GenomeNet

Database: PDB
Entry: 4ETA
LinkDB: 4ETA
Original site: 4ETA 
HEADER    HYDROLASE                               24-APR-12   4ETA              
TITLE     LYSOZYME, ROOM TEMPERATURE, 400 KGY DOSE                              
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 IV;           
COMPND   5 EC: 3.2.1.17                                                         
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;                                  
SOURCE   3 ORGANISM_COMMON: BANTAM,CHICKENS;                                    
SOURCE   4 ORGANISM_TAXID: 9031                                                 
KEYWDS    LYSOZYME, HYDROLASE                                                   
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.BOUTET,L.LOMB,G.WILLIAMS,T.BARENDS,A.AQUILA,R.B.DOAK,U.WEIERSTALL,  
AUTHOR   2 D.DEPONTE,J.STEINBRENER,R.SHOEMAN,M.MESSERSCHMIDT,A.BARTY,T.WHITE,   
AUTHOR   3 S.KASSEMEYER,R.KIRIAN,M.SEIBERT,P.MONTANEZ,C.KENNEY,R.HERBST,P.HART, 
AUTHOR   4 J.PINES,G.HALLER,S.GRUNER,H.PHILLLIP,M.TATE,M.HROMALIK,L.KOERNER,    
AUTHOR   5 N.VAN BAKEL,J.MORSE,W.GHONSALVES,D.ARNLUND,M.BOGAN,C.CALEMANN,       
AUTHOR   6 R.FROMME,C.HAMPTON,M.HUNTER,L.JOHANSSON,G.KATONA,C.KUPITZ,M.LIANG,   
AUTHOR   7 A.MARTIN,K.NASS,L.REDECKE,F.STELLATO,N.TIMNEANU,D.WANG,N.ZATSEPIN,   
AUTHOR   8 D.SCHAFER,K.DEFEVER,R.NEUTZE,P.FROMME,J.SPENCE,H.CHAPMAN,            
AUTHOR   9 I.SCHLICHTING                                                        
REVDAT   3   15-NOV-17 4ETA    1       REMARK                                   
REVDAT   2   08-AUG-12 4ETA    1       JRNL                                     
REVDAT   1   13-JUN-12 4ETA    0                                                
JRNL        AUTH   S.BOUTET,L.LOMB,G.J.WILLIAMS,T.R.BARENDS,A.AQUILA,R.B.DOAK,  
JRNL        AUTH 2 U.WEIERSTALL,D.P.DEPONTE,J.STEINBRENER,R.L.SHOEMAN,          
JRNL        AUTH 3 M.MESSERSCHMIDT,A.BARTY,T.A.WHITE,S.KASSEMEYER,R.A.KIRIAN,   
JRNL        AUTH 4 M.M.SEIBERT,P.A.MONTANEZ,C.KENNEY,R.HERBST,P.HART,J.PINES,   
JRNL        AUTH 5 G.HALLER,S.M.GRUNER,H.T.PHILIPP,M.W.TATE,M.HROMALIK,         
JRNL        AUTH 6 L.J.KOERNER,N.VAN BAKEL,J.MORSE,W.GHONSALVES,D.ARNLUND,      
JRNL        AUTH 7 M.J.BOGAN,C.CALEMAN,R.FROMME,C.Y.HAMPTON,M.S.HUNTER,         
JRNL        AUTH 8 L.C.JOHANSSON,G.KATONA,C.KUPITZ,M.LIANG,A.V.MARTIN,K.NASS,   
JRNL        AUTH 9 L.REDECKE,F.STELLATO,N.TIMNEANU,D.WANG,N.A.ZATSEPIN,         
JRNL        AUTH10 D.SCHAFER,J.DEFEVER,R.NEUTZE,P.FROMME,J.C.SPENCE,            
JRNL        AUTH11 H.N.CHAPMAN,I.SCHLICHTING                                    
JRNL        TITL   HIGH-RESOLUTION PROTEIN STRUCTURE DETERMINATION BY SERIAL    
JRNL        TITL 2 FEMTOSECOND CRYSTALLOGRAPHY.                                 
