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Database: PDB
Entry: 2VK5
LinkDB: 2VK5
Original site: 2VK5 
HEADER    HYDROLASE                               17-DEC-07   2VK5              
TITLE     THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND           
TITLE    2 ITS CATALYTIC INTERMEDIATES                                          
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: EXO-ALPHA-SIALIDASE;                                       
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 243-694;                        
COMPND   5 SYNONYM: SIALIDASE;                                                  
COMPND   6 EC: 3.2.1.18;                                                        
COMPND   7 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS;                        
SOURCE   3 ORGANISM_TAXID: 1502;                                                
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   5 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    HYDROLASE, SIALIDASE, GLYCOSIDASE, SIALIC ACID, CLOSTRIDIUM           
KEYWDS   2 PERFRINGENS                                                          
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.L.NEWSTEAD,J.A.POTTER,J.C.WILSON,G.XU,C.H.CHIEN,A.G.WATTS,          
AUTHOR   2 S.G.WITHERS,G.L.TAYLOR                                               
REVDAT   4   16-FEB-11 2VK5    1       VERSN                                    
REVDAT   3   24-FEB-09 2VK5    1       VERSN                                    
REVDAT   2   08-APR-08 2VK5    1       JRNL   REMARK                            
REVDAT   1   22-JAN-08 2VK5    0                                                
JRNL        AUTH   S.L.NEWSTEAD,J.A.POTTER,J.C.WILSON,G.XU,C.H.CHIEN,A.G.WATTS, 
JRNL        AUTH 2 S.G.WITHERS,G.L.TAYLOR                                       
JRNL        TITL   THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND  
JRNL        TITL 2 ITS CATALYTIC INTERMEDIATES.                                 
JRNL        REF    J.BIOL.CHEM.                  V. 283  9080 2008              
JRNL        REFN                   ISSN 0021-9258                               
JRNL        PMID   18218621                                                     
JRNL        DOI    10.1074/JBC.M710247200                                       
REMARK   2                                                                      
REMARK   2 RESOLUTION.    0.97 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : SHELX                                                
REMARK   3   AUTHORS     : G.M.SHELDRICK                                        
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 0.97                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20                             
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0                              
REMARK   3   COMPLETENESS FOR RANGE        (%) : 98                             
REMARK   3   CROSS-VALIDATION METHOD           : THROUGHOUT                     
REMARK   3   FREE R VALUE TEST SET SELECTION   : NULL                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).                         
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : NULL                   
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : NULL                   
REMARK   3   FREE R VALUE                  (NO CUTOFF) : NULL                   
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : NULL                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : NULL                   
REMARK   3                                                                      
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).                     
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : NULL                   
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : NULL                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 281317                 
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS      : 3584                                          
REMARK   3   NUCLEIC ACID ATOMS : 0                                             
REMARK   3   HETEROGEN ATOMS    : 14                                            
REMARK   3   SOLVENT ATOMS      : 1030                                          
REMARK   3                                                                      
REMARK   3  MODEL REFINEMENT.                                                   
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : NULL                    
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : NULL                    
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL                    
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : NULL                    
REMARK   3   NUMBER OF RESTRAINTS                     : NULL                    
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.                        
REMARK   3   BOND LENGTHS                         (A) : 0.017                   
REMARK   3   ANGLE DISTANCES                      (A) : 2.048                   
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL                    
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : NULL                    
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : NULL                    
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : NULL                    
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : NULL                    
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : NULL                    
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : NULL                    
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : NULL                    
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED: NULL                                                  
REMARK   3                                                                      
REMARK   3  STEREOCHEMISTRY TARGET VALUES : NULL                                
REMARK   3   SPECIAL CASE: NULL                                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2VK5 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-DEC-07.                  
