HEADER OXIDOREDUCTASE 04-FEB-09 3G4X
TITLE CRYSTAL STRUCTURE OF NISOD Y9F MUTANT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [NI];
COMPND 3 CHAIN: A, B, C;
COMPND 4 FRAGMENT: NISOD (UNP RESIDUES 15 TO 131);
COMPND 5 SYNONYM: NISOD, NICKEL-CONTAINING SUPEROXIDE DISMUTASE;
COMPND 6 EC: 1.15.1.1;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR;
SOURCE 3 ORGANISM_TAXID: 1902;
SOURCE 4 GENE: 2SC7G11.16C, SCO5254, SOD1, SODN;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET30
KEYWDS NICKEL, HEXAMER, SUPEROXIDE DISMUTASE, NISOD, SOD, ANTIOXIDANT,
KEYWDS 2 METAL-BINDING, OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.C.GARMAN,A.I.GUCE,R.W.HERBST,P.A.BRYNGELSON,D.E.CABELLI,
AUTHOR 2 K.A.HIGGINS,K.C.RYAN,M.J.MARONEY
REVDAT 5 06-SEP-23 3G4X 1 REMARK
REVDAT 4 20-OCT-21 3G4X 1 REMARK SEQADV
REVDAT 3 01-NOV-17 3G4X 1 REMARK
REVDAT 2 13-JUL-11 3G4X 1 VERSN
REVDAT 1 28-APR-09 3G4X 0
JRNL AUTH R.W.HERBST,A.GUCE,P.A.BRYNGELSON,K.A.HIGGINS,K.C.RYAN,
JRNL AUTH 2 D.E.CABELLI,S.C.GARMAN,M.J.MARONEY
JRNL TITL ROLE OF CONSERVED TYROSINE RESIDUES IN NISOD CATALYSIS: A
JRNL TITL 2 CASE OF CONVERGENT EVOLUTION
JRNL REF BIOCHEMISTRY V. 48 3354 2009
JRNL REFN ISSN 0006-2960
JRNL PMID 19183068
JRNL DOI 10.1021/BI802029T
REMARK 2
REMARK 2 RESOLUTION. 2.01 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0019
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) : 2.01
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.61
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 3 NUMBER OF REFLECTIONS : 24113
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) : 0.172
REMARK 3 R VALUE (WORKING SET) : 0.168
REMARK 3 FREE R VALUE : 0.237
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1300
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) : 2.01
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1709
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.77
REMARK 3 BIN R VALUE (WORKING SET) : 0.2620
REMARK 3 BIN FREE R VALUE SET COUNT : 86
REMARK 3 BIN FREE R VALUE : 0.3250
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2787
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 6
REMARK 3 SOLVENT ATOMS : 389
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.79
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.03000
REMARK 3 B22 (A**2) : -0.02000
REMARK 3 B33 (A**2) : -0.01000
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 OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.184
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.178
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.132
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2898 ; 0.018 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3926 ; 1.479 ; 1.940
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 352 ; 4.759 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;36.560 ;24.892
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 504 ;14.881 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;18.297 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 417 ; 0.109 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2225 ; 0.008 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1467 ; 0.229 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1964 ; 0.302 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 316 ; 0.173 ; 0.200
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): 135 ; 0.289 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 56 ; 0.227 ; 0.200
