HEADER    HYDROLASE                               19-FEB-04   1VAT              
TITLE     IODINE DERIVATIVE OF HEN EGG-WHITE LYSOZYME                           
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: LYSOZYME C;                                                
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C, ALLERGEN GAL D 4, GAL D IV;  
COMPND   5 EC: 3.2.1.17                                                         
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;                                  
SOURCE   3 ORGANISM_COMMON: CHICKEN;                                            
SOURCE   4 ORGANISM_TAXID: 9031;                                                
SOURCE   5 TISSUE: HEN EGG-WHITE                                                
KEYWDS    IODINE-DERIVATIVE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE,   
KEYWDS   2 RSGI, STRUCTURAL GENOMICS, HYDROLASE                                 
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    K.TAKEDA,H.MIYATAKE,S.Y.PARK,M.KAWAMOTO,N.KAMIYA,K.MIKI,RIKEN         
AUTHOR   2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)                     
REVDAT   5   23-OCT-24 1VAT    1       REMARK                                   
REVDAT   4   27-DEC-23 1VAT    1       REMARK                                   
REVDAT   3   23-JUN-09 1VAT    1       AUTHOR                                   
REVDAT   2   24-FEB-09 1VAT    1       VERSN                                    
REVDAT   1   08-MAR-05 1VAT    0                                                
JRNL        AUTH   K.TAKEDA,H.MIYATAKE,S.Y.PARK,M.KAWAMOTO,N.KAMIYA,K.MIKI      
JRNL        TITL   MULTI-WAVELENGTH ANOMALOUS DIFFRACTION METHOD FOR I AND XE   
JRNL        TITL 2 ATOMS USING ULTRA-HIGH-ENERGY X-RAYS FROM SPRING-8           
JRNL        REF    J.APPL.CRYSTALLOGR.           V.  37   925 2004              
JRNL        REFN                   ISSN 0021-8898                               
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.60 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS                                                  
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-              
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,              
REMARK   3               : READ,RICE,SIMONSON,WARREN                            
REMARK   3                                                                      
REMARK   3  REFINEMENT TARGET : ENGH & HUBER                                    
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 25.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL                           
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL                           
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 99.6                           
REMARK   3   NUMBER OF REFLECTIONS             : 15774                          
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 SET) : 0.205                           
REMARK   3   FREE R VALUE                     : 0.232                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL                            
REMARK   3   FREE R VALUE TEST SET COUNT      : 775                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL                            
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL                         
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.60                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.70                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 93.80                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL                         
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2210                       
REMARK   3   BIN FREE R VALUE                    : 0.2840                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 123                          
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.019                        
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 995                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 2                                       
REMARK   3   SOLVENT ATOMS            : 94                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 16.40                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 16.30                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -0.14000                                             
REMARK   3    B22 (A**2) : -0.14000                                             
REMARK   3    B33 (A**2) : 0.28000                                              
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : 0.00000                                              
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.18                            
REMARK   3   ESD FROM SIGMAA              (A) : 0.08                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.21                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.16                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.004                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.300                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL                            
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL                            
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : ISOTROPIC                                 
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED : NULL                                                 
REMARK   3   KSOL        : NULL                                                 
REMARK   3   BSOL        : NULL                                                 
REMARK   3                                                                      
REMARK   3  NCS MODEL : NULL                                                    
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT          
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL                 
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  PARAMETER FILE  1  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1VAT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-FEB-04.                  
