HEADER OXIDOREDUCTASE 02-APR-11 3RE0
TITLE CRYSTAL STRUCTURE OF HUMAN APO CU,ZN SUPEROXIDE DISMUTASE (SOD1)
TITLE 2 COMPLEXED WITH CISPLATIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [CU-ZN];
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 EC: 1.15.1.1;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: SOD1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS SOD1, CISPLATIN, ALS, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR I.BERTINI,O.BLAZEVITS,V.CALDERONE,M.JAIFEI,M.VIERU,I.AMORI,
AUTHOR 2 M.COZZOLINO,M.T.CARRI,L.BANCI
REVDAT 3 01-NOV-23 3RE0 1 REMARK LINK
REVDAT 2 03-JUL-13 3RE0 1 JRNL
REVDAT 1 25-APR-12 3RE0 0
JRNL AUTH L.BANCI,I.BERTINI,O.BLAZEVITS,V.CALDERONE,F.CANTINI,J.MAO,
JRNL AUTH 2 A.TRAPANANTI,M.VIERU,I.AMORI,M.COZZOLINO,M.T.CARRI
JRNL TITL INTERACTION OF CISPLATIN WITH HUMAN SUPEROXIDE DISMUTASE.
JRNL REF J.AM.CHEM.SOC. V. 134 7009 2012
JRNL REFN ISSN 0002-7863
JRNL PMID 22471402
JRNL DOI 10.1021/JA211591N
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH L.BANCI,I.BERTINI,M.BOCA,V.CALDERONE,F.CANTINI,S.GIROTTO,
REMARK 1 AUTH 2 M.VIERU
REMARK 1 TITL STRUCTURAL AND DYNAMIC ASPECTS RELATED TO OLIGOMERIZATION OF
REMARK 1 TITL 2 APO SOD1 AND ITS MUTANTS.
REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 106 6980 2009
REMARK 1 REFN ISSN 0027-8424
REMARK 1 PMID 19369197
REMARK 1 DOI 10.1073/PNAS.0809845106
REMARK 2
REMARK 2 RESOLUTION. 2.28 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.6.0117
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.32
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3
REMARK 3 NUMBER OF REFLECTIONS : 24261
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) : 0.216
REMARK 3 R VALUE (WORKING SET) : 0.209
REMARK 3 FREE R VALUE : 0.290
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2407
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.28
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1383
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.82
REMARK 3 BIN R VALUE (WORKING SET) : 0.3760
REMARK 3 BIN FREE R VALUE SET COUNT : 138
REMARK 3 BIN FREE R VALUE : 0.4700
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4027
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 12
REMARK 3 SOLVENT ATOMS : 96
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 35.90
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.30
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -2.92000
REMARK 3 B22 (A**2) : 5.14000
REMARK 3 B33 (A**2) : -4.38000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -2.84000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.363
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.283
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.215
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.075
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4110 ; 0.014 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5547 ; 1.825 ; 1.945
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 547 ; 8.493 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 171 ;40.440 ;25.556
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 659 ;19.509 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;11.238 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 621 ; 0.121 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3125 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 3RE0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-APR-11.
