GenomeNet

Database: PDB
Entry: 6B79
LinkDB: 6B79
Original site: 6B79 
HEADER    PROTEIN FIBRIL                          03-OCT-17   6B79              
TITLE     CURVED PAIR OF SHEETS FORMED FROM SOD1 RESIDUES 28-38 WITH FAMILIAL   
TITLE    2 MUTATION G37R.                                                       
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: SUPEROXIDE DISMUTASE [CU-ZN];                              
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 SYNONYM: SUPEROXIDE DISMUTASE 1,HSOD1;                               
COMPND   5 EC: 1.15.1.1;                                                        
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    AMYLOID FIBRIL, PROTEIN FIBRIL                                        
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.SANGWAN,M.R.SAWAYA,D.S.EISENBERG                                    
REVDAT   2   18-JUL-18 6B79    1       JRNL                                     
REVDAT   1   30-MAY-18 6B79    0                                                
JRNL        AUTH   S.SANGWAN,M.R.SAWAYA,K.A.MURRAY,M.P.HUGHES,D.S.EISENBERG     
JRNL        TITL   ATOMIC STRUCTURES OF CORKSCREW-FORMING SEGMENTS OF SOD1      
JRNL        TITL 2 REVEAL VARIED OLIGOMER CONFORMATIONS.                        
JRNL        REF    PROTEIN SCI.                  V.  27  1231 2018              
JRNL        REFN                   ESSN 1469-896X                               
JRNL        PMID   29453800                                                     
JRNL        DOI    10.1002/PRO.3391                                             
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.80 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : BUSTER 2.10.0                                        
REMARK   3   AUTHORS     : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,              
REMARK   3               : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,              
REMARK   3               : WOMACK,MATTHEWS,TEN EYCK,TRONRUD                     
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 35.73                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.9                           
REMARK   3   NUMBER OF REFLECTIONS             : 2327                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD           : THROUGHOUT                     
REMARK   3   FREE R VALUE TEST SET SELECTION   : RANDOM                         
REMARK   3   R VALUE     (WORKING + TEST SET)  : 0.234                          
REMARK   3   R VALUE            (WORKING SET)  : 0.230                          
REMARK   3   FREE R VALUE                      : 0.267                          
REMARK   3   FREE R VALUE TEST SET SIZE   (%)  : 9.580                          
REMARK   3   FREE R VALUE TEST SET COUNT       : 223                            
REMARK   3   ESTIMATED ERROR OF FREE R VALUE   : NULL                           
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED               : 5                        
REMARK   3   BIN RESOLUTION RANGE HIGH   (ANGSTROMS) : 1.80                     
REMARK   3   BIN RESOLUTION RANGE LOW    (ANGSTROMS) : 2.01                     
REMARK   3   BIN COMPLETENESS (WORKING+TEST)     (%) : 97.90                    
REMARK   3   REFLECTIONS IN BIN (WORKING + TEST SET) : 622                      
REMARK   3   BIN R VALUE        (WORKING + TEST SET) : 0.2764                   
REMARK   3   REFLECTIONS IN BIN        (WORKING SET) : 560                      
REMARK   3   BIN R VALUE               (WORKING SET) : 0.2727                   
REMARK   3   BIN FREE R VALUE                        : 0.3159                   
REMARK   3   BIN FREE R VALUE TEST SET SIZE      (%) : 9.97                     
REMARK   3   BIN FREE R VALUE TEST SET COUNT         : 62                       
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE     : 0.000                    
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 188                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 27                                      
REMARK   3   SOLVENT ATOMS            : 16                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 28.25                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 30.08                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -5.98750                                             
REMARK   3    B22 (A**2) : 7.08830                                              
REMARK   3    B33 (A**2) : -1.10080                                             
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : 7.27710                                              
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT                    (A) : 0.298               
REMARK   3   DPI (BLOW EQ-10) BASED ON R VALUE        (A) : 0.183               
REMARK   3   DPI (BLOW EQ-9) BASED ON FREE R VALUE    (A) : 0.158               
REMARK   3   DPI (CRUICKSHANK) BASED ON R VALUE       (A) : 0.168               
REMARK   3   DPI (CRUICKSHANK) BASED ON FREE R VALUE  (A) : 0.151               
REMARK   3                                                                      
REMARK   3   REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797                
REMARK   3               CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601     
REMARK   3                                                                      
REMARK   3 CORRELATION COEFFICIENTS.                                            
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.909                         
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.916                         
REMARK   3                                                                      
REMARK   3   NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15                    
REMARK   3   TERM                          COUNT    WEIGHT   FUNCTION.          
REMARK   3    BOND LENGTHS              : 219    ; 2.000  ; HARMONIC            
REMARK   3    BOND ANGLES               : 294    ; 2.000  ; HARMONIC            
REMARK   3    TORSION ANGLES            : 80     ; 2.000  ; SINUSOIDAL          
REMARK   3    TRIGONAL CARBON PLANES    : 2      ; 2.000  ; HARMONIC            
REMARK   3    GENERAL PLANES            : 29     ; 5.000  ; HARMONIC            
REMARK   3    ISOTROPIC THERMAL FACTORS : 219    ; 20.000 ; HARMONIC            
REMARK   3    BAD NON-BONDED CONTACTS   : NULL   ; NULL   ; NULL                
REMARK   3    IMPROPER TORSIONS         : NULL   ; NULL   ; NULL                
REMARK   3    PSEUDOROTATION ANGLES     : NULL   ; NULL   ; NULL                
REMARK   3    CHIRAL IMPROPER TORSION   : 22     ; 5.000  ; SEMIHARMONIC        
REMARK   3    SUM OF OCCUPANCIES        : NULL   ; NULL   ; NULL                
REMARK   3    UTILITY DISTANCES         : NULL   ; NULL   ; NULL                
REMARK   3    UTILITY ANGLES            : NULL   ; NULL   ; NULL                
REMARK   3    UTILITY TORSION           : NULL   ; NULL   ; NULL                
REMARK   3    IDEAL-DIST CONTACT TERM   : 274    ; 4.000  ; SEMIHARMONIC        
REMARK   3                                                                      
REMARK   3   RMS DEVIATIONS FROM IDEAL VALUES.                                  
