?

Promode Elastic




    Copyright ©  WASEDA Univ,Japan. All rights reserved.

    Header

    HEADER    OXIDOREDUCTASE                          23-JUL-14   4U4I              
    TITLE     MEGAVIRUS CHILENSIS SUPEROXIDE DISMUTASE                              
    COMPND    MOL_ID: 1;                                                            
    COMPND   2 MOLECULE: CU/ZN SUPEROXIDE DISMUTASE;                                
    COMPND   3 CHAIN: A, B;                                                         
    COMPND   4 EC: 1.15.1.1;                                                        
    COMPND   5 ENGINEERED: YES;                                                     
    COMPND   6 MUTATION: YES;                                                       
    COMPND   7 OTHER_DETAILS: THE LOOPS INVOLVED IN COPPER AND ZINC BINDING ARE     
    COMPND   8 DISRDERED IN THE CRYSTAL STRUCTURE                                   
    SOURCE    MOL_ID: 1;                                                            
    SOURCE   2 ORGANISM_SCIENTIFIC: MEGAVIRUS CHILIENSIS;                           
    SOURCE   3 ORGANISM_TAXID: 1094892;                                             
    SOURCE   4 GENE: MG277;                                                         
    SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);                       
    SOURCE   6 EXPRESSION_SYSTEM_TAXID: 469008;                                     
    SOURCE   7 EXPRESSION_SYSTEM_VARIANT: ROSETTA;                                  
    SOURCE   8 EXPRESSION_SYSTEM_PLASMID: MODIFIED PETDUET                          
    KEYWDS    CU-ZN SUPEROXIDE DISMUTASE, METAL-FREE, OXIDOREDUCTASE                
    EXPDTA    X-RAY DIFFRACTION                                                     
    AUTHOR    A.LARTIGUE,J.-M.CLAVERIE,B.BURLAT,B.COUTARD,C.ABERGEL                 
    REVDAT   3   24-DEC-14 4U4I    1       JRNL                                     
    REVDAT   2   12-NOV-14 4U4I    1       JRNL                                     
    REVDAT   1   05-NOV-14 4U4I    0                                                
    JRNL        AUTH   A.LARTIGUE,B.BURLAT,B.COUTARD,F.CHASPOUL,J.M.CLAVERIE,       
    JRNL        AUTH 2 C.ABERGEL                                                    
    JRNL        TITL   THE MEGAVIRUS CHILENSIS CU,ZN-SUPEROXIDE DISMUTASE: THE      
    JRNL        TITL 2 FIRST VIRAL STRUCTURE OF A TYPICAL CELLULAR COPPER           
    JRNL        TITL 3 CHAPERONE-INDEPENDENT HYPERSTABLE DIMERIC ENZYME.            
    JRNL        REF    J.VIROL.                      V.  89   824 2015              
    JRNL        REFN                   ESSN 1098-5514                               
    JRNL        PMID   25355875                                                     
    JRNL        DOI    10.1128/JVI.02588-14                                         
    REMARK   1                                                                      
    REMARK   1 REFERENCE 1                                                          
    REMARK   1  AUTH   A.LARTIGUE,N.PHILIPPE,S.JEUDY,C.ABERGEL                      
    REMARK   1  TITL   PRELIMINARY CRYSTALLOGRAPHIC ANALYSIS OF THE MEGAVIRUS       
    REMARK   1  TITL 2 SUPEROXIDE DISMUTASE.                                        
    REMARK   1  REF    ACTA CRYSTALLOGR. SECT. F     V.  68  1557 2012              
    REMARK   1  REF  2 STRUCT. BIOL. CRYST. COMMUN.                                 
    REMARK   1  REFN                   ESSN 1744-3091                               
    REMARK   1  PMID   23192047                                                     
    REMARK   1  DOI    10.1107/S174430911204657X                                    
    REMARK   2                                                                      
    REMARK   2 RESOLUTION.    2.20 ANGSTROMS.                                       
    REMARK   3                                                                      
    REMARK   3 REFINEMENT.                                                          
    REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.9_1692)                     
    REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
    REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
    REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
    REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
    REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
    REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
    REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
    REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
    REMARK   3                                                                      
    REMARK   3    REFINEMENT TARGET : ML                                            
    REMARK   3                                                                      
    REMARK   3  DATA USED IN REFINEMENT.                                            
    REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20                           
    REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 38.04                          
    REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.350                          
    REMARK   3   COMPLETENESS FOR RANGE        (%) : 100.0                          
    REMARK   3   NUMBER OF REFLECTIONS             : 15726                          
    REMARK   3                                                                      
    REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