REMARK 100 THE DEPOSITION ID IS D_1000064814.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-MAY-10
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 : ESRF
REMARK 200 BEAMLINE : ID14-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.93616
REMARK 200 MONOCHROMATOR : MIRRORS
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27768
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250
REMARK 200 RESOLUTION RANGE LOW (A) : 39.320
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6
REMARK 200 DATA REDUNDANCY : 4.900
REMARK 200 R MERGE (I) : 0.10000
REMARK 200 R SYM (I) : 0.10000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5
REMARK 200 DATA REDUNDANCY IN SHELL : 2.50
REMARK 200 R MERGE FOR SHELL (I) : 0.57000
REMARK 200 R SYM FOR SHELL (I) : 0.57000
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 1ECU
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.68
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.1M HEPES, PH 7.5,
REMARK 280 VAPOR DIFFUSION, SITTING 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 78.70600
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.40250
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 78.70600
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.40250
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1880 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14030 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1670 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11530 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 SER C 68
REMARK 465 ARG C 69
REMARK 465 LYS C 70
REMARK 465 HIS C 71
REMARK 465 GLY C 72
REMARK 465 GLY C 73
REMARK 465 PRO C 74
REMARK 465 LYS C 75
REMARK 465 ASP C 76
REMARK 465 GLU C 77
REMARK 465 GLU C 78
REMARK 465 ASP C 125
REMARK 465 LEU C 126
REMARK 465 GLY C 127
REMARK 465 LYS C 128
REMARK 465 GLY C 129
REMARK 465 GLY C 130
REMARK 465 ASN C 131
REMARK 465 GLU C 132
REMARK 465 GLU C 133
REMARK 465 SER C 134
REMARK 465 THR C 135
REMARK 465 LYS C 136
REMARK 465 THR C 137
REMARK 465 GLY C 138
REMARK 465 ASN C 139
REMARK 465 ALA C 140
REMARK 465 LEU D 67
REMARK 465 SER D 68
REMARK 465 ARG D 69
REMARK 465 LYS D 70
REMARK 465 HIS D 71
REMARK 465 GLY D 72
REMARK 465 GLY D 73
REMARK 465 PRO D 74
REMARK 465 LYS D 75
REMARK 465 ASP D 76
REMARK 465 GLU D 77
REMARK 465 GLU D 78
REMARK 465 ARG D 79
REMARK 465 ASP D 125
REMARK 465 LEU D 126
REMARK 465 GLY D 127
REMARK 465 LYS D 128
REMARK 465 GLY D 129
REMARK 465 GLY D 130
REMARK 465 ASN D 131
REMARK 465 GLU D 132
REMARK 465 GLU D 133
REMARK 465 SER D 134
REMARK 465 THR D 135
REMARK 465 LYS D 136
REMARK 465 THR D 137
REMARK 465 GLY D 138
REMARK 465 ASN D 139
REMARK 465 ALA D 140
REMARK 465 GLY D 141
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 LEU A 8 CA - CB - CG ANGL. DEV. = 15.2 DEGREES
REMARK 500 LEU A 38 CB - CG - CD1 ANGL. DEV. = 11.2 DEGREES
REMARK 500 THR A 39 C - N - CA ANGL. DEV. = 15.2 DEGREES
REMARK 500 GLU A 40 O - C - N ANGL. DEV. = 11.8 DEGREES
REMARK 500 VAL A 94 CA - CB - CG1 ANGL. DEV. = 10.5 DEGREES
REMARK 500 ASP A 96 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES
