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Database: PDB
Entry: 3VMM
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Original site: 3VMM 
HEADER    LIGASE                                  14-DEC-11   3VMM              
TITLE     CRYSTAL STRUCTURE OF BACD, AN L-AMINO ACID DIPEPTIDE LIGASE FROM      
TITLE    2 BACILLUS SUBTILIS                                                    
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: ALANINE-ANTICAPSIN LIGASE BACD;                            
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: BACILYSIN SYNTHETASE, L-AMINO ACID LIGASE;                  
COMPND   5 EC: 6.3.2.28;                                                        
COMPND   6 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS;                              
SOURCE   3 ORGANISM_TAXID: 1423;                                                
SOURCE   4 GENE: BACD, BSU37710, IPA-83D;                                       
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID                               
KEYWDS    ATP-GRASP DOMAIN, AMINO ACID LIGASE, ATP BINDING, LIGASE              
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    Y.SHOMURA,Y.HIGUCHI                                                   
REVDAT   1   11-APR-12 3VMM    0                                                
JRNL        AUTH   Y.SHOMURA,E.HINOKUCHI,H.IKEDA,A.SENOO,Y.TAKAHASHI,J.SAITO,   
JRNL        AUTH 2 H.KOMORI,N.SHIBATA,Y.YONETANI,Y.HIGUCHI                      
JRNL        TITL   STRUCTURAL AND ENZYMATIC CHARACTERIZATION OF BACD, AN        
JRNL        TITL 2 L-AMINO ACID DIPEPTIDE LIGASE FROM BACILLUS SUBTILIS         
JRNL        REF    PROTEIN SCI.                               2012              
JRNL        REFN                   ESSN 1469-896X                               
JRNL        PMID   22407814                                                     
JRNL        DOI    10.1002/PRO.2058                                             
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.50 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : REFMAC 5.5.0109                                      
REMARK   3   AUTHORS     : MURSHUDOV,VAGIN,DODSON                               
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 19.93                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL                           
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.3                           
REMARK   3   NUMBER OF REFLECTIONS             : 24770                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.194                           
REMARK   3   R VALUE            (WORKING SET) : 0.192                           
REMARK   3   FREE R VALUE                     : 0.229                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.100                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 1327                            
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 20                           
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.50                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.57                         
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 1755                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 97.19                        
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2520                       
REMARK   3   BIN FREE R VALUE SET COUNT          : 77                           
REMARK   3   BIN FREE R VALUE                    : 0.3850                       
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 3675                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 51                                      
REMARK   3   SOLVENT ATOMS            : 147                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 49.80                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 45.02                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : 0.07000                                              
REMARK   3    B22 (A**2) : 0.07000                                              
REMARK   3    B33 (A**2) : -0.11000                                             
REMARK   3    B12 (A**2) : 0.04000                                              
REMARK   3    B13 (A**2) : -0.00000                                             
REMARK   3    B23 (A**2) : -0.00000                                             
REMARK   3                                                                      
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.                                 
