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Database: PDB
Entry: 5VYG
LinkDB: 5VYG
Original site: 5VYG 
HEADER    TRANSFERASE, HYDROLASE                  25-MAY-17   5VYG              
TITLE     CRYSTAL STRUCTURE OF HFA9 EGF REPEAT WITH O-GLUCOSE TRISACCHARIDE     
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: COAGULATION FACTOR IX;                                     
COMPND   3 CHAIN: B, A, C;                                                      
COMPND   4 SYNONYM: CHRISTMAS FACTOR,PLASMA THROMBOPLASTIN COMPONENT,PTC;       
COMPND   5 EC: 3.4.21.22;                                                       
COMPND   6 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: F9;                                                            
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562                                         
KEYWDS    NOTCH REGULATION, EGF REPEAT, GLYCOSYLATION, TRANSFERASE-HYDROLASE    
KEYWDS   2 COMPLEX, TRANSFERASE, HYDROLASE                                      
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    H.J.YU,H.L.LI                                                         
REVDAT   2   28-FEB-18 5VYG    1       JRNL                                     
REVDAT   1   09-AUG-17 5VYG    0                                                
JRNL        AUTH   H.TAKEUCHI,H.YU,H.HAO,M.TAKEUCHI,A.ITO,H.LI,R.S.HALTIWANGER  
JRNL        TITL   O-GLYCOSYLATION MODULATES THE STABILITY OF EPIDERMAL GROWTH  
JRNL        TITL 2 FACTOR-LIKE REPEATS AND THEREBY REGULATES NOTCH TRAFFICKING  
JRNL        REF    J. BIOL. CHEM.                V. 292 15964 2017              
JRNL        REFN                   ESSN 1083-351X                               
JRNL        PMID   28729422                                                     
JRNL        DOI    10.1074/JBC.M117.800102                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.20 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : REFMAC 5.6.0117                                      
REMARK   3   AUTHORS     : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,              
REMARK   3               : NICHOLLS,WINN,LONG,VAGIN                             
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 46.16                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : NULL                           
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.8                           
REMARK   3   NUMBER OF REFLECTIONS             : 7814                           
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) : 0.214                           
REMARK   3   R VALUE            (WORKING SET) : 0.212                           
REMARK   3   FREE R VALUE                     : 0.259                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.600                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 377                             
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) : 2.20                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.26                         
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 546                          
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 100.0                        
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2600                       
REMARK   3   BIN FREE R VALUE SET COUNT          : 28                           
REMARK   3   BIN FREE R VALUE                    : 0.3320                       
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 958                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 90                                      
REMARK   3   SOLVENT ATOMS            : 37                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 37.00                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -0.02000                                             
REMARK   3    B22 (A**2) : -0.96000                                             
REMARK   3    B33 (A**2) : 0.96000                                              
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : -0.25000                                             
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.                                 
REMARK   3   ESU BASED ON R VALUE                            (A): 0.265         
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.216         
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.160         
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.412         
REMARK   3                                                                      
REMARK   3 CORRELATION COEFFICIENTS.                                            
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.939                         
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.913                         
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT      
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  1078 ; 0.009 ; 0.020       
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  1469 ; 1.490 ; 2.048       
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL       
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   125 ; 6.362 ; 5.000       
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):    53 ;44.180 ;27.736       
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   151 ;17.405 ;15.000       
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):  NULL ;  NULL ;  NULL       
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   165 ; 0.083 ; 0.200       
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):   784 ; 0.004 ; 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):  NULL ;  NULL ;  NULL       
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   MAIN-CHAIN ANGLE OTHER ATOMS   (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN ANGLE OTHER ATOMS   (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   LONG RANGE B REFINED ATOMS     (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   LONG RANGE B OTHER ATOMS       (A**2):  NULL ;  NULL ;  NULL       
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  : NULL                                       
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED : MASK                                                 
REMARK   3   PARAMETERS FOR MASK CALCULATION                                    
REMARK   3   VDW PROBE RADIUS   : 1.20                                          
REMARK   3   ION PROBE RADIUS   : 0.80                                          
REMARK   3   SHRINKAGE RADIUS   : 0.80                                          
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN    
REMARK   3  THE INPUT                                                           
REMARK   4                                                                      
REMARK   4 5VYG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-17.                  