    REMARK   3   R VALUE     (WORKING + TEST SET) : 0.190                           
    REMARK   3   R VALUE            (WORKING SET) : 0.186                           
    REMARK   3   FREE R VALUE                     : 0.226                           
    REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.000                          
    REMARK   3   FREE R VALUE TEST SET COUNT      : 1573                            
    REMARK   3                                                                      
    REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).                           
    REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE        
    REMARK   3     1 38.0461 -  4.8897    1.00     1415   157  0.2028 0.2314        
    REMARK   3     2  4.8897 -  3.8823    1.00     1323   147  0.1642 0.1884        
    REMARK   3     3  3.8823 -  3.3919    1.00     1293   144  0.1763 0.1934        
    REMARK   3     4  3.3919 -  3.0820    1.00     1283   142  0.1775 0.2320        
    REMARK   3     5  3.0820 -  2.8611    1.00     1270   142  0.1882 0.2638        
    REMARK   3     6  2.8611 -  2.6925    1.00     1270   141  0.1948 0.2614        
    REMARK   3     7  2.6925 -  2.5577    1.00     1270   141  0.2069 0.2717        
    REMARK   3     8  2.5577 -  2.4464    1.00     1255   140  0.1948 0.2331        
    REMARK   3     9  2.4464 -  2.3522    1.00     1255   139  0.1862 0.2201        
    REMARK   3    10  2.3522 -  2.2710    1.00     1256   140  0.1886 0.2568        
    REMARK   3    11  2.2710 -  2.2000    1.00     1263   140  0.2090 0.2767        
    REMARK   3                                                                      
    REMARK   3  BULK SOLVENT MODELLING.                                             
    REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
    REMARK   3   SOLVENT RADIUS     : 1.11                                          
    REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
    REMARK   3   K_SOL              : NULL                                          
    REMARK   3   B_SOL              : NULL                                          
    REMARK   3                                                                      
    REMARK   3  ERROR ESTIMATES.                                                    
    REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.190            
    REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.830           
    REMARK   3                                                                      
    REMARK   3  B VALUES.                                                           
    REMARK   3   FROM WILSON PLOT           (A**2) : 33.83                          
    REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 38.60                          
    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  TWINNING INFORMATION.                                               
    REMARK   3   FRACTION: NULL                                                     
    REMARK   3   OPERATOR: NULL                                                     
    REMARK   3                                                                      
    REMARK   3  DEVIATIONS FROM IDEAL VALUES.                                       
    REMARK   3                 RMSD          COUNT                                  
    REMARK   3   BOND      :  0.009           1980                                  
    REMARK   3   ANGLE     :  1.139           2671                                  
    REMARK   3   CHIRALITY :  0.053            289                                  
    REMARK   3   PLANARITY :  0.005            354                                  
    REMARK   3   DIHEDRAL  : 14.254            719                                  
    REMARK   3                                                                      
    REMARK   3  TLS DETAILS                                                         
    REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
    REMARK   3                                                                      
    REMARK   3  NCS DETAILS                                                         
    REMARK   3   NUMBER OF NCS GROUPS : NULL                                        
    REMARK   3                                                                      
    REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
    REMARK   4                                                                      
    REMARK   4 4U4I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
    REMARK 100                                                                      
    REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUL-14.                  
    REMARK 100 THE DEPOSITION ID IS D_1000202784.                                   
    REMARK 200                                                                      
    REMARK 200 EXPERIMENTAL DETAILS                                                 
    REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
    REMARK 200  DATE OF DATA COLLECTION        : 03-OCT-12                          
    REMARK 200  TEMPERATURE           (KELVIN) : 105                                
    REMARK 200  PH                             : 5.5                                
    REMARK 200  NUMBER OF CRYSTALS USED        : NULL                               
    REMARK 200                                                                      
    REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
    REMARK 200  RADIATION SOURCE               : ESRF                               