REMARK 500 LEU B 38 CA - CB - CG ANGL. DEV. = 16.3 DEGREES
REMARK 500 LYS B 91 O - C - N ANGL. DEV. = -12.5 DEGREES
REMARK 500 VAL B 94 C - N - CA ANGL. DEV. = 19.2 DEGREES
REMARK 500 ASP B 96 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES
REMARK 500 LEU C 38 CA - CB - CG ANGL. DEV. = 14.7 DEGREES
REMARK 500 ASP C 92 O - C - N ANGL. DEV. = -12.9 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 ASN A 65 55.86 -145.15
REMARK 500 ASP A 83 85.79 -67.22
REMARK 500 ASP A 90 -170.08 -69.83
REMARK 500 SER A 98 47.13 -143.03
REMARK 500 ALA A 123 138.76 -36.65
REMARK 500 ASN B 65 67.89 -157.89
REMARK 500 VAL B 94 88.90 54.64
REMARK 500 HIS B 110 24.77 -67.65
REMARK 500 ALA B 123 134.63 -38.45
REMARK 500 LEU B 126 31.14 78.69
REMARK 500 LYS B 128 41.93 -109.20
REMARK 500 THR B 137 -14.04 -141.55
REMARK 500 ASN B 139 59.28 37.72
REMARK 500 ALA C 55 51.48 -102.65
REMARK 500 ASP C 83 99.40 -69.11
REMARK 500 ASP C 90 -164.41 -67.60
REMARK 500 ASP C 92 -141.53 -93.87
REMARK 500 ALA D 55 39.77 -90.38
REMARK 500 ASP D 90 -162.23 -70.66
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 GLY C 93 VAL C 94 -63.53
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 VAL A 94 -14.41
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 CPT B 202
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 CPT B 201 PT1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 111 SG
REMARK 620 2 CPT B 201 N1 76.8
REMARK 620 3 CPT B 201 N2 134.8 91.0
REMARK 620 4 CPT B 201 CL2 104.3 178.2 87.2
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CPT B 201 PT1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 111 SG
REMARK 620 2 CPT B 201 N1 167.2
REMARK 620 3 CPT B 201 N2 132.9 36.6
REMARK 620 4 CPT B 201 CL2 116.0 51.5 22.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CPT C 201 PT1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS C 111 SG
REMARK 620 2 CPT C 201 N1 97.5
REMARK 620 3 CPT C 201 N2 170.0 90.0
REMARK 620 4 CPT C 201 CL2 81.3 178.7 91.3
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CPT C 201 PT1
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS D 111 SG
REMARK 620 2 CPT C 201 N1 143.4
REMARK 620 3 CPT C 201 N2 152.6 16.0
REMARK 620 4 CPT C 201 CL2 162.5 49.4 43.8
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPT B 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPT B 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPT C 201
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3ECU RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF HUMAN APO CU,ZN SUPEROXIDE DISMUTASE (SOD1)
REMARK 900 RELATED ID: 3ECV RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE ALS-RELATED PATHOLOGICAL MUTANT I113T OF
REMARK 900 HUMAN APO CU,ZN SUPEROXIDE DISMUTASE (SOD1)
REMARK 900 RELATED ID: 3ECW RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE ALS-RELATED PATHOLOGICAL MUTANT T54R OF
REMARK 900 HUMAN APO CU,ZN SUPEROXIDE DISMUTASE (SOD1)
DBREF 3RE0 A 1 153 UNP P00441 SODC_HUMAN 2 154
DBREF 3RE0 B 1 153 UNP P00441 SODC_HUMAN 2 154
DBREF 3RE0 C 1 153 UNP P00441 SODC_HUMAN 2 154
DBREF 3RE0 D 1 153 UNP P00441 SODC_HUMAN 2 154
SEQRES 1 A 153 ALA THR LYS ALA VAL CYS VAL LEU LYS GLY ASP GLY PRO