JRNL        REF    SCIENCE                       V. 337   362 2012              
JRNL        REFN                   ISSN 0036-8075                               
JRNL        PMID   22653729                                                     
JRNL        DOI    10.1126/SCIENCE.1217737                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.91 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.7.2_869)                    
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) : 1.91                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 35.46                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 2.050                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.6                           
REMARK   3   NUMBER OF REFLECTIONS             : 9851                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.161                           
REMARK   3   R VALUE            (WORKING SET) : 0.160                           
REMARK   3   FREE R VALUE                     : 0.180                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.090                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 501                             
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 35.4701 -  3.0315    0.99     2449   124  0.1660 0.1758        
REMARK   3     2  3.0315 -  2.4063    1.00     2337   128  0.1717 0.1909        
REMARK   3     3  2.4063 -  2.1022    1.00     2313   120  0.1426 0.1843        
REMARK   3     4  2.1022 -  1.9100    1.00     2251   129  0.1384 0.1669        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
REMARK   3   SOLVENT RADIUS     : 1.10                                          
REMARK   3   SHRINKAGE RADIUS   : 0.86                                          
REMARK   3   K_SOL              : 0.33                                          
REMARK   3   B_SOL              : 33.21                                         
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.220            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.720           
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) : -0.86700                                             
REMARK   3    B22 (A**2) : -0.86700                                             
REMARK   3    B33 (A**2) : 1.73390                                              
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  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      :  0.006           1025                                  
REMARK   3   ANGLE     :  1.010           1381                                  
REMARK   3   CHIRALITY :  0.078            144                                  
REMARK   3   PLANARITY :  0.003            181                                  
REMARK   3   DIHEDRAL  : 13.815            365                                  
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 4ETA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-12.                  
REMARK 100 THE DEPOSITION ID IS D_1000072041.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 26-AUG-11                          
REMARK 200  TEMPERATURE           (KELVIN) : 293                                
REMARK 200  PH                             : NULL                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SLS                                
REMARK 200  BEAMLINE                       : X10SA                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.97860                            
REMARK 200  MONOCHROMATOR                  : SI111                              
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : PSI PILATUS 6M                     
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : XDS                                
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 10022                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.900                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 39.600                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.6                               
REMARK 200  DATA REDUNDANCY                : NULL                               
REMARK 200  R MERGE                    (I) : NULL                               
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) : 1.90                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.00                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 99.7                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
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: FOURIER SYNTHESIS            
REMARK 200 SOFTWARE USED: PHENIX                                                
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 41.30                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: GROWN IN LINBRO PLATES IN HANGING OR     
REMARK 280  SITTING DROP GEOMETRY. DROPS OF EQUAL VOLUME OF PROTEIN (20 MG/     
REMARK 280  ML) AND RESERVOIR SOLUTION (1 M NAAC PH 3.0, 9-10 % NACL, 6 %       
REMARK 280  PEG 6000) WERE MIXED. FOR THE MEASUREMENTS, THE CRYSTALS WERE       
REMARK 280  EQUILIBRATED IN 1 M NAAC PH 3.4, 10 % NACL, VAPOR DIFFUSION,        
REMARK 280  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       19.10000            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       39.65000            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       39.65000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       28.65000            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       39.65000            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       39.65000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000        9.55000            
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       39.65000            
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       39.65000            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       28.65000            
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       39.65000            
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       39.65000            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000        9.55000            
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       19.10000            
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 201                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 4ET8   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 4ET9   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 4ETB   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 4ETC   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 4ETD   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 4ETE   RELATED DB: PDB                                   
DBREF  4ETA 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     CL  A 201       1                                                       
HETNAM      CL CHLORIDE ION                                                     
FORMUL   2   CL    CL 1-                                                        
FORMUL   3  HOH   *87(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  ILE A  124  5                                   6    
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  2.01  
SSBOND   2 CYS A   30    CYS A  115                          1555   1555  2.03  
SSBOND   3 CYS A   64    CYS A   80                          1555   1555  2.03  
SSBOND   4 CYS A   76    CYS A   94                          1555   1555  2.04  
SITE     1 AC1  2 TYR A  23  ASN A 113                                          
CRYST1   79.300   79.300   38.200  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      0.012610  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.012610  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.026178        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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