    REMARK 200  BEAMLINE                       : BM30A                              
    REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
    REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
    REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9792                             
    REMARK 200  MONOCHROMATOR                  : NULL                               
    REMARK 200  OPTICS                         : NULL                               
    REMARK 200                                                                      
    REMARK 200  DETECTOR TYPE                  : CCD                                
    REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315R                  
    REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
    REMARK 200  DATA SCALING SOFTWARE          : SCALA                              
    REMARK 200                                                                      
    REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 15785                              
    REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.200                              
    REMARK 200  RESOLUTION RANGE LOW       (A) : 39.140                             
    REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
    REMARK 200                                                                      
    REMARK 200 OVERALL.                                                             
    REMARK 200  COMPLETENESS FOR RANGE     (%) : 100.0                              
    REMARK 200  DATA REDUNDANCY                : 14.90                              
    REMARK 200  R MERGE                    (I) : 0.11000                            
    REMARK 200  R SYM                      (I) : NULL                               
    REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 6.3000                             
    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       : 15.00                              
    REMARK 200  R MERGE FOR SHELL          (I) : 0.80000                            
    REMARK 200  R SYM FOR SHELL            (I) : NULL                               
    REMARK 200  <I/SIGMA(I)> FOR SHELL         : 1.000                              
    REMARK 200                                                                      
    REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
    REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD                          
    REMARK 200 SOFTWARE USED: PHENIX                                                
    REMARK 200 STARTING MODEL: NULL                                                 
    REMARK 200                                                                      
    REMARK 200 REMARK: RODS                                                         
    REMARK 280                                                                      
    REMARK 280 CRYSTAL                                                              
    REMARK 280 SOLVENT CONTENT, VS   (%): 40.55                                     
    REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10                     
    REMARK 280                                                                      
    REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE BUFFER, 20%(W/V)    
    REMARK 280  PEG 4000, 20%(V/V) MPD                                              
    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       58.71300            
    REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       35.31300            
    REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       35.31300            
    REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       88.06950            
    REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       35.31300            
    REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       35.31300            
    REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       29.35650            
    REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       35.31300            
    REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       35.31300            
    REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       88.06950            
    REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       35.31300            
    REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       35.31300            
    REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000       29.35650            
    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       58.71300            
    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: DIMERIC                           
    REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC                    
    REMARK 350 SOFTWARE USED: PISA                                                  
    REMARK 350 TOTAL BURIED SURFACE AREA: 1850 ANGSTROM**2                          
    REMARK 350 SURFACE AREA OF THE COMPLEX: 11910 ANGSTROM**2                       
    REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL                          
    REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 465                                                                      
    REMARK 465 MISSING RESIDUES                                                     
    REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
    REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
    REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
    REMARK 465                                                                      