SEQRES 2 A 153 VAL GLN GLY ILE ILE ASN PHE GLU GLN LYS GLU SER ASN
SEQRES 3 A 153 GLY PRO VAL LYS VAL TRP GLY SER ILE LYS GLY LEU THR
SEQRES 4 A 153 GLU GLY LEU HIS GLY PHE HIS VAL HIS GLU PHE GLY ASP
SEQRES 5 A 153 ASN THR ALA GLY CYS THR SER ALA GLY PRO HIS PHE ASN
SEQRES 6 A 153 PRO LEU SER ARG LYS HIS GLY GLY PRO LYS ASP GLU GLU
SEQRES 7 A 153 ARG HIS VAL GLY ASP LEU GLY ASN VAL THR ALA ASP LYS
SEQRES 8 A 153 ASP GLY VAL ALA ASP VAL SER ILE GLU ASP SER VAL ILE
SEQRES 9 A 153 SER LEU SER GLY ASP HIS CYS ILE ILE GLY ARG THR LEU
SEQRES 10 A 153 VAL VAL HIS GLU LYS ALA ASP ASP LEU GLY LYS GLY GLY
SEQRES 11 A 153 ASN GLU GLU SER THR LYS THR GLY ASN ALA GLY SER ARG
SEQRES 12 A 153 LEU ALA CYS GLY VAL ILE GLY ILE ALA GLN
SEQRES 1 B 153 ALA THR LYS ALA VAL CYS VAL LEU LYS GLY ASP GLY PRO
SEQRES 2 B 153 VAL GLN GLY ILE ILE ASN PHE GLU GLN LYS GLU SER ASN
SEQRES 3 B 153 GLY PRO VAL LYS VAL TRP GLY SER ILE LYS GLY LEU THR
SEQRES 4 B 153 GLU GLY LEU HIS GLY PHE HIS VAL HIS GLU PHE GLY ASP
SEQRES 5 B 153 ASN THR ALA GLY CYS THR SER ALA GLY PRO HIS PHE ASN
SEQRES 6 B 153 PRO LEU SER ARG LYS HIS GLY GLY PRO LYS ASP GLU GLU
SEQRES 7 B 153 ARG HIS VAL GLY ASP LEU GLY ASN VAL THR ALA ASP LYS
SEQRES 8 B 153 ASP GLY VAL ALA ASP VAL SER ILE GLU ASP SER VAL ILE
SEQRES 9 B 153 SER LEU SER GLY ASP HIS CYS ILE ILE GLY ARG THR LEU
SEQRES 10 B 153 VAL VAL HIS GLU LYS ALA ASP ASP LEU GLY LYS GLY GLY
SEQRES 11 B 153 ASN GLU GLU SER THR LYS THR GLY ASN ALA GLY SER ARG
SEQRES 12 B 153 LEU ALA CYS GLY VAL ILE GLY ILE ALA GLN
SEQRES 1 C 153 ALA THR LYS ALA VAL CYS VAL LEU LYS GLY ASP GLY PRO
SEQRES 2 C 153 VAL GLN GLY ILE ILE ASN PHE GLU GLN LYS GLU SER ASN
SEQRES 3 C 153 GLY PRO VAL LYS VAL TRP GLY SER ILE LYS GLY LEU THR
SEQRES 4 C 153 GLU GLY LEU HIS GLY PHE HIS VAL HIS GLU PHE GLY ASP
SEQRES 5 C 153 ASN THR ALA GLY CYS THR SER ALA GLY PRO HIS PHE ASN
SEQRES 6 C 153 PRO LEU SER ARG LYS HIS GLY GLY PRO LYS ASP GLU GLU
SEQRES 7 C 153 ARG HIS VAL GLY ASP LEU GLY ASN VAL THR ALA ASP LYS
SEQRES 8 C 153 ASP GLY VAL ALA ASP VAL SER ILE GLU ASP SER VAL ILE
SEQRES 9 C 153 SER LEU SER GLY ASP HIS CYS ILE ILE GLY ARG THR LEU
SEQRES 10 C 153 VAL VAL HIS GLU LYS ALA ASP ASP LEU GLY LYS GLY GLY
SEQRES 11 C 153 ASN GLU GLU SER THR LYS THR GLY ASN ALA GLY SER ARG
SEQRES 12 C 153 LEU ALA CYS GLY VAL ILE GLY ILE ALA GLN
SEQRES 1 D 153 ALA THR LYS ALA VAL CYS VAL LEU LYS GLY ASP GLY PRO
SEQRES 2 D 153 VAL GLN GLY ILE ILE ASN PHE GLU GLN LYS GLU SER ASN
SEQRES 3 D 153 GLY PRO VAL LYS VAL TRP GLY SER ILE LYS GLY LEU THR
SEQRES 4 D 153 GLU GLY LEU HIS GLY PHE HIS VAL HIS GLU PHE GLY ASP
SEQRES 5 D 153 ASN THR ALA GLY CYS THR SER ALA GLY PRO HIS PHE ASN
SEQRES 6 D 153 PRO LEU SER ARG LYS HIS GLY GLY PRO LYS ASP GLU GLU
SEQRES 7 D 153 ARG HIS VAL GLY ASP LEU GLY ASN VAL THR ALA ASP LYS
SEQRES 8 D 153 ASP GLY VAL ALA ASP VAL SER ILE GLU ASP SER VAL ILE
SEQRES 9 D 153 SER LEU SER GLY ASP HIS CYS ILE ILE GLY ARG THR LEU
SEQRES 10 D 153 VAL VAL HIS GLU LYS ALA ASP ASP LEU GLY LYS GLY GLY
SEQRES 11 D 153 ASN GLU GLU SER THR LYS THR GLY ASN ALA GLY SER ARG
SEQRES 12 D 153 LEU ALA CYS GLY VAL ILE GLY ILE ALA GLN