REMARK 100 THE PDBE ID CODE IS EBI-34803.                                       
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : NULL                               
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : NULL                               
REMARK 200  NUMBER OF CRYSTALS USED        : NULL                               
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : ESRF                               
REMARK 200  BEAMLINE                       : ID14-1                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.934                              
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ADSC                               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : MOSFLM                             
REMARK 200  DATA SCALING SOFTWARE          : NULL                               
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 281317                             
REMARK 200  RESOLUTION RANGE HIGH      (A) : 0.97                               
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.00                              
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.0                                
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.0                               
REMARK 200  DATA REDUNDANCY                : 4.6                                
REMARK 200  R MERGE                    (I) : 0.07                               
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 15.60                              
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.02                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 95.0                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.1                                
REMARK 200  R MERGE FOR SHELL          (I) : 0.33                               
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 3.60                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: CNS                                                   
REMARK 200 STARTING MODEL: PDB ENTRY 1SLL                                       
REMARK 200                                                                      
REMARK 200 REMARK: NONE                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 34                                        
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.9                      
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL                                     
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
REMARK 290       4555   X+1/2,-Y+1/2,-Z                                         
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       48.44600            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       36.40400            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       34.50950            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       36.40400            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       48.44600            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       34.50950            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PQS                                                   
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     ALA A  1692                                                      
REMARK 465     ASN A  1693                                                      
REMARK 465     LYS A  1694                                                      
REMARK 470                                                                      
REMARK 470 MISSING ATOM                                                         
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;           
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 470 I=INSERTION CODE):                                                   
REMARK 470   M RES CSSEQI  ATOMS                                                
REMARK 470     GLY A1691    CA   C    O                                         
REMARK 480                                                                      
REMARK 480 ZERO OCCUPANCY ATOM                                                  
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO                  
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS                
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER;                                