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): 1773 ; 0.827 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2858 ; 1.423 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1125 ; 2.568 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1068 ; 3.968 ; 4.500
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 : 6
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 1 A 7
REMARK 3 ORIGIN FOR THE GROUP (A): -14.0183 20.9258 28.6046
REMARK 3 T TENSOR
REMARK 3 T11: .1143 T22: .0699
REMARK 3 T33: .1712 T12: .0260
REMARK 3 T13: .0353 T23: .0130
REMARK 3 L TENSOR
REMARK 3 L11: 4.6648 L22: 1.1383
REMARK 3 L33: 3.4384 L12: -2.3041
REMARK 3 L13: -4.0033 L23: 1.9766
REMARK 3 S TENSOR
REMARK 3 S11: -.1103 S12: -.0517 S13: -.0249
REMARK 3 S21: .0707 S22: .0523 S23: .0108
REMARK 3 S31: .1039 S32: .0407 S33: .0580
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : A 8 A 116
REMARK 3 ORIGIN FOR THE GROUP (A): 1.0128 24.3996 16.2163
REMARK 3 T TENSOR
REMARK 3 T11: .0766 T22: .0328
REMARK 3 T33: .0369 T12: -.0042
REMARK 3 T13: .0402 T23: .0150
REMARK 3 L TENSOR
REMARK 3 L11: 1.4796 L22: .6742
REMARK 3 L33: .2642 L12: -.3305
REMARK 3 L13: .0148 L23: .0374
REMARK 3 S TENSOR
REMARK 3 S11: .0189 S12: -.0016 S13: .0590
REMARK 3 S21: -.1159 S22: .0227 S23: -.0252
REMARK 3 S31: -.0964 S32: .0086 S33: -.0416
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 1 B 7
REMARK 3 ORIGIN FOR THE GROUP (A): -13.8784 -3.9164 27.8616
REMARK 3 T TENSOR
REMARK 3 T11: .0748 T22: .1411
REMARK 3 T33: .2415 T12: -.0453
REMARK 3 T13: -.0063 T23: .1122
REMARK 3 L TENSOR
REMARK 3 L11: 2.5649 L22: 8.5571
REMARK 3 L33: 2.8403 L12: 1.0430
REMARK 3 L13: -.6254 L23: 4.4210
REMARK 3 S TENSOR
REMARK 3 S11: -.2013 S12: .5371 S13: .6544
REMARK 3 S21: .2851 S22: -.0335 S23: .9039
REMARK 3 S31: .2754 S32: -.2894 S33: .2348
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : B 8 B 116
REMARK 3 ORIGIN FOR THE GROUP (A): .8616 -8.0308 16.3168
REMARK 3 T TENSOR
REMARK 3 T11: .0741 T22: .0564
REMARK 3 T33: .0111 T12: .0024
REMARK 3 T13: .0168 T23: -.0014
REMARK 3 L TENSOR
REMARK 3 L11: 1.3753 L22: 1.0003
REMARK 3 L33: 1.2129 L12: 1.0482
REMARK 3 L13: -.9276 L23: -.4973
REMARK 3 S TENSOR
REMARK 3 S11: -.0811 S12: .0936 S13: .0239
REMARK 3 S21: -.0889 S22: .0520 S23: .0430
REMARK 3 S31: .1206 S32: -.0468 S33: .0291
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : C 1 C 7
REMARK 3 ORIGIN FOR THE GROUP (A): -2.1233 7.9842 46.3197
REMARK 3 T TENSOR
REMARK 3 T11: .0896 T22: .0477
REMARK 3 T33: .0882 T12: .0082
REMARK 3 T13: .0532 T23: -.0213
REMARK 3 L TENSOR
REMARK 3 L11: 5.7206 L22: .0018
REMARK 3 L33: 3.5409 L12: -.0368
REMARK 3 L13: 1.1018 L23: -.0761
REMARK 3 S TENSOR
REMARK 3 S11: -.2478 S12: -.2314 S13: .0534
REMARK 3 S21: -.0046 S22: .0347 S23: -.0062
REMARK 3 S31: .1497 S32: -.0386 S33: .2132
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 NUMBER OF COMPONENTS GROUP : 1
REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI
REMARK 3 RESIDUE RANGE : C 8 C 116
REMARK 3 ORIGIN FOR THE GROUP (A): 16.1785 8.5195 39.8301
REMARK 3 T TENSOR
REMARK 3 T11: .0211 T22: .0589
REMARK 3 T33: .0583 T12: -.0024
REMARK 3 T13: -.0268 T23: -.0085
REMARK 3 L TENSOR
REMARK 3 L11: .4625 L22: .8229
REMARK 3 L33: 1.3240 L12: -.2078
REMARK 3 L13: -.5634 L23: .3519
REMARK 3 S TENSOR
REMARK 3 S11: -.0061 S12: -.0210 S13: .0323
REMARK 3 S21: .1149 S22: .0074 S23: -.1279
REMARK 3 S31: .0311 S32: .0789 S33: -.0013
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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 3G4X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-09.