    REMARK 465   M RES C SSSEQI                                                     
    REMARK 465     GLY A     1                                                      
    REMARK 465     PRO A     2                                                      
    REMARK 465     GLY A     3                                                      
    REMARK 465     SER A     4                                                      
    REMARK 465     SER A     5                                                      
    REMARK 465     ARG A     6                                                      
    REMARK 465     TYR A     7                                                      
    REMARK 465     ASP A     8                                                      
    REMARK 465     GLY A    77                                                      
    REMARK 465     VAL A    78                                                      
    REMARK 465     HIS A    79                                                      
    REMARK 465     LYS A    80                                                      
    REMARK 465     ASP A    81                                                      
    REMARK 465     ILE A    82                                                      
    REMARK 465     ASN A    83                                                      
    REMARK 465     ILE A    84                                                      
    REMARK 465     GLN A    85                                                      
    REMARK 465     HIS A    86                                                      
    REMARK 465     ASN A    87                                                      
    REMARK 465     HIS A    88                                                      
    REMARK 465     LEU A   134                                                      
    REMARK 465     GLY A   135                                                      
    REMARK 465     MSE A   136                                                      
    REMARK 465     THR A   137                                                      
    REMARK 465     ASN A   138                                                      
    REMARK 465     HIS A   139                                                      
    REMARK 465     PRO A   140                                                      
    REMARK 465     ASP A   141                                                      
    REMARK 465     SER A   142                                                      
    REMARK 465     LYS A   143                                                      
    REMARK 465     THR A   144                                                      
    REMARK 465     THR A   145                                                      
    REMARK 465     GLY A   146                                                      
    REMARK 465     ASN A   147                                                      
    REMARK 465     SER A   148                                                      
    REMARK 465     GLY B     1                                                      
    REMARK 465     PRO B     2                                                      
    REMARK 465     GLY B     3                                                      
    REMARK 465     SER B     4                                                      
    REMARK 465     SER B     5                                                      
    REMARK 465     ARG B     6                                                      
    REMARK 465     ASN B    76                                                      
    REMARK 465     GLY B    77                                                      
    REMARK 465     VAL B    78                                                      
    REMARK 465     HIS B    79                                                      
    REMARK 465     LYS B    80                                                      
    REMARK 465     ASP B    81                                                      
    REMARK 465     ILE B    82                                                      
    REMARK 465     ASN B    83                                                      
    REMARK 465     ILE B    84                                                      
    REMARK 465     GLN B    85                                                      
    REMARK 465     HIS B    86                                                      
    REMARK 465     ASN B    87                                                      
    REMARK 465     HIS B    88                                                      
    REMARK 465     LEU B    89                                                      
    REMARK 465     GLY B    90                                                      
    REMARK 465     ASP B    91                                                      
    REMARK 465     ASP B   133                                                      
    REMARK 465     LEU B   134                                                      
    REMARK 465     GLY B   135                                                      
    REMARK 465     MSE B   136                                                      
    REMARK 465     THR B   137                                                      
    REMARK 465     ASN B   138                                                      
    REMARK 465     HIS B   139                                                      
    REMARK 465     PRO B   140                                                      