REMARK 480 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;          
REMARK 480 I=INSERTION CODE):                                                   
REMARK 480   M RES CSSEQI  ATOMS                                                
REMARK 480     GLU A1313   OE1  OE2                                             
REMARK 480     VAL A1344   CG1                                                  
REMARK 480     GLU A1632   OE2                                                  
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   N    VAL A  1243  -  O    HOH A  2241              1.86            
REMARK 500   NE   ARG A  1286  -  O    HOH A  2302              1.87            
REMARK 500   CZ   ARG A  1286  -  O    HOH A  2302              1.56            
REMARK 500   NH1  ARG A  1286  -  O    HOH A  2302              1.47            
REMARK 500   OD1  ASP A  1296  -  O    HOH A  2329              1.94            
REMARK 500   C    MET A  1318  -  O    HOH A  2373              1.92            
REMARK 500   N    ASP A  1319  -  O    HOH A  2373              1.88            
REMARK 500   O    TYR A  1320  -  O    HOH A  2329              2.14            
REMARK 500   N    VAL A  1326  -  O    HOH A  2386              2.20            
REMARK 500   CG1  ILE A  1340  -  O    HOH A  2409              1.07            
REMARK 500   CD1  ILE A  1340  -  O    HOH A  2409              2.08            
REMARK 500   N    LEU A  1342  -  O    HOH A  2410              1.88            
REMARK 500   CA   LEU A  1342  -  O    HOH A  2410              0.89            
REMARK 500   C    LEU A  1342  -  O    HOH A  2410              1.85            
REMARK 500   CB   LEU A  1342  -  O    HOH A  2410              2.18            
REMARK 500   N    THR A  1345  -  O    HOH A  2412              1.91            
REMARK 500   CA   THR A  1345  -  O    HOH A  2412              0.96            
REMARK 500   C    THR A  1345  -  O    HOH A  2412              2.08            
REMARK 500   CB   THR A  1345  -  O    HOH A  2412              2.17            
REMARK 500   CB   ASN A  1364  -  O    HOH A  2442              1.67            
REMARK 500   CG   ASN A  1364  -  O    HOH A  2442              1.54            
REMARK 500   OD1  ASN A  1364  -  O    HOH A  2442              1.48            
REMARK 500   CG   LYS A  1368  -  O    HOH A  2458              2.04            
REMARK 500   CA   SER A  1376  -  O    HOH A  2473              2.09            
REMARK 500   CB   SER A  1376  -  O    HOH A  2473              1.42            
REMARK 500   N    SER A  1429  -  O    HOH A  2572              1.98            
REMARK 500   CA   SER A  1429  -  O    HOH A  2572              1.04            
REMARK 500   C    SER A  1429  -  O    HOH A  2572              2.17            
REMARK 500   CB   SER A  1429  -  O    HOH A  2572              2.18            
REMARK 500   OD1  ASN A  1432  -  O    HOH A  2575              1.27            
REMARK 500   C    SER A  1444  -  O    HOH A  2599              2.03            
REMARK 500   N    GLU A  1445  -  O    HOH A  2599              1.05            
REMARK 500   CA   GLU A  1445  -  O    HOH A  2599              2.19            
REMARK 500   OE2  GLU A  1445  -  O    HOH A  2606              1.35            
REMARK 500   CB   GLN A  1447  -  O    HOH A  2612              1.49            
REMARK 500   CG   GLN A  1447  -  O    HOH A  2612              1.96            
REMARK 500   CG   LYS A  1455  -  O    HOH A  2622              1.39            
REMARK 500   CE   LYS A  1455  -  O    HOH A  2624              1.75            
REMARK 500   CB   ASP A  1456  -  O    HOH A  2626              1.90            
REMARK 500   CB   LYS A  1459  -  O    HOH A  2630              1.36            
REMARK 500   CG   LYS A  1459  -  O    HOH A  2630              1.84            
REMARK 500   CD   LYS A  1459  -  O    HOH A  2632              1.63            
REMARK 500   N    LEU A  1461  -  O    HOH A  2634              2.06            
REMARK 500   CA   LEU A  1461  -  O    HOH A  2634              1.04            
REMARK 500   C    LEU A  1461  -  O    HOH A  2634              2.14            
REMARK 500   CB   LEU A  1461  -  O    HOH A  2634              2.13            
REMARK 500   CB   ARG A  1467  -  O    HOH A  2639              1.14            
REMARK 500   CG   ARG A  1467  -  O    HOH A  2639              1.39            