REMARK   3   ESU BASED ON R VALUE                            (A): NULL          
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.232         
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.176         
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.920        
REMARK   3                                                                      
REMARK   3 CORRELATION COEFFICIENTS.                                            
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.950                         
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.927                         
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT      
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  3804 ; 0.009 ; 0.022       
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  5166 ; 1.297 ; 1.981       
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL       
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   470 ; 5.956 ; 5.000       
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   172 ;39.076 ;25.523       
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   645 ;17.771 ;15.000       
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    12 ;15.692 ;15.000       
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   576 ; 0.089 ; 0.200       
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  2870 ; 0.005 ; 0.021       
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):  NULL ;  NULL ;  NULL       
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL       
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL       
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT      
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  2354 ; 0.336 ; 1.500       
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  3792 ; 0.694 ; 2.000       
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1450 ; 1.263 ; 3.000       
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1374 ; 2.173 ; 4.500       
REMARK   3                                                                      
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT       
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS STATISTICS                                           
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL                              
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : 1                                          
REMARK   3                                                                      
REMARK   3   TLS GROUP : 1                                                      
REMARK   3    NUMBER OF COMPONENTS GROUP : 3                                    
REMARK   3    COMPONENTS        C SSSEQI   TO  C SSSEQI                         
REMARK   3    RESIDUE RANGE :   A     2        A   472                          
REMARK   3    RESIDUE RANGE :   A   501        A   504                          
REMARK   3    RESIDUE RANGE :   A   601        A   747                          
REMARK   3    ORIGIN FOR THE GROUP (A):  -1.2620 -46.1950  -9.8030              
REMARK   3    T TENSOR                                                          
REMARK   3      T11:   0.1408 T22:   0.0546                                     
REMARK   3      T33:   0.2168 T12:   0.0041                                     
REMARK   3      T13:  -0.1254 T23:  -0.0189                                     
REMARK   3    L TENSOR                                                          
REMARK   3      L11:   1.7772 L22:   2.0765                                     
REMARK   3      L33:   0.7530 L12:  -0.9044                                     
REMARK   3      L13:   0.3995 L23:  -0.5482                                     
REMARK   3    S TENSOR                                                          
REMARK   3      S11:  -0.2051 S12:  -0.0723 S13:   0.4367                       
REMARK   3      S21:   0.3005 S22:   0.0358 S23:  -0.5227                       
REMARK   3      S31:  -0.0506 S32:  -0.0034 S33:   0.1692                       
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED : BABINET MODEL WITH MASK                              
REMARK   3   PARAMETERS FOR MASK CALCULATION                                    
REMARK   3   VDW PROBE RADIUS   : 1.40                                          
REMARK   3   ION PROBE RADIUS   : 0.80                                          
REMARK   3   SHRINKAGE RADIUS   : 0.80                                          
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING   
REMARK   3  POSITIONS                                                           
REMARK   4                                                                      
REMARK   4 3VMM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JAN-12.                  
REMARK 100 THE RCSB ID CODE IS RCSB095234.                                      