    REMARK 465     ASP B   141                                                      
    REMARK 465     SER B   142                                                      
    REMARK 465     LYS B   143                                                      
    REMARK 465     THR B   144                                                      
    REMARK 465     THR B   145                                                      
    REMARK 465     GLY B   146                                                      
    REMARK 465     ASN B   147                                                      
    REMARK 465     SER B   148                                                      
    REMARK 465     GLY B   149                                                      
    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     TYR B   7    O                                                   
    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   O    HOH A   252     O    HOH A   253              1.84            
    REMARK 500   OD1  ASN A    11     O    HOH A   201              1.98            
    REMARK 500   O    HOH A   215     O    HOH A   224              2.02            
    REMARK 500   O    HOH A   219     O    HOH A   234              2.10            
    REMARK 500   O    HOH B   225     O    HOH B   236              2.10            
    REMARK 500   O    ASP A   133     O    HOH A   202              2.16            
    REMARK 500   O    HOH A   222     O    HOH A   227              2.17            
    REMARK 500                                                                      
    REMARK 500 REMARK: NULL                                                         
    REMARK 500                                                                      
    REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
    REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
    REMARK 500                                                                      
    REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC             
    REMARK 500 SYMMETRY ARE IN CLOSE CONTACT.  AN ATOM LOCATED WITHIN 0.15          
    REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A           
    REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375             
    REMARK 500 INSTEAD OF REMARK 500.  ATOMS WITH NON-BLANK ALTERNATE               
    REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.            
    REMARK 500                                                                      
    REMARK 500 DISTANCE CUTOFF:                                                     
    REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS              
    REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS                  
    REMARK 500                                                                      
    REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI  SSYMOP   DISTANCE          
    REMARK 500   O    HOH A   227     O    HOH B   222     4555     1.72            
    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    CYS A  36      137.86   -172.68                                   
    REMARK 500    ARG A 123     -162.61   -111.01                                   
    REMARK 500    ASN B  63       41.38   -100.40                                   
    REMARK 500    PRO B  74       12.68    -69.90                                   
    REMARK 500    LEU B 112       80.58   -162.84                                   
    REMARK 500                                                                      
    REMARK 500 REMARK: NULL                                                         
    REMARK 500                                                                      
    REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
    REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS                                         
    REMARK 500                                                                      
    REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH          
    REMARK 500 CIS AND TRANS CONFORMATION.  CIS BONDS, IF ANY, ARE LISTED           
    REMARK 500 ON CISPEP RECORDS.  TRANS IS DEFINED AS 180 +/- 30 AND               
    REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.                                  
    REMARK 500                                 MODEL     OMEGA                      
    REMARK 500 ASP A   35     CYS A   36                 -149.99                    
    REMARK 500                                                                      
    REMARK 500 REMARK: NULL                                                         
    DBREF  4U4I A    5   161  UNP    G5CS11   G5CS11_9VIRU     2    158             
    DBREF  4U4I B    5   161  UNP    G5CS11   G5CS11_9VIRU     2    158             
    SEQADV 4U4I GLY A    1  UNP  G5CS11              EXPRESSION TAG                 
    SEQADV 4U4I PRO A    2  UNP  G5CS11              EXPRESSION TAG                 
    SEQADV 4U4I GLY A    3  UNP  G5CS11              EXPRESSION TAG                 
    SEQADV 4U4I SER A    4  UNP  G5CS11              EXPRESSION TAG                 
    SEQADV 4U4I GLY B    1  UNP  G5CS11              EXPRESSION TAG                 
    SEQADV 4U4I PRO B    2  UNP  G5CS11              EXPRESSION TAG                 
    SEQADV 4U4I GLY B    3  UNP  G5CS11              EXPRESSION TAG                 
    SEQADV 4U4I SER B    4  UNP  G5CS11              EXPRESSION TAG                 
    SEQRES   1 A  161  GLY PRO GLY SER SER ARG TYR ASP PHE PHE ASN VAL VAL          