REMARK 100 THE DEPOSITION ID IS D_1000228144.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 06-SEP-15                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : NULL                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : APS                                
REMARK 200  BEAMLINE                       : 31-ID                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9793                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : RAYONIX MX225HE                    
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : SCALA                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 7814                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.200                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.8                               
REMARK 200  DATA REDUNDANCY                : 7.500                              
REMARK 200  R MERGE                    (I) : 0.10400                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 12.6000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.32                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0                              
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.51500                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 4.500                              
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: 1EDM                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 47.69                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 15% GLYCEROL, 1.6 M   
REMARK 280  (NH4)2SO4, 5% 2,2,2-TRIFLUOROETHANOL, VAPOR DIFFUSION, HANGING      
REMARK 280  DROP, TEMPERATURE 293K                                              
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1                          
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,Y,-Z                                                 
REMARK 290       3555   X+1/2,Y+1/2,Z                                           
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        0.00000            
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   3  1.000000  0.000000  0.000000       46.20850            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       23.42000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       46.20850            
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000       23.42000            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1, 2, 3                                                 
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: PISA                                                  
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B                                     
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 350                                                                      
REMARK 350 BIOMOLECULE: 2                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
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 350                                                                      
REMARK 350 BIOMOLECULE: 3                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C                                     
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     GLU B    86                                                      
REMARK 465     HIS B    87                                                      
REMARK 465     HIS B    88                                                      
REMARK 465     HIS B    89                                                      
REMARK 465     HIS B    90                                                      
REMARK 465     HIS B    91                                                      
REMARK 465     HIS B    92                                                      
REMARK 465     GLU A    86                                                      
REMARK 465     HIS A    87                                                      
REMARK 465     HIS A    88                                                      
REMARK 465     HIS A    89                                                      
REMARK 465     HIS A    90                                                      
REMARK 465     HIS A    91                                                      
REMARK 465     HIS A    92                                                      
REMARK 465     MET C    43                                                      
REMARK 465     GLU C    86                                                      
REMARK 465     HIS C    87                                                      
REMARK 465     HIS C    88                                                      
REMARK 465     HIS C    89                                                      
REMARK 465     HIS C    90                                                      
REMARK 465     HIS C    91                                                      
REMARK 465     HIS C    92                                                      
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     LEU B  85    CG   CD1  CD2                                       
REMARK 470     MET A  43    CG   SD   CE                                        
REMARK 470     ASP A  44    CG   OD1  OD2                                       
REMARK 470     ILE A  45    CG1  CG2  CD1                                       
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   OG   SER A    53     O51  GXX A   101              1.75            
REMARK 500   OG   SER B    53     O51  GXX B   101              2.00            
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    SER A  68      170.95    179.64                                   
REMARK 500    PHE C  75      123.93    -36.92                                   
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 B 102  CA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 ASP B  47   OD2                                                    