REMARK 500   CD   ARG A  1467  -  O    HOH A  2639              1.76            
REMARK 500   N    VAL A  1482  -  O    HOH A  2661              1.92            
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     152 CLOSE CONTACTS                                
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC             
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15          
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A           
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375             
REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE               
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.            
REMARK 500                                                                      
REMARK 500 DISTANCE CUTOFF:                                                     
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS              
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS                  
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE          
REMARK 500                                                                      
REMARK 500   O    HOH A  2136     O    HOH A  3024     2655      2.09           
REMARK 500   O    HOH A  2401     O    HOH A  3008     3755      1.81           
REMARK 500   O    HOH A  2452     O    HOH A  2881     3755      1.72           
REMARK 500   O    HOH A  2563     O    HOH A  2724     4455      1.43           
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS                                      
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)               
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   RES CSSEQI ATM2   DEVIATION                     
REMARK 500    GLU A1676   CD    GLU A1676   OE1     0.068                       
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500    ASP A1253   CB  -  CG  -  OD1 ANGL. DEV. =  -5.9 DEGREES          
REMARK 500    ASP A1283   CB  -  CG  -  OD2 ANGL. DEV. =  -5.8 DEGREES          
REMARK 500    ARG A1286   NE  -  CZ  -  NH2 ANGL. DEV. =  -5.2 DEGREES          
REMARK 500    ARG A1286   NH1 -  CZ  -  NH2 ANGL. DEV. =   7.8 DEGREES          
REMARK 500    ARG A1302   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.8 DEGREES          
REMARK 500    ASP A1335   CA  -  CB  -  CG  ANGL. DEV. =  16.3 DEGREES          
REMARK 500    ASP A1335   CB  -  CG  -  OD1 ANGL. DEV. =   6.8 DEGREES          
REMARK 500    ASP A1366   CB  -  CG  -  OD2 ANGL. DEV. =  -6.7 DEGREES          
REMARK 500    ARG A1384   NE  -  CZ  -  NH2 ANGL. DEV. =  -4.7 DEGREES          
REMARK 500    LEU A1433   CB  -  CG  -  CD2 ANGL. DEV. =  15.1 DEGREES          
REMARK 500    ASP A1456   CB  -  CG  -  OD1 ANGL. DEV. =  -8.3 DEGREES          
REMARK 500    ARG A1613   CD  -  NE  -  CZ  ANGL. DEV. =  40.2 DEGREES          
REMARK 500    ARG A1613   NE  -  CZ  -  NH1 ANGL. DEV. =   3.7 DEGREES          
REMARK 500    TYR A1655   CB  -  CG  -  CD1 ANGL. DEV. =   4.2 DEGREES          
REMARK 500    TYR A1655   CB  -  CG  -  CD2 ANGL. DEV. =  -4.4 DEGREES          
REMARK 500    GLU A1676   CG  -  CD  -  OE1 ANGL. DEV. =  13.9 DEGREES          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: TORSION ANGLES                                             
REMARK 500                                                                      
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:            
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                    
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-           
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400            
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        PSI       PHI                                   
REMARK 500    ILE A1267       74.84     77.27                                   
REMARK 500    ASN A1294       48.91    -90.50                                   
REMARK 500    ASN A1295     -178.88   -170.50                                   
REMARK 500    ASP A1328       84.75     75.18                                   
REMARK 500    LYS A1350       -4.36     83.86                                   
REMARK 500    ASP A1414     -159.98   -171.38                                   
REMARK 500    LYS A1459      -68.55    -92.93                                   
REMARK 500    THR A1538     -122.13   -125.70                                   
REMARK 500    TYR A1587       67.03     79.05                                   
