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Database: PDB
Entry: 1DI3
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Original site: 1DI3 
HEADER    HYDROLASE                               28-NOV-99   1DI3              
TITLE     ROLE OF AMINO ACID RESIDUES AT TURNS IN THE CONFORMATIONAL STABILITY  
TITLE    2 AND FOLDING OF HUMAN LYSOZYME                                        
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: LYSOZYME C;                                                
COMPND   3 CHAIN: A;                                                            
COMPND   4 EC: 3.2.1.17;                                                        
COMPND   5 ENGINEERED: YES;                                                     
COMPND   6 MUTATION: YES                                                        
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE;                         
SOURCE   6 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST;                             
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 4932;                                       
SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PGEL125                                   
KEYWDS    STABILITY, TURN, MUTANT, HYDROLASE                                    
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    K.TAKANO,Y.YAMAGATA,K.YUTANI                                          
REVDAT   4   03-NOV-21 1DI3    1       REMARK SEQADV LINK                       
REVDAT   3   24-FEB-09 1DI3    1       VERSN                                    
REVDAT   2   23-AUG-00 1DI3    1       JRNL                                     
REVDAT   1   08-DEC-99 1DI3    0                                                
JRNL        AUTH   K.TAKANO,Y.YAMAGATA,K.YUTANI                                 
JRNL        TITL   ROLE OF AMINO ACID RESIDUES AT TURNS IN THE CONFORMATIONAL   
JRNL        TITL 2 STABILITY AND FOLDING OF HUMAN LYSOZYME.                     
JRNL        REF    BIOCHEMISTRY                  V.  39  8655 2000              
JRNL        REFN                   ISSN 0006-2960                               
JRNL        PMID   10913274                                                     
JRNL        DOI    10.1021/BI9928694                                            
REMARK   1                                                                      
REMARK   1 REFERENCE 1                                                          
REMARK   1  AUTH   K.TAKANO,Y.YAMAGATA,J.FUNAHASHI,Y.HIOKI,S.KURAMITSU,K.YUTANI 
REMARK   1  TITL   CONTRIBUTION OF INTRA-AND INTERMOLECULAR HYDROGEN BONDS TO   
REMARK   1  TITL 2 THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME               
REMARK   1  REF    BIOCHEMISTRY                  V.  38 12698 1999              
REMARK   1  REFN                   ISSN 0006-2960                               
REMARK   1  DOI    10.1021/BI9910169                                            
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.80 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.1                                           
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 8.00                           
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 3.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL                           
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL                           
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 86.6                           
REMARK   3   NUMBER OF REFLECTIONS             : 9573                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : NULL                            
REMARK   3   FREE R VALUE TEST SET SELECTION  : NULL                            
REMARK   3   R VALUE            (WORKING SET) : 0.190                           
REMARK   3   FREE R VALUE                     : NULL                            
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL                            
REMARK   3   FREE R VALUE TEST SET COUNT      : NULL                            
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) : NULL                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL                         
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL                         
REMARK   3   BIN R VALUE           (WORKING SET) : NULL                         
REMARK   3   BIN FREE R VALUE                    : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL                         
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL                         
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 1022                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 1                                       
REMARK   3   SOLVENT ATOMS            : 224                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL                            
REMARK   3   ESD FROM SIGMAA              (A) : NULL                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : NULL                            
REMARK   3   BOND ANGLES            (DEGREES) : NULL                            
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL                            
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL                            
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : NULL                                      
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  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 1DI3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-99.                  
