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Database: PDB
Entry: 4NIN
LinkDB: 4NIN
Original site: 4NIN 
HEADER    PROTEIN FIBRIL                          06-NOV-13   4NIN              
TITLE     DSVISLS SEGMENT 101-107 FROM HUMAN SUPEROXIDE DISMUTASE               
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DSVISLS SEGMENT FROM SUPEROXIDE DISMUTASE [CU-ZN];         
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: UNP RESIDUES 102-108;                                      
COMPND   5 SYNONYM: SUPEROXIDE DISMUTASE 1, HSOD1;                              
COMPND   6 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   4 ORGANISM_COMMON: HUMAN;                                              
SOURCE   5 ORGANISM_TAXID: 9606                                                 
KEYWDS    STERIC ZIPPER, CROSS-BETA SPINE, AMYLOID FIBER, PROTEIN FIBRIL        
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.A.SIEVERS,M.R.SAWAYA,D.EISENBERG                                    
REVDAT   3   22-NOV-17 4NIN    1       REMARK                                   
REVDAT   2   22-JAN-14 4NIN    1       JRNL                                     
REVDAT   1   04-DEC-13 4NIN    0                                                
JRNL        AUTH   M.I.IVANOVA,S.A.SIEVERS,E.L.GUENTHER,L.M.JOHNSON,            
JRNL        AUTH 2 D.D.WINKLER,A.GALALELDEEN,M.R.SAWAYA,P.J.HART,D.S.EISENBERG  
JRNL        TITL   AGGREGATION-TRIGGERING SEGMENTS OF SOD1 FIBRIL FORMATION     
JRNL        TITL 2 SUPPORT A COMMON PATHWAY FOR FAMILIAL AND SPORADIC ALS.      
JRNL        REF    PROC.NATL.ACAD.SCI.USA        V. 111   197 2014              
JRNL        REFN                   ISSN 0027-8424                               
JRNL        PMID   24344300                                                     
JRNL        DOI    10.1073/PNAS.1320786110                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.40 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.7.1_743                                     
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) : 1.40                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 22.67                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.660                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 74.1                           
REMARK   3   NUMBER OF REFLECTIONS             : 705                            
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.191                           
REMARK   3   R VALUE            (WORKING SET) : 0.187                           
REMARK   3   FREE R VALUE                     : 0.228                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 9.220                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 65                              
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 22.6715 -  1.4023    0.74      640    65  0.1872 0.2281        
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   : 0.83                                          
REMARK   3   K_SOL              : 0.44                                          
REMARK   3   B_SOL              : 58.79                                         
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.000            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.160           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 11.41                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 19.28                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -4.91060                                             
REMARK   3    B22 (A**2) : -5.65070                                             
REMARK   3    B33 (A**2) : 10.56130                                             
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : -2.58500                                             
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             49                                  
REMARK   3   ANGLE     :  0.923             66                                  
REMARK   3   CHIRALITY :  0.061             10                                  
REMARK   3   PLANARITY :  0.002              8                                  
REMARK   3   DIHEDRAL  : 10.205             17                                  
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 4NIN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-NOV-13.                  
REMARK 100 THE DEPOSITION ID IS D_1000083250.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 22-JUL-11                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 6.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : APS                                
REMARK 200  BEAMLINE                       : 24-ID-E                            
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                  : CRYOGENICALLY-COOLED SINGLE        
REMARK 200                                   CRYSTAL SI(220)                    
REMARK 200  OPTICS                         : MIRRORS                            
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315                   
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 717                                
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.400                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 100.000                            
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 73.6                               
REMARK 200  DATA REDUNDANCY                : 3.700                              
REMARK 200  R MERGE                    (I) : 0.18600                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 24.1000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.51                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 28.4                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 1.50                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.16600                            
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: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER 2.1.4                                          
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 26.84                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.0, 20% PEG 6000, AND 5    
REMARK 280  MM ZNCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K           
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,Y+1/2,-Z                                             
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000       22.66850            
REMARK 290   SMTRY3   2  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 300 REMARK: BIOLOGICAL UNIT IS A PAIR OF BETA-SHEETS FORMED BY THE       
REMARK 300 SYMMETRY OPERATORS X,Y,Z AND X,Y,Z-1 WITH POSITIVE AND NEGATIVE      
REMARK 300 UNIT CELL TRANSLATIONS ALONG THE X AXIS. FOR EXAMPLE ONE SHEET IS    
REMARK 300 COMPOSED OF SYMMETRY OPERATORS X,Y,Z; X+1,Y,Z; X-1,Y,Z; X+2,Y,Z; X-  
REMARK 300 2,Y,Z: THE OPPOSING SHEET IS COMPOSED OF SYMMETRY OPERATORS X,Y,Z-1; 
REMARK 300 X+1,Y,Z-1; X-1,Y,Z-1; X+2,Y,Z-1; X-2,Y,Z-1, ETC.                     