    SEQRES   2 A  161  THR ALA ILE CYS GLN LEU ASP LYS PRO HIS ASP TYR GLY          
    SEQRES   3 A  161  TYR ALA ILE PHE THR GLN LEU PRO ASP CYS THR GLU ILE          
    SEQRES   4 A  161  GLN PHE HIS LEU LYS ASN LEU PRO PRO GLY LYS HIS GLY          
    SEQRES   5 A  161  CYS HIS ILE HIS LYS SER GLY ASP ARG ARG ASN GLY CYS          
    SEQRES   6 A  161  THR SER MSE GLY PRO HIS PHE ASN PRO PHE ASN GLY VAL          
    SEQRES   7 A  161  HIS LYS ASP ILE ASN ILE GLN HIS ASN HIS LEU GLY ASP          
    SEQRES   8 A  161  LEU GLY ASN ILE VAL VAL ASN ASN ASN GLY GLU CYS ASN          
    SEQRES   9 A  161  GLU ILE ILE CYS VAL LYS TYR LEU PRO LEU THR GLY SER          
    SEQRES  10 A  161  ASN GLN ILE ILE GLY ARG GLY LEU VAL ILE HIS GLU LYS          
    SEQRES  11 A  161  GLU ASP ASP LEU GLY MSE THR ASN HIS PRO ASP SER LYS          
    SEQRES  12 A  161  THR THR GLY ASN SER GLY ASP ARG ILE ALA CYS GLY ILE          
    SEQRES  13 A  161  ILE ALA TYR LEU ASN                                          
    SEQRES   1 B  161  GLY PRO GLY SER SER ARG TYR ASP PHE PHE ASN VAL VAL          
    SEQRES   2 B  161  THR ALA ILE CYS GLN LEU ASP LYS PRO HIS ASP TYR GLY          
    SEQRES   3 B  161  TYR ALA ILE PHE THR GLN LEU PRO ASP CYS THR GLU ILE          
    SEQRES   4 B  161  GLN PHE HIS LEU LYS ASN LEU PRO PRO GLY LYS HIS GLY          
    SEQRES   5 B  161  CYS HIS ILE HIS LYS SER GLY ASP ARG ARG ASN GLY CYS          
    SEQRES   6 B  161  THR SER MSE GLY PRO HIS PHE ASN PRO PHE ASN GLY VAL          
    SEQRES   7 B  161  HIS LYS ASP ILE ASN ILE GLN HIS ASN HIS LEU GLY ASP          
    SEQRES   8 B  161  LEU GLY ASN ILE VAL VAL ASN ASN ASN GLY GLU CYS ASN          
    SEQRES   9 B  161  GLU ILE ILE CYS VAL LYS TYR LEU PRO LEU THR GLY SER          
    SEQRES  10 B  161  ASN GLN ILE ILE GLY ARG GLY LEU VAL ILE HIS GLU LYS          
    SEQRES  11 B  161  GLU ASP ASP LEU GLY MSE THR ASN HIS PRO ASP SER LYS          
    SEQRES  12 B  161  THR THR GLY ASN SER GLY ASP ARG ILE ALA CYS GLY ILE          
    SEQRES  13 B  161  ILE ALA TYR LEU ASN                                          
    MODRES 4U4I MSE A   68  MET  MODIFIED RESIDUE                                   
    MODRES 4U4I MSE B   68  MET  MODIFIED RESIDUE                                   
    HET    MSE  A  68       8                                                       
    HET    MSE  B  68       8                                                       
    HETNAM     MSE SELENOMETHIONINE                                                 
    FORMUL   1  MSE    2(C5 H11 N O2 SE)                                            
    FORMUL   3  HOH   *107(H2 O)                                                    
    HELIX    1 AA1 ASN A   63  GLY A   69  5                                   7    
    HELIX    2 AA2 ASN B   63  GLY B   69  5                                   7    
    SHEET    1 AA1 8 ASP A  91  VAL A  97  0                                        
    SHEET    2 AA1 8 GLY A  49  HIS A  56 -1  N  GLY A  49   O  VAL A  97           
    SHEET    3 AA1 8 GLY A 124  HIS A 128 -1  O  HIS A 128   N  GLY A  52           
    SHEET    4 AA1 8 ARG A 151  TYR A 159 -1  O  ALA A 153   N  ILE A 127           
    SHEET    5 AA1 8 VAL A  13  GLN A  18 -1  N  ILE A  16   O  ALA A 158           
    SHEET    6 AA1 8 GLY A  26  LEU A  33 -1  O  PHE A  30   N  ALA A  15           
    SHEET    7 AA1 8 CYS A  36  LEU A  43 -1  O  GLU A  38   N  THR A  31           
    SHEET    8 AA1 8 ILE A 106  VAL A 109 -1  O  ILE A 107   N  ILE A  39           
    SHEET    1 AA2 8 ASN B  94  VAL B  97  0                                        
    SHEET    2 AA2 8 GLY B  49  HIS B  56 -1  N  GLY B  49   O  VAL B  97           
    SHEET    3 AA2 8 GLY B 124  HIS B 128 -1  O  VAL B 126   N  HIS B  54           
    SHEET    4 AA2 8 ARG B 151  TYR B 159 -1  O  ALA B 153   N  ILE B 127           
    SHEET    5 AA2 8 VAL B  13  GLN B  18 -1  N  ILE B  16   O  ALA B 158           
    SHEET    6 AA2 8 GLY B  26  LEU B  33 -1  O  PHE B  30   N  ALA B  15           
    SHEET    7 AA2 8 CYS B  36  LEU B  43 -1  O  GLN B  40   N  ILE B  29           
    SHEET    8 AA2 8 ILE B 106  VAL B 109 -1  O  VAL B 109   N  THR B  37           
    SSBOND   1 CYS A   36    CYS A  108                          1555   1555  2.01  
    SSBOND   2 CYS A   65    CYS A  154                          1555   1555  2.08  
    SSBOND   3 CYS B   36    CYS B  108                          1555   1555  2.04  
    SSBOND   4 CYS B   65    CYS B  154                          1555   1555  2.07  
    LINK         C   SER A  67                 N   MSE A  68     1555   1555  1.34  
    LINK         C   MSE A  68                 N   GLY A  69     1555   1555  1.33  
    LINK         C   SER B  67                 N   MSE B  68     1555   1555  1.33  
    LINK         C   MSE B  68                 N   GLY B  69     1555   1555  1.33  
    CISPEP   1 PHE A   10    ASN A   11          0        -8.34                     
    CISPEP   2 LYS A   21    PRO A   22          0        -3.41                     
    CISPEP   3 LYS B   21    PRO B   22          0        -1.18                     
    CRYST1   70.626   70.626  117.426  90.00  90.00  90.00 P 43 21 2    16          
    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      0.014159  0.000000  0.000000        0.00000                         
    SCALE2      0.000000  0.014159  0.000000        0.00000                         
    SCALE3      0.000000  0.000000  0.008516        0.00000                         