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 29-JAN-11                          
REMARK 200  TEMPERATURE           (KELVIN) : 90                                 
REMARK 200  PH                             : NULL                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SPRING-8                           
REMARK 200  BEAMLINE                       : BL44XU                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.900                              
REMARK 200  MONOCHROMATOR                  : SI(111)                            
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : RAYONIX MX-225                     
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                           
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000                           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 26252                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.500                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.9                               
REMARK 200  DATA REDUNDANCY                : 5.900                              
REMARK 200  R MERGE                    (I) : 0.08100                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 11.6000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.54                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 1.0                                
REMARK 200  DATA REDUNDANCY IN SHELL       : 6.00                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.48700                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 4.400                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: MOLREP                                                
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 64.62                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.48                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM BIS-TRIS PROPANE, 60MM SODIUM      
REMARK 280  CITRATE, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE   
REMARK 280  293K                                                                
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -Y,X-Y,Z+2/3                                            
REMARK 290       3555   -X+Y,-X,Z+1/3                                           
REMARK 290       4555   -X,-Y,Z+1/2                                             
REMARK 290       5555   Y,-X+Y,Z+1/6                                            
REMARK 290       6555   X-Y,X,Z+5/6                                             
REMARK 290       7555   Y,X,-Z+2/3                                              
REMARK 290       8555   X-Y,-Y,-Z                                               
REMARK 290       9555   -X,-X+Y,-Z+1/3                                          
REMARK 290      10555   -Y,-X,-Z+1/6                                            
REMARK 290      11555   -X+Y,Y,-Z+1/2                                           
REMARK 290      12555   X,X-Y,-Z+5/6                                            
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 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       98.49467            
REMARK 290   SMTRY1   3 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   3 -0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       49.24733            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       73.87100            
REMARK 290   SMTRY1   5  0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   5 -0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   5  0.000000  0.000000  1.000000       24.62367            
REMARK 290   SMTRY1   6  0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   6  0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   6  0.000000  0.000000  1.000000      123.11833            
REMARK 290   SMTRY1   7 -0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   7  0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000       98.49467            
REMARK 290   SMTRY1   8  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   8  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   9 -0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2   9 -0.866025  0.500000  0.000000        0.00000            
REMARK 290   SMTRY3   9  0.000000  0.000000 -1.000000       49.24733            
REMARK 290   SMTRY1  10  0.500000 -0.866025  0.000000        0.00000            
REMARK 290   SMTRY2  10 -0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3  10  0.000000  0.000000 -1.000000       24.62367            
REMARK 290   SMTRY1  11 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2  11  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3  11  0.000000  0.000000 -1.000000       73.87100            
REMARK 290   SMTRY1  12  0.500000  0.866025  0.000000        0.00000            