REMARK 100 THE DEPOSITION ID IS D_1000006411.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 26-APR-01                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 5.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SPRING-8                           
REMARK 200  BEAMLINE                       : BL41XU                             
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.5400, 0.3746, 0.3734             
REMARK 200  MONOCHROMATOR                  : SI (111)                           
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH                        
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                           
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 15776                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.600                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 25.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.5                               
REMARK 200  DATA REDUNDANCY                : 12.10                              
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : 0.06100                            
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 32.2000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.66                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 99.9                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : 0.21200                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 5.500                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: MAD                                            
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD                          
REMARK 200 SOFTWARE USED: SHARP                                                 
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 34.27                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 50MG/ML HEWL, 20%(W/V) PEG4000, 100MM    
REMARK 280  SODIUM CITRATE (PH 5.5), 100MM SODIUM IODIDE, AND 20%(V/V)          
REMARK 280  GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K           
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2                        
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,-Y,Z+1/2                                             
REMARK 290       3555   -Y+1/2,X+1/2,Z+3/4                                      
REMARK 290       4555   Y+1/2,-X+1/2,Z+1/4                                      
REMARK 290       5555   -X+1/2,Y+1/2,-Z+3/4                                     
REMARK 290       6555   X+1/2,-Y+1/2,-Z+1/4                                     
REMARK 290       7555   Y,X,-Z                                                  
REMARK 290       8555   -Y,-X,-Z+1/2                                            
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       18.77000            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       39.17500            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       39.17500            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       28.15500            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       39.17500            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       39.17500            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000        9.38500            
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       39.17500            
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       39.17500            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       28.15500            
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       39.17500            
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       39.17500            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000        9.38500            
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       18.77000            
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 375                                                                      
REMARK 375 SPECIAL POSITION                                                     
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS            
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL          
REMARK 375 POSITIONS.                                                           
REMARK 375                                                                      
REMARK 375 ATOM RES CSSEQI                                                      
REMARK 375      HOH A 395  LIES ON A SPECIAL POSITION.                          
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     ARG A  61    CG   CD   NE   CZ   NH1  NH2                        
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 301                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1VAU   RELATED DB: PDB                                   
REMARK 900 XENON DERIVATIVE                                                     
REMARK 900 RELATED ID: MY_001000041.1   RELATED DB: TARGETDB                    
DBREF  1VAT A    1   129  UNP    P00698   LYSC_CHICK      19    147             
SEQRES   1 A  129  LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS          
SEQRES   2 A  129  ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY          
SEQRES   3 A  129  ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN          
SEQRES   4 A  129  THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP          
SEQRES   5 A  129  TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN          
SEQRES   6 A  129  ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE          
SEQRES   7 A  129  PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER          
SEQRES   8 A  129  VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY          
SEQRES   9 A  129  MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY          
SEQRES  10 A  129  THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU              
HET    IOD  A 300       1                                                       
HET    IOD  A 301       1                                                       
HETNAM     IOD IODIDE ION                                                       
FORMUL   2  IOD    2(I 1-)                                                      
FORMUL   4  HOH   *94(H2 O)                                                     
HELIX    1   1 GLY A    4  HIS A   15  1                                  12    
HELIX    2   2 ASN A   19  TYR A   23  5                                   5    
HELIX    3   3 SER A   24  ASN A   37  1                                  14    
HELIX    4   4 PRO A   79  SER A   85  5                                   7    
HELIX    5   5 ILE A   88  SER A  100  1                                  13    
HELIX    6   6 ASN A  103  ALA A  107  5                                   5    
HELIX    7   7 TRP A  108  CYS A  115  1                                   8    
HELIX    8   8 ASP A  119  ARG A  125  5                                   7    
SHEET    1   A 3 THR A  43  ARG A  45  0                                        
SHEET    2   A 3 THR A  51  TYR A  53 -1  O  ASP A  52   N  ASN A  44           
SHEET    3   A 3 ILE A  58  ASN A  59 -1  O  ILE A  58   N  TYR A  53           
SSBOND   1 CYS A    6    CYS A  127                          1555   1555  2.03  
SSBOND   2 CYS A   30    CYS A  115                          1555   1555  2.03  
SSBOND   3 CYS A   64    CYS A   80                          1555   1555  2.04  
SSBOND   4 CYS A   76    CYS A   94                          1555   1555  2.04  
SITE     1 AC1  3 ARG A  21  TYR A  23  ASN A 113                               
CRYST1   78.350   78.350   37.540  90.00  90.00  90.00 P 43 21 2     8          
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      0.012763  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.012763  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.026638        0.00000