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Database: PDB
Entry: 5DLI
LinkDB: 5DLI
Original site: 5DLI 
HEADER    UNKNOWN FUNCTION                        05-SEP-15   5DLI              
TITLE     CORKSCREW ASSEMBLY OF SOD1 RESIDUES 28-38                             
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: SUPEROXIDE DISMUTASE [CU-ZN];                              
COMPND   3 CHAIN: A, B, C, D, E, F, G, H;                                       
COMPND   4 FRAGMENT: RESIDUES 29-39;                                            
COMPND   5 SYNONYM: SUPEROXIDE DISMUTASE 1,HSOD1;                               
COMPND   6 EC: 1.15.1.1;                                                        
COMPND   7 ENGINEERED: YES;                                                     
COMPND   8 MUTATION: 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;                                                
SOURCE   6 OTHER_DETAILS: SYNTHESIZED                                           
KEYWDS    AMYLOID-RELATED OLIGOMER, UNKNOWN FUNCTION                            
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    S.SANGWAN,A.ZHAO,M.R.SAWAYA,D.EISENBERG                               
REVDAT   3   09-JAN-19 5DLI    1       JRNL                                     
REVDAT   2   20-SEP-17 5DLI    1       REMARK                                   
REVDAT   1   14-SEP-16 5DLI    0                                                
JRNL        AUTH   S.SANGWAN,A.ZHAO,K.L.ADAMS,C.K.JAYSON,M.R.SAWAYA,            
JRNL        AUTH 2 E.L.GUENTHER,A.C.PAN,J.NGO,D.M.MOORE,A.B.SORIAGA,T.D.DO,     
JRNL        AUTH 3 L.GOLDSCHMIDT,R.NELSON,M.T.BOWERS,C.M.KOEHLER,D.E.SHAW,      
JRNL        AUTH 4 B.G.NOVITCH,D.S.EISENBERG                                    
JRNL        TITL   ATOMIC STRUCTURE OF A TOXIC, OLIGOMERIC SEGMENT OF SOD1      
JRNL        TITL 2 LINKED TO AMYOTROPHIC LATERAL SCLEROSIS (ALS).               
JRNL        REF    PROC. NATL. ACAD. SCI.        V. 114  8770 2017              
JRNL        REF  2 U.S.A.                                                       
JRNL        REFN                   ESSN 1091-6490                               
JRNL        PMID   28760994                                                     
JRNL        DOI    10.1073/PNAS.1705091114                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.10 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : BUSTER-TNT 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) : 2.10                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 19.33                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 95.8                           
REMARK   3   NUMBER OF REFLECTIONS             : 6249                           
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)  : 0.215                          
REMARK   3   R VALUE            (WORKING SET)  : 0.213                          
REMARK   3   FREE R VALUE                      : 0.262                          
REMARK   3   FREE R VALUE TEST SET SIZE   (%)  : 5.010                          
REMARK   3   FREE R VALUE TEST SET COUNT       : 313                            
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) : 2.10                     
REMARK   3   BIN RESOLUTION RANGE LOW    (ANGSTROMS) : 2.35                     
REMARK   3   BIN COMPLETENESS (WORKING+TEST)     (%) : 95.84                    
REMARK   3   REFLECTIONS IN BIN (WORKING + TEST SET) : 1747                     
REMARK   3   BIN R VALUE        (WORKING + TEST SET) : 0.1744                   
REMARK   3   REFLECTIONS IN BIN        (WORKING SET) : 1660                     
REMARK   3   BIN R VALUE               (WORKING SET) : 0.1716                   
REMARK   3   BIN FREE R VALUE                        : 0.2292                   
REMARK   3   BIN FREE R VALUE TEST SET SIZE      (%) : 4.98                     
REMARK   3   BIN FREE R VALUE TEST SET COUNT         : 87                       
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE     : NULL                     
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 688                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 8                                       
REMARK   3   SOLVENT ATOMS            : 50                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 21.81                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 23.83                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -4.35590                                             
REMARK   3    B22 (A**2) : -2.35110                                             
REMARK   3    B33 (A**2) : 6.70710                                              
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  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT                    (A) : 0.243               
REMARK   3   DPI (BLOW EQ-10) BASED ON R VALUE        (A) : 0.234               
REMARK   3   DPI (BLOW EQ-9) BASED ON FREE R VALUE    (A) : 0.198               
REMARK   3   DPI (CRUICKSHANK) BASED ON R VALUE       (A) : 0.219               
REMARK   3   DPI (CRUICKSHANK) BASED ON FREE R VALUE  (A) : 0.194               
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      : 0.922                         
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.921                         
REMARK   3                                                                      
REMARK   3   NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15                    
REMARK   3   TERM                          COUNT    WEIGHT   FUNCTION.          
REMARK   3    BOND LENGTHS              : 715    ; 2.000  ; HARMONIC            
REMARK   3    BOND ANGLES               : 947    ; 2.000  ; HARMONIC            
REMARK   3    TORSION ANGLES            : 254    ; 2.000  ; SINUSOIDAL          
REMARK   3    TRIGONAL CARBON PLANES    : 8      ; 2.000  ; HARMONIC            
REMARK   3    GENERAL PLANES            : 91     ; 5.000  ; HARMONIC            
REMARK   3    ISOTROPIC THERMAL FACTORS : 715    ; 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   : 81     ; 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   : 778    ; 4.000  ; SEMIHARMONIC        
REMARK   3                                                                      
REMARK   3   RMS DEVIATIONS FROM IDEAL VALUES.                                  