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: DECAMERIC                         
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 350   BIOMT1   2  1.000000  0.000000  0.000000        4.80500            
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000            
REMARK 350   BIOMT1   3  1.000000  0.000000  0.000000        9.61000            
REMARK 350   BIOMT2   3  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   3  0.000000  0.000000  1.000000        0.00000            
REMARK 350   BIOMT1   4  1.000000  0.000000  0.000000       -9.61000            
REMARK 350   BIOMT2   4  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   4  0.000000  0.000000  1.000000        0.00000            
REMARK 350   BIOMT1   5  1.000000  0.000000  0.000000       -4.80500            
REMARK 350   BIOMT2   5  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   5  0.000000  0.000000  1.000000        0.00000            
REMARK 350   BIOMT1   6  1.000000  0.000000  0.000000        2.06314            
REMARK 350   BIOMT2   6  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   6  0.000000  0.000000  1.000000      -11.11006            
REMARK 350   BIOMT1   7  1.000000  0.000000  0.000000        6.86814            
REMARK 350   BIOMT2   7  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   7  0.000000  0.000000  1.000000      -11.11006            
REMARK 350   BIOMT1   8  1.000000  0.000000  0.000000       11.67314            
REMARK 350   BIOMT2   8  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   8  0.000000  0.000000  1.000000      -11.11006            
REMARK 350   BIOMT1   9  1.000000  0.000000  0.000000       -7.54686            
REMARK 350   BIOMT2   9  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   9  0.000000  0.000000  1.000000      -11.11006            
REMARK 350   BIOMT1  10  1.000000  0.000000  0.000000       -2.74186            
REMARK 350   BIOMT2  10  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3  10  0.000000  0.000000  1.000000      -11.11006            
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                              ZN A 101  ZN                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 ASP A   1   OD1                                                    
REMARK 620 2 HOH A 202   O    80.3                                              
REMARK 620 3 HOH A 201   O    85.9  86.9                                        
REMARK 620 4 HOH A 203   O   103.2 176.5  93.9                                  
REMARK 620 5 ASP A   1   N    89.0  76.7 163.4 102.6                            
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 ZN A 101                  
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 4NIO   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 4NIP   RELATED DB: PDB                                   
DBREF  4NIN A    1     7  UNP    P00441   SODC_HUMAN     102    108             
SEQRES   1 A    7  ASP SER VAL ILE SER LEU SER                                  
HET     ZN  A 101       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   2   ZN    ZN 2+                                                        
FORMUL   3  HOH   *4(H2 O)                                                      
LINK         OD1 ASP A   1                ZN    ZN A 101     1555   1555  2.05  
LINK        ZN    ZN A 101                 O   HOH A 202     1555   1555  2.06  
LINK        ZN    ZN A 101                 O   HOH A 201     1555   1555  2.17  
LINK        ZN    ZN A 101                 O   HOH A 203     1555   1555  2.22  
LINK         N   ASP A   1                ZN    ZN A 101     1555   1555  2.25  
SITE     1 AC1  4 ASP A   1  HOH A 201  HOH A 202  HOH A 203                    
CRYST1    4.805   45.337   11.300  90.00 100.52  90.00 P 1 21 1      2          
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      0.208117  0.000000  0.038632        0.00000                         
SCALE2      0.000000  0.022057  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.090007        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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