REMARK 100 THE DEPOSITION ID IS D_1000010103.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : NULL                               
REMARK 200  TEMPERATURE           (KELVIN) : 100.0                              
REMARK 200  PH                             : 4.5                                
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) : 0.708                              
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : NULL                               
REMARK 200  DETECTOR MANUFACTURER          : NULL                               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : NULL                               
REMARK 200  DATA SCALING SOFTWARE          : NULL                               
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 10060                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.800                              
REMARK 200  RESOLUTION RANGE LOW       (A) : NULL                               
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 90.8                               
REMARK 200  DATA REDUNDANCY                : NULL                               
REMARK 200  R MERGE                    (I) : 0.04500                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : NULL                               
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.83                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 90.0                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.08900                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL                         
REMARK 200 SOFTWARE USED: X-PLOR                                                
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 37.45                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM PHOSPHATE, SODIUM CHLORIDE, PH    
REMARK 280  4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K                
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
REMARK 290       4555   X+1/2,-Y+1/2,-Z                                         
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       28.14000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       16.23000            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       31.48000            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       16.23000            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       28.14000            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       31.48000            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
REMARK 350 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 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                              NA A 601  NA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 SER A  61   O                                                      
REMARK 620 2 CYS A  65   O    87.3                                              
REMARK 620 3 VAL A  74   O   104.4 102.7                                        
REMARK 620 4 HOH A 173   O    90.4  89.8 160.9                                  
REMARK 620 5 HOH A 235   O   158.8 108.1  86.8  75.4                            
REMARK 620 N                    1     2     3     4                             
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 601                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1CJ6   RELATED DB: PDB                                   
REMARK 900 1CJ6 CONTAINS OTHER MUTANT HUMAN LYSOZYME                            
REMARK 900 RELATED ID: 1DI4   RELATED DB: PDB                                   
REMARK 900 HUMAN LYSOZYME, RESIDUES 47-48 DELETED                               
REMARK 900 RELATED ID: 1DI5   RELATED DB: PDB                                   
REMARK 900 HUMAN LYSOZYME, RESIDUE 101 DELETED                                  
DBREF  1DI3 A    1   130  UNP    P61626   LYSC_HUMAN      19    148             
SEQADV 1DI3 GLY A   50  UNP  P61626    ARG    68 ENGINEERED MUTATION            
SEQRES   1 A  130  LYS VAL PHE GLU ARG CYS GLU LEU ALA ARG THR LEU LYS          
SEQRES   2 A  130  ARG LEU GLY MET ASP GLY TYR ARG GLY ILE SER LEU ALA          
SEQRES   3 A  130  ASN TRP MET CYS LEU ALA LYS TRP GLU SER GLY TYR ASN          
SEQRES   4 A  130  THR ARG ALA THR ASN TYR ASN ALA GLY ASP GLY SER THR          
SEQRES   5 A  130  ASP TYR GLY ILE PHE GLN ILE ASN SER ARG TYR TRP CYS          
SEQRES   6 A  130  ASN ASP GLY LYS THR PRO GLY ALA VAL ASN ALA CYS HIS          
SEQRES   7 A  130  LEU SER CYS SER ALA LEU LEU GLN ASP ASN ILE ALA ASP          
SEQRES   8 A  130  ALA VAL ALA CYS ALA LYS ARG VAL VAL ARG ASP PRO GLN          
SEQRES   9 A  130  GLY ILE ARG ALA TRP VAL ALA TRP ARG ASN ARG CYS GLN          
SEQRES  10 A  130  ASN ARG ASP VAL ARG GLN TYR VAL GLN GLY CYS GLY VAL          
HET     NA  A 601       1                                                       
HETNAM      NA SODIUM ION                                                       
FORMUL   2   NA    NA 1+                                                        
FORMUL   3  HOH   *224(H2 O)                                                    
HELIX    1   1 GLU A    4  LEU A   15  1                                  12    
HELIX    2   2 SER A   24  GLY A   37  1                                  14    
HELIX    3   3 CYS A   81  GLN A   86  5                                   6    
HELIX    4   4 ILE A   89  ARG A  101  1                                  13    
HELIX    5   5 GLN A  104  ALA A  108  5                                   5    
HELIX    6   6 TRP A  109  CYS A  116  1                                   8    
HELIX    7   7 VAL A  121  VAL A  125  5                                   5    
SHEET    1   A 3 THR A  43  ASN A  46  0                                        
SHEET    2   A 3 SER A  51  TYR A  54 -1  O  SER A  51   N  ASN A  46           
SHEET    3   A 3 ILE A  59  ASN A  60 -1  O  ILE A  59   N  TYR A  54           
SSBOND   1 CYS A    6    CYS A  128                          1555   1555  2.04  
SSBOND   2 CYS A   30    CYS A  116                          1555   1555  2.03  
SSBOND   3 CYS A   65    CYS A   81                          1555   1555  2.05  
SSBOND   4 CYS A   77    CYS A   95                          1555   1555  2.03  
LINK         O   SER A  61                NA    NA A 601     1555   1555  2.21  
LINK         O   CYS A  65                NA    NA A 601     1555   1555  2.32  
LINK         O   VAL A  74                NA    NA A 601     1555   1555  2.37  
LINK         O   HOH A 173                NA    NA A 601     1555   1555  2.47  
LINK         O   HOH A 235                NA    NA A 601     1555   1555  2.42  
SITE     1 AC1  6 SER A  61  CYS A  65  ALA A  73  VAL A  74                    
SITE     2 AC1  6 HOH A 173  HOH A 235                                          
CRYST1   56.280   62.960   32.460  90.00  90.00  90.00 P 21 21 21    4          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.017768  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.015883  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.030807        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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