REMARK 290   SMTRY2  12  0.866025 -0.500000  0.000000        0.00000            
REMARK 290   SMTRY3  12  0.000000  0.000000 -1.000000      123.11833            
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 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     GLY A    -1                                                      
REMARK 465     ALA A     0                                                      
REMARK 465     MET A     1                                                      
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   OE1  GLU A   324     O    HOH A   721              2.18            
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                                                                      
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    ASP A  11     -168.00   -162.61                                   
REMARK 500    HIS A  78       46.81    -90.94                                   
REMARK 500    LYS A 151      118.13    -36.95                                   
REMARK 500    THR A 159      -54.30   -121.73                                   
REMARK 500    GLU A 170      -70.59    -66.93                                   
REMARK 500    LEU A 182     -152.34   -104.01                                   
REMARK 500    TYR A 242     -151.97   -104.06                                   
REMARK 500    ASP A 254       53.24     32.44                                   
REMARK 500    ILE A 260      -59.81   -120.03                                   
REMARK 500    GLN A 304      -61.61   -101.08                                   
REMARK 500    ALA A 327       37.57    -87.72                                   
REMARK 500    TRP A 332     -146.74     55.46                                   
REMARK 500    TYR A 372     -178.55   -178.94                                   
REMARK 500    ASP A 396       66.82     37.08                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CHIRAL CENTERS                                             
REMARK 500                                                                      
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL                     
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY                      
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR                        
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE                                    
REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)       
REMARK 500                                                                      
REMARK 500  M RES CSSEQI    IMPROPER   EXPECTED   FOUND DETAILS                 
REMARK 500    THR A   5        24.9      L          L   OUTSIDE RANGE           
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                              MG A 501  MG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 GLU A 324   OE2                                                    
REMARK 620 2 ADP A 503   O1B 106.7                                              
REMARK 620 3 P0D A 504   O5P 121.0  96.7                                        
REMARK 620 4 GLU A 311   OE1  78.8 161.9  95.0                                  
REMARK 620 5 ADP A 503   O1A  68.7  77.5 170.1  88.9                            
REMARK 620 6 HOH A 719   O   142.6  86.8  90.7  79.2  81.1                      
REMARK 620 N                    1     2     3     4     5                       
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              MG A 502  MG                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 GLU A 324   OE1                                                    
REMARK 620 2 HOH A 721   O    52.8                                              
REMARK 620 3 ADP A 503   O3B  57.9 106.2                                        
REMARK 620 4 GLU A 109   OE2 122.1  78.6 169.3                                  
REMARK 620 5 P0D A 504   O3P  60.7  66.5  60.1 130.2                            
REMARK 620 6 LEU A 182   O   133.0 172.7  81.0  94.0 119.4                      
REMARK 620 N                    1     2     3     4     5                       
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 501                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 503                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC4                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P0D A 504                 
DBREF  3VMM A    1   472  UNP    P39641   BACD_BACSU       1    472             
SEQADV 3VMM GLY A   -1  UNP  P39641              EXPRESSION TAG                 
SEQADV 3VMM ALA A    0  UNP  P39641              EXPRESSION TAG                 
SEQRES   1 A  474  GLY ALA MET GLU ARG LYS THR VAL LEU VAL ILE ALA ASP          
SEQRES   2 A  474  LEU GLY GLY CYS PRO PRO HIS MET PHE TYR LYS SER ALA          
SEQRES   3 A  474  ALA GLU LYS TYR ASN LEU VAL SER PHE ILE PRO ARG PRO          