HET CPT B 201 8
HET CPT B 202 4
HET CPT C 201 8
HETNAM CPT CISPLATIN
HETSYN CPT DIAMMINE(DICHLORO)PLATINUM
FORMUL 5 CPT 3(CL2 H6 N2 PT)
FORMUL 8 HOH *96(H2 O)
HELIX 1 1 ALA A 55 GLY A 61 5 7
HELIX 2 2 SER A 107 CYS A 111 5 5
HELIX 3 3 GLU A 132 LYS A 136 5 5
HELIX 4 4 GLY B 56 GLY B 61 5 6
HELIX 5 5 ASN B 131 THR B 137 1 7
HELIX 6 6 ALA C 55 GLY C 61 5 7
HELIX 7 7 ALA D 55 GLY D 61 5 7
HELIX 8 8 SER D 107 CYS D 111 5 5
SHEET 1 A 5 ALA A 95 ASP A 101 0
SHEET 2 A 5 VAL A 29 LYS A 36 -1 N ILE A 35 O ALA A 95
SHEET 3 A 5 GLN A 15 GLU A 21 -1 N GLU A 21 O LYS A 30
SHEET 4 A 5 LYS A 3 LEU A 8 -1 N CYS A 6 O ILE A 18
SHEET 5 A 5 GLY A 150 ILE A 151 -1 O GLY A 150 N VAL A 5
SHEET 1 B 4 ASP A 83 ALA A 89 0
SHEET 2 B 4 GLY A 41 HIS A 48 -1 N GLY A 41 O ALA A 89
SHEET 3 B 4 THR A 116 HIS A 120 -1 O HIS A 120 N GLY A 44
SHEET 4 B 4 ARG A 143 VAL A 148 -1 O GLY A 147 N LEU A 117
SHEET 1 C 9 LYS B 3 LEU B 8 0
SHEET 2 C 9 GLN B 15 GLN B 22 -1 O GLY B 16 N LEU B 8
SHEET 3 C 9 VAL B 29 LYS B 36 -1 O LYS B 30 N GLU B 21
SHEET 4 C 9 ALA B 95 ASP B 101 -1 O ILE B 99 N VAL B 31
SHEET 5 C 9 ASP B 83 ALA B 89 -1 O THR B 88 N ASP B 96
SHEET 6 C 9 GLY B 41 HIS B 48 -1 N GLY B 41 O ALA B 89
SHEET 7 C 9 THR B 116 HIS B 120 -1 O THR B 116 N HIS B 48
SHEET 8 C 9 ARG B 143 ILE B 151 -1 O ALA B 145 N VAL B 119
SHEET 9 C 9 LYS B 3 LEU B 8 -1 N VAL B 5 O GLY B 150
SHEET 1 D 5 ALA C 95 ASP C 101 0
SHEET 2 D 5 VAL C 29 LYS C 36 -1 N GLY C 33 O VAL C 97
SHEET 3 D 5 GLN C 15 GLN C 22 -1 N GLN C 15 O LYS C 36
SHEET 4 D 5 LYS C 3 LEU C 8 -1 N LEU C 8 O GLY C 16
SHEET 5 D 5 GLY C 150 ILE C 151 -1 O GLY C 150 N VAL C 5
SHEET 1 E 4 ASP C 83 ALA C 89 0
SHEET 2 E 4 GLY C 41 HIS C 48 -1 N GLY C 41 O ALA C 89
SHEET 3 E 4 THR C 116 HIS C 120 -1 O THR C 116 N HIS C 48
SHEET 4 E 4 ARG C 143 VAL C 148 -1 O ALA C 145 N VAL C 119
SHEET 1 F 5 ALA D 95 ASP D 101 0
SHEET 2 F 5 VAL D 29 LYS D 36 -1 N VAL D 29 O ASP D 101
SHEET 3 F 5 GLN D 15 GLU D 21 -1 N ASN D 19 O TRP D 32
SHEET 4 F 5 LYS D 3 LEU D 8 -1 N LEU D 8 O GLY D 16
SHEET 5 F 5 GLY D 150 ILE D 151 -1 O GLY D 150 N VAL D 5
SHEET 1 G 4 ASP D 83 ALA D 89 0
SHEET 2 G 4 GLY D 41 HIS D 48 -1 N GLY D 41 O ALA D 89
SHEET 3 G 4 THR D 116 HIS D 120 -1 O VAL D 118 N HIS D 46
SHEET 4 G 4 ARG D 143 VAL D 148 -1 O GLY D 147 N LEU D 117
SSBOND 1 CYS A 57 CYS A 146 1555 1555 2.14
SSBOND 2 CYS B 57 CYS B 146 1555 1555 2.13
SSBOND 3 CYS C 57 CYS C 146 1555 1555 2.15
SSBOND 4 CYS D 57 CYS D 146 1555 1555 2.11
LINK SG CYS A 111 PT1 ACPT B 201 1555 1555 2.25
LINK SG CYS B 111 PT1 BCPT B 201 1555 1555 2.21
LINK SG CYS C 111 PT1 CCPT C 201 1555 1555 2.18
LINK PT1 DCPT C 201 SG CYS D 111 1555 1555 2.37
CISPEP 1 GLY B 93 VAL B 94 0 23.03
SITE 1 AC1 4 LEU A 106 CYS A 111 LEU B 106 CYS B 111
SITE 1 AC2 2 ASP B 109 GLU C 24
SITE 1 AC3 3 CYS C 111 CYS D 111 ILE D 113
CRYST1 157.412 34.805 115.225 90.00 112.28 90.00 C 1 2 1 16
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.006353 0.000000 0.002603 0.00000
SCALE2 0.000000 0.028732 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009379 0.00000
(ATOM LINES ARE NOT SHOWN.)
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