REMARK 500    ALA A1654     -114.44   -121.47                                   
REMARK 500    SER A1675       27.90   -158.57                                   
REMARK 500    GLU A1676      -97.20   -119.91                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620  (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;              
REMARK 620   SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                           
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              CA A  10  CA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 HOH A2710   O                                                      
REMARK 620 2 TRP A1573   O    80.0                                              
REMARK 620 3 ASP A1515   O    86.0 162.1                                        
REMARK 620 4 HOH A2713   O    95.4  89.7 102.6                                  
REMARK 620 5 HOH A2704   O    95.0  84.2  86.1 166.9                            
REMARK 620 6 HOH A2708   O   169.1 108.9  84.0  91.0  80.1                      
REMARK 620 N                    1     2     3     4     5                       
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              CA A  17  CA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 HOH A2330   O                                                      
REMARK 620 2 ASP A1296   OD1  80.2                                              
REMARK 620 3 HOH A2329   O   105.9  56.5                                        
REMARK 620 4 ASP A1298   OD1 146.9 104.1 103.5                                  
REMARK 620 5 ASP A1319   OD1  88.7 167.1 133.9  81.7                            
REMARK 620 6 TYR A1320   O    74.0 100.6  61.5 135.0  82.3                      
REMARK 620 7 HOH A2332   O    71.5  86.2 141.9  76.0  84.1 143.1                
REMARK 620 8 HOH A2384   O   143.9  85.3  40.3  68.8 107.5  76.5 140.4          
REMARK 620 N                    1     2     3     4     5     6     7           
REMARK 700                                                                      
REMARK 700 SHEET                                                                
REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN               
REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW,          
REMARK 700 TWO SHEETS ARE DEFINED.                                              
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A   1                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A   6                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  CA A  10                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC4                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE  CA A  17                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 2BF6   RELATED DB: PDB                                   
REMARK 900  ATOMIC RESOLUTION STRUCTURE OF THE BACTERIAL SIALIDASE              
REMARK 900  NANI FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH ALPHA             
REMARK 900  -SIALIC ACID (NEU5AC).                                              
REMARK 900 RELATED ID: 2VK7   RELATED DB: PDB                                   
REMARK 900  THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE             
REMARK 900  AND ITS CATALYTIC INTERMEDIATES                                     
REMARK 900 RELATED ID: 2VK6   RELATED DB: PDB                                   
REMARK 900  THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE             
REMARK 900  AND ITS CATALYTIC INTERMEDIATES                                     
DBREF  2VK5 A 1243  1694  UNP    Q59310   Q59310_CLOPE   243    694             
SEQADV 2VK5 SER A 1393  UNP  Q59310    GLY   393 CONFLICT                       
SEQRES   1 A  452  VAL GLU GLY ALA VAL LYS THR GLU PRO VAL ASP LEU PHE          
SEQRES   2 A  452  HIS PRO GLY PHE LEU ASN SER SER ASN TYR ARG ILE PRO          
SEQRES   3 A  452  ALA LEU PHE LYS THR LYS GLU GLY THR LEU ILE ALA SER          
SEQRES   4 A  452  ILE ASP ALA ARG ARG HIS GLY GLY ALA ASP ALA PRO ASN          
SEQRES   5 A  452  ASN ASP ILE ASP THR ALA VAL ARG ARG SER GLU ASP GLY          
SEQRES   6 A  452  GLY LYS THR TRP ASP GLU GLY GLN ILE ILE MET ASP TYR          
SEQRES   7 A  452  PRO ASP LYS SER SER VAL ILE ASP THR THR LEU ILE GLN          
SEQRES   8 A  452  ASP ASP GLU THR GLY ARG ILE PHE LEU LEU VAL THR HIS          