SEQRES   4 A  474  PHE ALA ILE THR ALA SER HIS ALA ALA LEU ILE GLU LYS          
SEQRES   5 A  474  TYR SER VAL ALA VAL ILE LYS ASP LYS ASP TYR PHE LYS          
SEQRES   6 A  474  SER LEU ALA ASP PHE GLU HIS PRO ASP SER ILE TYR TRP          
SEQRES   7 A  474  ALA HIS GLU ASP HIS ASN LYS PRO GLU GLU GLU VAL VAL          
SEQRES   8 A  474  GLU GLN ILE VAL LYS VAL ALA GLU MET PHE GLY ALA ASP          
SEQRES   9 A  474  ALA ILE THR THR ASN ASN GLU LEU PHE ILE ALA PRO MET          
SEQRES  10 A  474  ALA LYS ALA CYS GLU ARG LEU GLY LEU ARG GLY ALA GLY          
SEQRES  11 A  474  VAL GLN ALA ALA GLU ASN ALA ARG ASP LYS ASN LYS MET          
SEQRES  12 A  474  ARG ASP ALA PHE ASN LYS ALA GLY VAL LYS SER ILE LYS          
SEQRES  13 A  474  ASN LYS ARG VAL THR THR LEU GLU ASP PHE ARG ALA ALA          
SEQRES  14 A  474  LEU GLU GLU ILE GLY THR PRO LEU ILE LEU LYS PRO THR          
SEQRES  15 A  474  TYR LEU ALA SER SER ILE GLY VAL THR LEU ILE THR ASP          
SEQRES  16 A  474  THR GLU THR ALA GLU ASP GLU PHE ASN ARG VAL ASN ASP          
SEQRES  17 A  474  TYR LEU LYS SER ILE ASN VAL PRO LYS ALA VAL THR PHE          
SEQRES  18 A  474  GLU ALA PRO PHE ILE ALA GLU GLU PHE LEU GLN GLY GLU          
SEQRES  19 A  474  TYR GLY ASP TRP TYR GLN THR GLU GLY TYR SER ASP TYR          
SEQRES  20 A  474  ILE SER ILE GLU GLY ILE MET ALA ASP GLY GLU TYR PHE          
SEQRES  21 A  474  PRO ILE ALA ILE HIS ASP LYS THR PRO GLN ILE GLY PHE          
SEQRES  22 A  474  THR GLU THR SER HIS ILE THR PRO SER ILE LEU ASP GLU          
SEQRES  23 A  474  GLU ALA LYS LYS LYS ILE VAL GLU ALA ALA LYS LYS ALA          
SEQRES  24 A  474  ASN GLU GLY LEU GLY LEU GLN ASN CYS ALA THR HIS THR          
SEQRES  25 A  474  GLU ILE LYS LEU MET LYS ASN ARG GLU PRO GLY LEU ILE          
SEQRES  26 A  474  GLU SER ALA ALA ARG PHE ALA GLY TRP ASN MET ILE PRO          
SEQRES  27 A  474  ASN ILE LYS LYS VAL PHE GLY LEU ASP MET ALA GLN LEU          
SEQRES  28 A  474  LEU LEU ASP VAL LEU CYS PHE GLY LYS ASP ALA ASP LEU          
SEQRES  29 A  474  PRO ASP GLY LEU LEU ASP GLN GLU PRO TYR TYR VAL ALA          
SEQRES  30 A  474  ASP CYS HIS LEU TYR PRO GLN HIS PHE LYS GLN ASN GLY          
SEQRES  31 A  474  GLN ILE PRO GLU THR ALA GLU ASP LEU VAL ILE GLU ALA          
SEQRES  32 A  474  ILE ASP ILE PRO ASP GLY LEU LEU LYS GLY ASP THR GLU          
SEQRES  33 A  474  ILE VAL SER PHE SER ALA ALA ALA PRO GLY THR SER VAL          
SEQRES  34 A  474  ASP LEU THR LEU PHE GLU ALA PHE ASN SER ILE ALA ALA          
SEQRES  35 A  474  PHE GLU LEU LYS GLY SER ASN SER GLN ASP VAL ALA GLU          
SEQRES  36 A  474  SER ILE ARG GLN ILE GLN GLN HIS ALA LYS LEU THR ALA          
SEQRES  37 A  474  LYS TYR VAL LEU PRO VAL                                      
HET     MG  A 501       1                                                       
HET     MG  A 502       1                                                       
HET    ADP  A 503      27                                                       
HET    P0D  A 504      22                                                       
HETNAM      MG MAGNESIUM ION                                                    
HETNAM     ADP ADENOSINE-5'-DIPHOSPHATE                                         
HETNAM     P0D (2S)-3-[(S)-[(1R)-1-AMINOETHYL](PHOSPHONOOXY)                    
HETNAM   2 P0D  PHOSPHORYL]-2-BENZYLPROPANOIC ACID                              
FORMUL   2   MG    2(MG 2+)                                                     
FORMUL   4  ADP    C10 H15 N5 O10 P2                                            
FORMUL   5  P0D    C12 H19 N O7 P2                                              
FORMUL   6  HOH   *147(H2 O)                                                    
HELIX    1   1 PRO A   16  GLU A   26  1                                  11    
HELIX    2   2 ARG A   36  ILE A   40  5                                   5    
HELIX    3   3 THR A   41  TYR A   51  1                                  11    
HELIX    4   4 LYS A   59  PHE A   62  5                                   4    
HELIX    5   5 SER A   64  GLU A   69  5                                   6    
HELIX    6   6 PRO A   84  PHE A   99  1                                  16    
HELIX    7   7 ASN A  108  LEU A  110  5                                   3    
HELIX    8   8 PHE A  111  LEU A  122  1                                  12    
HELIX    9   9 GLY A  128  ALA A  135  1                                   8    
HELIX   10  10 ASP A  137  ALA A  148  1                                  12    
HELIX   11  11 THR A  160  ILE A  171  1                                  12    
HELIX   12  12 THR A  196  LYS A  209  1                                  14    
HELIX   13  13 GLU A  232  TYR A  237  1                                   6    
HELIX   14  14 ASP A  283  GLY A  302  1                                  20    