REMARK 620 2 GLY B  48   O    94.1                                              
REMARK 620 3 GLN B  50   OE1  77.8  88.2                                        
REMARK 620 4 ASP B  64   OD1 150.0  92.4  73.2                                  
REMARK 620 5 ASP B  64   OD2 155.7  91.4 126.0  52.9                            
REMARK 620 6 ASP B  65   O    87.0 173.0  85.3  83.3  90.4                      
REMARK 620 7 ASN C  58   OD1  75.8  98.9 153.0 131.9  80.0  88.1                
REMARK 620 N                    1     2     3     4     5     6                 
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              CA B 103  CA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 ASN B  58   OD1                                                    
REMARK 620 2 ASP A  47   OD1  71.7                                              
REMARK 620 3 GLY A  48   O    97.0  91.6                                        
REMARK 620 4 GLN A  50   OE1 158.1  86.4  84.6                                  
REMARK 620 5 ASP A  64   OD1 128.5 158.9  91.7  73.1                            
REMARK 620 6 ASP A  64   OD2  76.3 147.9  95.2 125.4  52.3                      
REMARK 620 7 ASP A  65   O    94.6  87.5 167.4  82.8  84.8  92.2                
REMARK 620 N                    1     2     3     4     5     6                 
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              CA C 102  CA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 ASP C  47   OD2                                                    
REMARK 620 2 GLY C  48   O   100.0                                              
REMARK 620 3 GLN C  50   OE1  89.0  84.8                                        
REMARK 620 4 ASP C  64   OD1 160.1  85.3  72.3                                  
REMARK 620 5 ASP C  64   OD2 146.7  93.9 122.5  50.4                            
REMARK 620 6 ASP C  65   O    88.1 168.4  87.1  84.4  83.5                      
REMARK 620 7 ASN A  58   OD1 101.4  52.3  33.5  66.6 110.9 118.2                
REMARK 620 N                    1     2     3     4     5     6                 
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue GXX B 101                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 102                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 103                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC4                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue CA C 102                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC5                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide GXX A 101 and SER A    
REMARK 800  53                                                                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC6                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide GXX C 101 and SER C    
REMARK 800  53                                                                  
DBREF  5VYG B   46    84  UNP    P00740   FA9_HUMAN       92    130             
DBREF  5VYG A   46    84  UNP    P00740   FA9_HUMAN       92    130             
DBREF  5VYG C   46    84  UNP    P00740   FA9_HUMAN       92    130             
SEQADV 5VYG MET B   43  UNP  P00740              INITIATING METHIONINE          
SEQADV 5VYG ASP B   44  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG ILE B   45  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG LEU B   85  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG GLU B   86  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS B   87  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS B   88  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS B   89  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS B   90  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS B   91  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS B   92  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG MET A   43  UNP  P00740              INITIATING METHIONINE          
SEQADV 5VYG ASP A   44  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG ILE A   45  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG LEU A   85  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG GLU A   86  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS A   87  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS A   88  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS A   89  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS A   90  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS A   91  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS A   92  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG MET C   43  UNP  P00740              INITIATING METHIONINE          
SEQADV 5VYG ASP C   44  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG ILE C   45  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG LEU C   85  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG GLU C   86  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS C   87  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS C   88  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS C   89  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS C   90  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS C   91  UNP  P00740              EXPRESSION TAG                 
SEQADV 5VYG HIS C   92  UNP  P00740              EXPRESSION TAG                 
SEQRES   1 B   50  MET ASP ILE VAL ASP GLY ASP GLN CYS GLU SER ASN PRO          
SEQRES   2 B   50  CYS LEU ASN GLY GLY SER CYS LYS ASP ASP ILE ASN SER          
SEQRES   3 B   50  TYR GLU CYS TRP CYS PRO PHE GLY PHE GLU GLY LYS ASN          
SEQRES   4 B   50  CYS GLU LEU LEU GLU HIS HIS HIS HIS HIS HIS                  
SEQRES   1 A   50  MET ASP ILE VAL ASP GLY ASP GLN CYS GLU SER ASN PRO          
SEQRES   2 A   50  CYS LEU ASN GLY GLY SER CYS LYS ASP ASP ILE ASN SER          
SEQRES   3 A   50  TYR GLU CYS TRP CYS PRO PHE GLY PHE GLU GLY LYS ASN          
SEQRES   4 A   50  CYS GLU LEU LEU GLU HIS HIS HIS HIS HIS HIS                  