SEQRES   9 A  452  PHE PRO SER LYS TYR GLY PHE TRP ASN ALA GLY LEU GLY          
SEQRES  10 A  452  SER GLY PHE LYS ASN ILE ASP GLY LYS GLU TYR LEU CYS          
SEQRES  11 A  452  LEU TYR ASP SER SER GLY LYS GLU PHE THR VAL ARG GLU          
SEQRES  12 A  452  ASN VAL VAL TYR ASP LYS ASP SER ASN LYS THR GLU TYR          
SEQRES  13 A  452  THR THR ASN ALA LEU GLY ASP LEU PHE LYS ASN GLY THR          
SEQRES  14 A  452  LYS ILE ASP ASN ILE ASN SER SER THR ALA PRO LEU LYS          
SEQRES  15 A  452  ALA LYS GLY THR SER TYR ILE ASN LEU VAL TYR SER ASP          
SEQRES  16 A  452  ASP ASP GLY LYS THR TRP SER GLU PRO GLN ASN ILE ASN          
SEQRES  17 A  452  PHE GLN VAL LYS LYS ASP TRP MET LYS PHE LEU GLY ILE          
SEQRES  18 A  452  ALA PRO GLY ARG GLY ILE GLN ILE LYS ASN GLY GLU HIS          
SEQRES  19 A  452  LYS GLY ARG ILE VAL VAL PRO VAL TYR TYR THR ASN GLU          
SEQRES  20 A  452  LYS GLY LYS GLN SER SER ALA VAL ILE TYR SER ASP ASP          
SEQRES  21 A  452  SER GLY LYS ASN TRP THR ILE GLY GLU SER PRO ASN ASP          
SEQRES  22 A  452  ASN ARG LYS LEU GLU ASN GLY LYS ILE ILE ASN SER LYS          
SEQRES  23 A  452  THR LEU SER ASP ASP ALA PRO GLN LEU THR GLU CYS GLN          
SEQRES  24 A  452  VAL VAL GLU MET PRO ASN GLY GLN LEU LYS LEU PHE MET          
SEQRES  25 A  452  ARG ASN LEU SER GLY TYR LEU ASN ILE ALA THR SER PHE          
SEQRES  26 A  452  ASP GLY GLY ALA THR TRP ASP GLU THR VAL GLU LYS ASP          
SEQRES  27 A  452  THR ASN VAL LEU GLU PRO TYR CYS GLN LEU SER VAL ILE          
SEQRES  28 A  452  ASN TYR SER GLN LYS VAL ASP GLY LYS ASP ALA VAL ILE          
SEQRES  29 A  452  PHE SER ASN PRO ASN ALA ARG SER ARG SER ASN GLY THR          
SEQRES  30 A  452  VAL ARG ILE GLY LEU ILE ASN GLN VAL GLY THR TYR GLU          
SEQRES  31 A  452  ASN GLY GLU PRO LYS TYR GLU PHE ASP TRP LYS TYR ASN          
SEQRES  32 A  452  LYS LEU VAL LYS PRO GLY TYR TYR ALA TYR SER CYS LEU          
SEQRES  33 A  452  THR GLU LEU SER ASN GLY ASN ILE GLY LEU LEU TYR GLU          
SEQRES  34 A  452  GLY THR PRO SER GLU GLU MET SER TYR ILE GLU MET ASN          
SEQRES  35 A  452  LEU LYS TYR LEU GLU SER GLY ALA ASN LYS                      
HET    GOL  A   1       6                                                       
HET    GOL  A   6       6                                                       
HET     CA  A  10       1                                                       
HET     CA  A  17       1                                                       
HETNAM     GOL GLYCEROL                                                         
HETNAM      CA CALCIUM ION                                                      
FORMUL   2  GOL    2(C3 H8 O3)                                                  
FORMUL   3   CA    2(CA 2+)                                                     
FORMUL   4  HOH   *1030(H2 O)                                                   
HELIX    1   1 GLY A 1258  SER A 1262  5                                   5    
HELIX    2   2 ILE A 1449  LYS A 1454  1                                   6    
HELIX    3   3 ASN A 1473  LYS A 1477  5                                   5    
HELIX    4   4 ASN A 1684  GLU A 1689  1                                   6    
SHEET    1  AA 4 VAL A1252  PHE A1255  0                                        
SHEET    2  AA 4 MET A1678  MET A1683 -1  O  MET A1678   N  LEU A1254           
SHEET    3  AA 4 ILE A1666  TYR A1670 -1  O  ILE A1666   N  MET A1683           
SHEET    4  AA 4 SER A1656  GLU A1660 -1  O  CYS A1657   N  LEU A1669           
SHEET    1  AB 4 ASN A1264  LYS A1272  0                                        
SHEET    2  AB 4 LEU A1278  ARG A1285 -1  O  ILE A1279   N  PHE A1271           
SHEET    3  AB 4 ILE A1297  SER A1304 -1  O  ASP A1298   N  ALA A1284           
SHEET    4  AB 4 GLN A1315  MET A1318 -1  O  GLN A1315   N  VAL A1301           
SHEET    1  AC 5 GLN A1447  ASN A1448  0                                        
SHEET    2  AC 5 TYR A1430  SER A1436 -1  O  LEU A1433   N  GLN A1447           
SHEET    3  AC 5 ARG A1339  PHE A1347 -1  O  ILE A1340   N  SER A1436           
SHEET    4  AC 5 SER A1325  ASP A1334 -1  O  SER A1325   N  PHE A1347           
SHEET    5  AC 5 GLY A1466  ARG A1467  1  O  GLY A1466   N  LEU A1331           
SHEET    1  AD 7 PHE A1362  ILE A1365  0                                        
SHEET    2  AD 7 LYS A1368  TYR A1374 -1  O  LYS A1368   N  ILE A1365           