REMARK   3    BOND LENGTHS                       (A) : 0.010                    
REMARK   3    BOND ANGLES                  (DEGREES) : 0.89                     
REMARK   3    PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.43                     
REMARK   3    OTHER TORSION ANGLES         (DEGREES) : 15.32                    
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 5DLI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-15.                  
REMARK 100 THE DEPOSITION ID IS D_1000213382.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 09-DEC-12                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 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) : 0.9791                             
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   : 6261                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.100                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 19.330                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 95.3                               
REMARK 200  DATA REDUNDANCY                : 6.900                              
REMARK 200  R MERGE                    (I) : 0.10300                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 14.4000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.15                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 96.8                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 7.05                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.44300                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 4.880                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS                        
REMARK 200 SOFTWARE USED: SHELX                                                 
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 54.33                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONTAINED 13% PEG 6000, 0.2M   
REMARK 280  SODIUM CITRATE, PH 5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE    
REMARK 280  298K                                                                
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21                       
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X+1/2,-Y,Z+1/2                                         
REMARK 290       3555   -X,Y+1/2,-Z+1/2                                         
REMARK 290       4555   X+1/2,-Y+1/2,-Z                                         
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000       16.54500            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       35.71500            
REMARK 290   SMTRY1   3 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  0.000000  1.000000  0.000000       22.19500            
REMARK 290   SMTRY3   3  0.000000  0.000000 -1.000000       35.71500            
REMARK 290   SMTRY1   4  1.000000  0.000000  0.000000       16.54500            
REMARK 290   SMTRY2   4  0.000000 -1.000000  0.000000       22.19500            
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, C, D, E, F, G, H                
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 GOL B 101                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue IOD D 101                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue IOD D 102                 
DBREF  5DLI A   28    38  UNP    P00441   SODC_HUMAN      29     39             
DBREF  5DLI B   28    38  UNP    P00441   SODC_HUMAN      29     39             
DBREF  5DLI C   28    38  UNP    P00441   SODC_HUMAN      29     39             
DBREF  5DLI D   28    38  UNP    P00441   SODC_HUMAN      29     39             
DBREF  5DLI E   28    38  UNP    P00441   SODC_HUMAN      29     39             
DBREF  5DLI F   28    38  UNP    P00441   SODC_HUMAN      29     39             
DBREF  5DLI G   28    38  UNP    P00441   SODC_HUMAN      29     39             
DBREF  5DLI H   28    38  UNP    P00441   SODC_HUMAN      29     39             
SEQADV 5DLI LYS A   28  UNP  P00441    PRO    29 ENGINEERED MUTATION            
SEQADV 5DLI LYS B   28  UNP  P00441    PRO    29 ENGINEERED MUTATION            
SEQADV 5DLI LYS C   28  UNP  P00441    PRO    29 ENGINEERED MUTATION            
SEQADV 5DLI LYS D   28  UNP  P00441    PRO    29 ENGINEERED MUTATION            
SEQADV 5DLI LYS E   28  UNP  P00441    PRO    29 ENGINEERED MUTATION            
SEQADV 5DLI LYS F   28  UNP  P00441    PRO    29 ENGINEERED MUTATION            
SEQADV 5DLI LYS G   28  UNP  P00441    PRO    29 ENGINEERED MUTATION            
SEQADV 5DLI LYS H   28  UNP  P00441    PRO    29 ENGINEERED MUTATION            
SEQRES   1 A   11  LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU                  
SEQRES   1 B   11  LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU                  
SEQRES   1 C   11  LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU                  
SEQRES   1 D   11  LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU                  
SEQRES   1 E   11  LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU                  
SEQRES   1 F   11  LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU                  
SEQRES   1 G   11  LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU                  
SEQRES   1 H   11  LYS VAL LYS VAL TRP GLY SER ILE LYS GLY LEU                  
HET    GOL  B 101       6                                                       
HET    IOD  D 101       2                                                       
HET    IOD  D 102       2                                                       
HETNAM     GOL GLYCEROL                                                         
HETNAM     IOD IODIDE ION                                                       
HETSYN     GOL GLYCERIN; PROPANE-1,2,3-TRIOL                                    
FORMUL   9  GOL    C3 H8 O3                                                     
FORMUL  10  IOD    2(I 1-)                                                      
FORMUL  12  HOH   *50(H2 O)                                                     
SHEET    1 AA1 8 VAL A  29  GLY A  33  0                                        
SHEET    2 AA1 8 VAL B  29  SER B  34 -1  O  TRP B  32   N  LYS A  30           
SHEET    3 AA1 8 VAL C  29  SER C  34 -1  O  GLY C  33   N  VAL B  31           
SHEET    4 AA1 8 VAL D  29  SER D  34 -1  O  LYS D  30   N  TRP C  32           
SHEET    5 AA1 8 VAL E  29  SER E  34 -1  O  VAL E  31   N  GLY D  33           
SHEET    6 AA1 8 VAL F  29  SER F  34 -1  O  TRP F  32   N  LYS E  30           
SHEET    7 AA1 8 VAL G  29  SER G  34 -1  O  VAL G  31   N  GLY F  33           
SHEET    8 AA1 8 VAL H  29  GLY H  33 -1  O  LYS H  30   N  TRP G  32           
SITE     1 AC1  6 LYS A  28  LYS A  30  LYS B  28  GLY H  33                    
SITE     2 AC1  6 SER H  34  HOH H 102                                          
SITE     1 AC2  3 LYS D  30  TRP G  32  LYS H  30                               
SITE     1 AC3  4 TRP D  32  LYS E  30  LYS F  28  SER G  34                    
CRYST1   33.090   44.390   71.430  90.00  90.00  90.00 P 21 21 21   32          
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      0.030221  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.022528  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.014000        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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