    3D molecular view of vibration

    Displacement vectors
    Display
    Animation
    Display

    Still image of displacement vectors and GIF animation


    Mode 1

    Time-average properties and properties of the 10 lowest-frequency modes

    Fluctuation of atoms:
    Time average and for the 3 lowest-frequency modes.
    Fluctuation of dihedral angles:
    Time average and for the 3 lowest-frequency modes.
    Fluctuation of atomsFluctuation of dihedral angles

    Correlations between fluctuations of atoms

    Mode 1
    Correlations between fluctuations of atoms - Mode 1
    Time Average
    Time Average
    Distance map
    Distance map

    Calculation note

    PDB file name : pdb4u4i.ent

    Chains and HETATMs selected: 
      ATOM        A
      ATOM        B
      HETATM  MSE A
      HETATM  MSE B

    The following atoms are removed from PDB data on concern that they may have 
    abnormally large fluctuations, because they interact with few atoms.
      ATOM    699  CG  LYS A 110      63.514   9.441  51.437  1.00 46.92           C  
      ATOM    700  CD  LYS A 110      64.917   9.896  51.068  1.00 56.72           C  
      ATOM    701  CE  LYS A 110      65.981   8.920  51.582  1.00 67.08           C  
      ATOM    702  NZ  LYS A 110      65.493   8.065  52.709  1.00 69.19           N  
      ATOM   1668  CG  LYS B 110      30.449  30.014  43.628  1.00 54.18           C  
      ATOM   1669  CD  LYS B 110      29.828  31.346  44.031  1.00 61.96           C  
      ATOM   1670  CE  LYS B 110      30.895  32.325  44.529  1.00 63.47           C  
      ATOM   1671  NZ  LYS B 110      32.140  32.294  43.698  1.00 65.79           N  

    = Normal mode analysis calculation =

    No. of modes used in the calculation : All modes.

    Parameters of potential energies:
      1-4 and 1-5 non-bonded interactions: E(d) = A*exp(-d(PDB)**2/B**2)(d-d(PDB))**2.
      Loop-closing potential:              E(d) = A*(d-d(PDB))**2.
        for a disulfide bond and one of the bonds in the DNA and RNA sugar ring.
      where d and d(PDB) are distances between atoms in calculation and in PDB data, 
      respectively.

      Interaction type   A       B      Cutoff distance (A)
        1-4             1.00    5.00      100.00
        1-5             1.00    5.00      100.00
        Loop-closing  100.00

    Temperature adjustment by magnitude of fluctuation:
      Set to mean displacements of atoms       0.500 A

    Animation
      No. of frames: 11
      Mean displacements (A):    0.50

    Displacement vector
      Mean length of vectors (A):    3.00