SHEET    3  AD 7 GLU A1380  ARG A1384 -1  O  PHE A1381   N  LEU A1373           
SHEET    4  AD 7 VAL A1387  TYR A1389 -1  O  VAL A1387   N  ARG A1384           
SHEET    5  AD 7 LYS A1395  THR A1400 -1  N  THR A1396   O  VAL A1388           
SHEET    6  AD 7 ASP A1405  LYS A1408 -1  O  PHE A1407   N  THR A1399           
SHEET    7  AD 7 THR A1411  ASN A1415 -1  O  THR A1411   N  LYS A1408           
SHEET    1  AE 3 PHE A1362  ILE A1365  0                                        
SHEET    2  AE 3 LYS A1368  TYR A1374 -1  O  LYS A1368   N  ILE A1365           
SHEET    3  AE 3 LYS A1424  ALA A1425 -1  O  LYS A1424   N  TYR A1374           
SHEET    1  AF 3 LEU A1461  ILE A1463  0                                        
SHEET    2  AF 3 ILE A1480  THR A1487 -1  O  TYR A1485   N  GLY A1462           
SHEET    3  AF 3 ILE A1469  GLN A1470 -1  O  ILE A1469   N  VAL A1481           
SHEET    1  AG 4 LEU A1461  ILE A1463  0                                        
SHEET    2  AG 4 ILE A1480  THR A1487 -1  O  TYR A1485   N  GLY A1462           
SHEET    3  AG 4 GLN A1493  SER A1500 -1  O  SER A1494   N  TYR A1486           
SHEET    4  AG 4 THR A1508  ILE A1509 -1  O  THR A1508   N  TYR A1499           
SHEET    1  AH 2 ARG A1517  LYS A1518  0                                        
SHEET    2  AH 2 ILE A1524  ILE A1525 -1  N  ILE A1525   O  ARG A1517           
SHEET    1  AI 4 LEU A1537  GLU A1544  0                                        
SHEET    2  AI 4 LEU A1550  ASN A1556 -1  O  LYS A1551   N  VAL A1543           
SHEET    3  AI 4 TYR A1560  SER A1566 -1  O  ASN A1562   N  MET A1554           
SHEET    4  AI 4 GLU A1578  LEU A1584 -1  O  GLU A1578   N  ILE A1563           
SHEET    1  AJ 4 SER A1591  ASN A1594  0                                        
SHEET    2  AJ 4 ALA A1604  PRO A1610 -1  O  ILE A1606   N  ILE A1593           
SHEET    3  AJ 4 SER A1616  THR A1630 -1  O  THR A1619   N  ASN A1609           
SHEET    4  AJ 4 PRO A1636  TYR A1652 -1  O  LYS A1637   N  VAL A1628           
LINK        CA    CA A  10                 O   HOH A2710     1555   1555  2.49  
LINK        CA    CA A  10                 O   TRP A1573     1555   1555  2.56  
LINK        CA    CA A  10                 O   ASP A1515     1555   1555  2.46  
LINK        CA    CA A  10                 O   HOH A2713     1555   1555  2.13  
LINK        CA    CA A  10                 O   HOH A2704     1555   1555  2.63  
LINK        CA    CA A  10                 O   HOH A2708     1555   1555  2.56  
LINK        CA    CA A  17                 O   HOH A2329     1555   1555  1.50  
LINK        CA    CA A  17                 OD1 ASP A1296     1555   1555  2.31  
LINK        CA    CA A  17                 OD1 ASP A1298     1555   1555  2.41  
LINK        CA    CA A  17                 OD1 ASP A1319     1555   1555  2.35  
LINK        CA    CA A  17                 O   TYR A1320     1555   1555  2.40  
LINK        CA    CA A  17                 O   HOH A2332     1555   1555  2.48  
LINK        CA    CA A  17                 O   HOH A2384     1555   1555  2.50  
LINK        CA    CA A  17                 O   HOH A2330     1555   1555  2.49  
CISPEP   1 ALA A 1292    PRO A 1293          0         7.86                     
SITE     1 AC1  9 LYS A1551  GLU A1578  TYR A1631  GLU A1639                    
SITE     2 AC1  9 HOH A2225  HOH A2226  HOH A2227  HOH A2228                    
SITE     3 AC1  9 HOH A2797                                                     
SITE     1 AC2  9 GLU A1578  LYS A1579  ASP A1580  THR A1581                    
SITE     2 AC2  9 ASN A1582  GLU A1639  HOH A2233  HOH A2235                    
SITE     3 AC2  9 HOH A2814                                                     
SITE     1 AC3  6 ASP A1515  TRP A1573  HOH A2704  HOH A2708                    
SITE     2 AC3  6 HOH A2710  HOH A2713                                          
SITE     1 AC4  8 ASP A1296  ASP A1298  ASP A1319  TYR A1320                    
SITE     2 AC4  8 HOH A2329  HOH A2330  HOH A2332  HOH A2384                    
CRYST1   96.892   69.019   72.808  90.00  90.00  90.00 P 21 21 21    4          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.010321  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.014489  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.013735        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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