HELIX   15  15 LYS A  316  ARG A  318  5                                   3    
HELIX   16  16 ASN A  333  GLY A  343  1                                  11    
HELIX   17  17 ASP A  345  GLY A  357  1                                  13    
HELIX   18  18 LYS A  358  ALA A  360  5                                   3    
HELIX   19  19 TYR A  380  ASN A  387  1                                   8    
HELIX   20  20 PHE A  432  ASN A  436  5                                   5    
HELIX   21  21 ASN A  447  ALA A  462  1                                  16    
SHEET    1   A 4 SER A  52  LYS A  57  0                                        
SHEET    2   A 4 TYR A  28  ILE A  34  1  N  SER A  32   O  ILE A  56           
SHEET    3   A 4 LYS A   4  ILE A   9  1  N  VAL A   8   O  PHE A  33           
SHEET    4   A 4 ALA A 103  THR A 106  1  O  ALA A 103   N  LEU A   7           
SHEET    1   B 4 ASN A 155  VAL A 158  0                                        
SHEET    2   B 4 PHE A 223  GLU A 227 -1  O  PHE A 223   N  VAL A 158           
SHEET    3   B 4 LEU A 175  PRO A 179 -1  N  ILE A 176   O  GLU A 226           
SHEET    4   B 4 THR A 189  ILE A 191 -1  O  THR A 189   N  LEU A 177           
SHEET    1   C 8 GLU A 319  ALA A 326  0                                        
SHEET    2   C 8 CYS A 306  MET A 315 -1  N  LYS A 313   O  GLY A 321           
SHEET    3   C 8 TYR A 245  ALA A 253 -1  N  MET A 252   O  CYS A 306           
SHEET    4   C 8 GLU A 256  LYS A 265 -1  O  ALA A 261   N  GLU A 249           
SHEET    5   C 8 SER A 275  THR A 278 -1  O  ILE A 277   N  ASP A 264           
SHEET    6   C 8 TYR A 373  LEU A 379 -1  O  VAL A 374   N  THR A 278           
SHEET    7   C 8 ALA A 439  GLY A 445 -1  O  GLY A 445   N  TYR A 373           
SHEET    8   C 8 GLU A 414  ALA A 420 -1  N  SER A 419   O  ALA A 440           
SHEET    1   D 3 THR A 425  VAL A 427  0                                        
SHEET    2   D 3 GLU A 395  ASP A 403 -1  N  LEU A 397   O  VAL A 427           
SHEET    3   D 3 LYS A 463  VAL A 469 -1  O  LYS A 467   N  VAL A 398           
LINK         OE2 GLU A 324                MG    MG A 501     1555   1555  2.01  
LINK        MG    MG A 501                 O1B ADP A 503     1555   1555  2.02  
LINK        MG    MG A 501                 O5P P0D A 504     1555   1555  2.03  
LINK         OE1 GLU A 311                MG    MG A 501     1555   1555  2.06  
LINK        MG    MG A 501                 O1A ADP A 503     1555   1555  2.20  
LINK        MG    MG A 501                 O   HOH A 719     1555   1555  2.25  
LINK         OE1 GLU A 324                MG    MG A 502     1555   1555  2.37  
LINK        MG    MG A 502                 O   HOH A 721     1555   1555  2.52  
LINK        MG    MG A 502                 O3B ADP A 503     1555   1555  2.60  
LINK         OE2 GLU A 109                MG    MG A 502     1555   1555  2.73  
LINK        MG    MG A 502                 O3P P0D A 504     1555   1555  2.82  
LINK         O   LEU A 182                MG    MG A 502     1555   1555  2.90  
CISPEP   1 THR A  173    PRO A  174          0        -5.57                     
CISPEP   2 THR A  278    PRO A  279          0        -9.84                     
SITE     1 AC1  5 GLU A 311  GLU A 324  ADP A 503  P0D A 504                    
SITE     2 AC1  5 HOH A 719                                                     
SITE     1 AC2  8 GLU A 109  LYS A 138  LEU A 182  ALA A 183                    
SITE     2 AC2  8 GLU A 324  ADP A 503  P0D A 504  HOH A 721                    
SITE     1 AC3 24 LYS A 138  ILE A 176  LYS A 178  LEU A 182                    
SITE     2 AC3 24 ALA A 183  SER A 184  SER A 185  VAL A 188                    
SITE     3 AC3 24 GLU A 226  GLU A 227  PHE A 228  LEU A 229                    
SITE     4 AC3 24 GLN A 268  PHE A 271  GLU A 311  ILE A 323                    
SITE     5 AC3 24 GLU A 324   MG A 501   MG A 502  P0D A 504                    
SITE     6 AC3 24 HOH A 631  HOH A 685  HOH A 706  HOH A 719                    
SITE     1 AC4 19 LEU A  12  GLY A  13  GLY A  14  ALA A 183                    
SITE     2 AC4 19 SER A 184  GLU A 273  HIS A 309  GLU A 311                    
SITE     3 AC4 19 GLU A 324  ARG A 328  GLY A 331   MG A 501                    
SITE     4 AC4 19  MG A 502  ADP A 503  HOH A 650  HOH A 719                    
SITE     5 AC4 19 HOH A 721  HOH A 744  HOH A 745                               
CRYST1  130.787  130.787  147.742  90.00  90.00 120.00 P 65 2 2     12          
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      0.007646  0.004414  0.000000        0.00000                         
SCALE2      0.000000  0.008829  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.006769        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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