SEQRES   1 C   50  MET ASP ILE VAL ASP GLY ASP GLN CYS GLU SER ASN PRO          
SEQRES   2 C   50  CYS LEU ASN GLY GLY SER CYS LYS ASP ASP ILE ASN SER          
SEQRES   3 C   50  TYR GLU CYS TRP CYS PRO PHE GLY PHE GLU GLY LYS ASN          
SEQRES   4 C   50  CYS GLU LEU LEU GLU HIS HIS HIS HIS HIS HIS                  
HET    GXX  B 101      29                                                       
HET     CA  B 102       1                                                       
HET     CA  B 103       1                                                       
HET    GXX  A 101      29                                                       
HET    GXX  C 101      29                                                       
HET     CA  C 102       1                                                       
HETNAM     GXX ALPHA-D-XYLOPYRANOSYL-(1->3)-ALPHA-D-XYLOPYRANOSYL-(1-           
HETNAM   2 GXX  >3)-BETA-D-GLUCOPYRANOSE                                        
HETNAM      CA CALCIUM ION                                                      
FORMUL   4  GXX    3(C16 H28 O14)                                               
FORMUL   5   CA    3(CA 2+)                                                     
FORMUL  10  HOH   *37(H2 O)                                                     
SHEET    1 AA1 2 SER B  61  ASP B  64  0                                        
SHEET    2 AA1 2 TYR B  69  TRP B  72 -1  O  TRP B  72   N  SER B  61           
SHEET    1 AA2 2 SER A  61  ASP A  65  0                                        
SHEET    2 AA2 2 SER A  68  TRP A  72 -1  O  TRP A  72   N  SER A  61           
SHEET    1 AA3 2 SER C  61  ASP C  65  0                                        
SHEET    2 AA3 2 SER C  68  TRP C  72 -1  O  TRP C  72   N  SER C  61           
SSBOND   1 CYS B   51    CYS B   62                          1555   1555  2.06  
SSBOND   2 CYS B   56    CYS B   71                          1555   1555  2.03  
SSBOND   3 CYS B   73    CYS B   82                          1555   1555  2.07  
SSBOND   4 CYS A   51    CYS A   62                          1555   1555  2.07  
SSBOND   5 CYS A   56    CYS A   71                          1555   1555  2.04  
SSBOND   6 CYS A   73    CYS A   82                          1555   1555  2.08  
SSBOND   7 CYS C   51    CYS C   62                          1555   1555  2.07  
SSBOND   8 CYS C   56    CYS C   71                          1555   1555  2.03  
SSBOND   9 CYS C   73    CYS C   82                          1555   1555  2.09  
LINK         OD2 ASP B  47                CA    CA B 102     1555   1555  2.59  
LINK         O   GLY B  48                CA    CA B 102     1555   1555  2.36  
LINK         OE1 GLN B  50                CA    CA B 102     1555   1555  2.44  
LINK         OG  SER B  53                 C11 GXX B 101     1555   1555  1.21  
LINK         OD1 ASN B  58                CA    CA B 103     1555   1555  2.29  
LINK         OD1 ASP B  64                CA    CA B 102     1555   1555  2.50  
LINK         OD2 ASP B  64                CA    CA B 102     1555   1555  2.45  
LINK         O   ASP B  65                CA    CA B 102     1555   1555  2.30  
LINK         OD1 ASP A  47                CA    CA B 103     1555   1555  2.68  
LINK         O   GLY A  48                CA    CA B 103     1555   1555  2.39  
LINK         OE1 GLN A  50                CA    CA B 103     1555   1555  2.34  
LINK         OG  SER A  53                 C11 GXX A 101     1555   1555  1.42  
LINK         OD1 ASP A  64                CA    CA B 103     1555   1555  2.49  
LINK         OD2 ASP A  64                CA    CA B 103     1555   1555  2.50  
LINK         O   ASP A  65                CA    CA B 103     1555   1555  2.42  
LINK         OD2 ASP C  47                CA    CA C 102     1555   1555  2.91  
LINK         O   GLY C  48                CA    CA C 102     1555   1555  2.40  
LINK         OE1 GLN C  50                CA    CA C 102     1555   1555  2.37  
LINK         OG  SER C  53                 C11 GXX C 101     1555   1555  1.30  
LINK         OD1 ASN C  58                CA    CA B 102     1555   1555  2.26  
LINK         OD1 ASP C  64                CA    CA C 102     1555   1555  2.49  
LINK         OD2 ASP C  64                CA    CA C 102     1555   1555  2.61  
LINK         O   ASP C  65                CA    CA C 102     1555   1555  2.34  
LINK         OD1 ASN A  58                CA    CA C 102     1555   1556  2.40  
SITE     1 AC1  6 GLN B  50  SER B  53  ASN B  67  SER B  68                    
SITE     2 AC1  6 TYR B  69  LYS B  80                                          
SITE     1 AC2  6 ASP B  47  GLY B  48  GLN B  50  ASP B  64                    
SITE     2 AC2  6 ASP B  65  ASN C  58                                          
SITE     1 AC3  6 ASP A  47  GLY A  48  GLN A  50  ASP A  64                    
SITE     2 AC3  6 ASP A  65  ASN B  58                                          
SITE     1 AC4  6 ASN A  58  ASP C  47  GLY C  48  GLN C  50                    
SITE     2 AC4  6 ASP C  64  ASP C  65                                          
SITE     1 AC5 13 GLN A  50  CYS A  51  GLU A  52  ASN A  54                    
SITE     2 AC5 13 PRO A  55  ASN A  67  SER A  68  TYR A  69                    
SITE     3 AC5 13 PRO A  74  PHE A  75  LYS A  80  HOH A 203                    
SITE     4 AC5 13 HOH A 207                                                     
SITE     1 AC6 10 GLN C  50  CYS C  51  GLU C  52  ASN C  54                    
SITE     2 AC6 10 PRO C  55  ASN C  67  SER C  68  TYR C  69                    
SITE     3 AC6 10 LYS C  80  HOH C 207                                          
CRYST1   92.417   46.840   37.259  90.00  92.58  90.00 C 1 2 1      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      0.010820  0.000000  0.000487        0.00000                         
SCALE2      0.000000  0.021349  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.026867        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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