REMARK   3    BOND LENGTHS                       (A) : 0.010                    
REMARK   3    BOND ANGLES                  (DEGREES) : 1.25                     
REMARK   3    PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.77                     
REMARK   3    OTHER TORSION ANGLES         (DEGREES) : 17.03                    
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 6B79 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-17.                  
REMARK 100 THE DEPOSITION ID IS D_1000230391.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 03-APR-14                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7.5                                
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                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 315                   
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : XSCALE                             
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 2330                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.800                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 35.730                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 96.6                               
REMARK 200  DATA REDUNDANCY                : 3.088                              
REMARK 200  R MERGE                    (I) : 0.17500                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 4.0600                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.84                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 74.1                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.40                               
REMARK 200  R MERGE FOR SHELL          (I) : 1.57900                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 0.480                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER                                                
REMARK 200 STARTING MODEL: 5DLI                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 42.06                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES PH 7.5, SODIUM CITRATE, 2-METHYL   
REMARK 280  -2,4-PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K   
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1                          
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,Y,-Z                                                 
REMARK 290       3555   X+1/2,Y+1/2,Z                                           
REMARK 290       4555   -X+1/2,Y+1/2,-Z                                         
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   3  1.000000  0.000000  0.000000       28.47000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000        5.82000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   4 -1.000000  0.000000  0.000000       28.47000            
REMARK 290   SMTRY2   4  0.000000  1.000000  0.000000        5.82000            
REMARK 290   SMTRY3   4  0.000000  0.000000 -1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: OCTAMERIC                         
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 350   BIOMT1   2  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000       11.64000            
REMARK 350   BIOMT3   2  0.000000  0.000000  1.000000        0.00000            
REMARK 350   BIOMT1   3 -1.000000  0.000000  0.000000        0.00000            
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        0.00000            
REMARK 350   BIOMT2   4  0.000000  1.000000  0.000000       11.64000            
REMARK 350   BIOMT3   4  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 ORA A 101                 
DBREF  6B79 A    1    11  UNP    P00441   SODC_HUMAN      29     39             
DBREF  6B79 B    1    11  UNP    P00441   SODC_HUMAN      29     39             
SEQADV 6B79 LYS A    1  UNP  P00441    PRO    29 CONFLICT                       
SEQADV 6B79 ARG A   10  UNP  P00441    GLY    38 ENGINEERED MUTATION            
SEQADV 6B79 LYS B    1  UNP  P00441    PRO    29 CONFLICT                       
SEQADV 6B79 ARG B   10  UNP  P00441    GLY    38 ENGINEERED MUTATION            
SEQRES   1 A   11  LYS A8E LYS VAL TRP GLY SER ILE LYS ARG LEU                  
SEQRES   1 B   11  LYS A8E LYS VAL TRP GLY SER ILE LYS ARG LEU                  
MODRES 6B79 A8E A    2  VAL  MODIFIED RESIDUE                                   
MODRES 6B79 A8E B    2  VAL  MODIFIED RESIDUE                                   
HET    A8E  A   2       8                                                       
HET    A8E  B   2       8                                                       
HET    ORA  A 101      27                                                       
HETNAM     A8E (2S)-2-AMINO-4-BROMOPENT-4-ENOIC ACID                            
HETNAM     ORA 7-HYDROXY-8-[(E)-PHENYLDIAZENYL]NAPHTHALENE-1,3-                 
HETNAM   2 ORA  DISULFONIC ACID                                                 
HETSYN     ORA ORANGE G                                                         
FORMUL   1  A8E    2(C5 H8 BR N O2)                                             
FORMUL   3  ORA    C16 H12 N2 O7 S2                                             
FORMUL   4  HOH   *16(H2 O)                                                     
SHEET    1 AA1 2 VAL A   4  GLY A   6  0                                        
SHEET    2 AA1 2 VAL B   4  GLY B   6 -1  O  VAL B   4   N  GLY A   6           
LINK         C   LYS A   1                 N   A8E A   2     1555   1555  1.34  
LINK         C   A8E A   2                 N   LYS A   3     1555   1555  1.35  
LINK         C   LYS B   1                 N   A8E B   2     1555   1555  1.33  
LINK         C   A8E B   2                 N   LYS B   3     1555   1555  1.34  
SITE     1 AC1  9 LYS A   3  VAL A   4  TRP A   5  LYS A   9                    
SITE     2 AC1  9 HOH A 201  HOH A 203  LYS B   3  TRP B   5                    
SITE     3 AC1  9 GLY B   6                                                     
CRYST1   56.940   11.640   44.930  90.00 127.32  90.00 C 1 2 1       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      0.017562  0.000000  0.013389        0.00000                         
SCALE2      0.000000  0.085911  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.027987        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
DBGET integrated database retrieval system