REMARK 100 THE DEPOSITION ID IS D_1000051427.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-NOV-06
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : RIGAKU
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : OSMIC BLUE
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25440
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 200 DATA REDUNDANCY : 4.700
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.05400
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3
REMARK 200 DATA REDUNDANCY IN SHELL : 4.40
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.51500
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100
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: PDB ENTRY 1T6U
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 48.48
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 550 MME, CACL2, BIS-TRIS, PH 6.5,
REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 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 55.93300
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.93300
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.04450
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.28400
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.04450
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.28400
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.93300
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.04450
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.28400
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.93300
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.04450
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.28400
REMARK 290 SMTRY3 8 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: HEXAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 14260 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 26560 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 55.93300
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH C 208 LIES ON A SPECIAL POSITION.
REMARK 375 HOH C 299 LIES ON A SPECIAL POSITION.
REMARK 375 HOH C 347 LIES ON A SPECIAL POSITION.
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 ALA C 117
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O HOH B 129 O HOH B 275 2.16
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH B 213 O HOH B 213 3555 1.63
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 ASP B 3 20.74 85.89
REMARK 500 ASP B 10 116.91 -163.11
REMARK 500 ASP C 3 12.57 82.65
REMARK 500 ASP C 10 119.40 -160.61
REMARK 500 PRO C 11 -7.00 -59.28
REMARK 500
REMARK 500 REMARK: NULL
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 NI A 201N NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 1 N
REMARK 620 2 HIS A 1 N 22.0
REMARK 620 3 HIS A 1 ND1 67.3 87.6
REMARK 620 4 CYS A 2 N 84.3 78.5 81.3
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NI B 202N NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS B 1 N
REMARK 620 2 HIS B 1 N 15.7
REMARK 620 3 CYS B 2 N 83.4 81.1
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NI C 203N NI
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS C 1 N
REMARK 620 2 HIS C 1 N 9.7
REMARK 620 3 HIS C 1 ND1 72.4 81.2
REMARK 620 4 CYS C 2 N 82.2 80.0 75.8
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 NI A 201N
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 301C
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 202N
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 302C
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI C 203N
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 303C
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1T6U RELATED DB: PDB
REMARK 900 NICKEL SUPEROXIDE DISMUTASE (NISOD) NATIVE AT 1.30 A
REMARK 900 RELATED ID: 3G4Z RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF NISOD Y9F MUTANT
REMARK 900 RELATED ID: 3G50 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF NISOD D3A MUTANT
DBREF 3G4X A 1 117 UNP P80735 SODN_STRCO 15 131
DBREF 3G4X B 1 117 UNP P80735 SODN_STRCO 15 131
DBREF 3G4X C 1 117 UNP P80735 SODN_STRCO 15 131
SEQADV 3G4X PHE A 9 UNP P80735 TYR 23 ENGINEERED MUTATION
SEQADV 3G4X PHE B 9 UNP P80735 TYR 23 ENGINEERED MUTATION
SEQADV 3G4X PHE C 9 UNP P80735 TYR 23 ENGINEERED MUTATION
SEQRES 1 A 117 HIS CYS ASP LEU PRO CYS GLY VAL PHE ASP PRO ALA GLN
SEQRES 2 A 117 ALA ARG ILE GLU ALA GLU SER VAL LYS ALA VAL GLN GLU
SEQRES 3 A 117 LYS MET ALA GLY ASN ASP ASP PRO HIS PHE GLN THR ARG
SEQRES 4 A 117 ALA THR VAL ILE LYS GLU GLN ARG ALA GLU LEU ALA LYS
SEQRES 5 A 117 HIS HIS VAL SER VAL LEU TRP SER ASP TYR PHE LYS PRO
SEQRES 6 A 117 PRO HIS PHE GLU LYS TYR PRO GLU LEU HIS GLN LEU VAL
SEQRES 7 A 117 ASN ASP THR LEU LYS ALA LEU SER ALA ALA LYS GLY SER
SEQRES 8 A 117 LYS ASP PRO ALA THR GLY GLN LYS ALA LEU ASP TYR ILE
SEQRES 9 A 117 ALA GLN ILE ASP LYS ILE PHE TRP GLU THR LYS LYS ALA
SEQRES 1 B 117 HIS CYS ASP LEU PRO CYS GLY VAL PHE ASP PRO ALA GLN
SEQRES 2 B 117 ALA ARG ILE GLU ALA GLU SER VAL LYS ALA VAL GLN GLU
SEQRES 3 B 117 LYS MET ALA GLY ASN ASP ASP PRO HIS PHE GLN THR ARG
SEQRES 4 B 117 ALA THR VAL ILE LYS GLU GLN ARG ALA GLU LEU ALA LYS
SEQRES 5 B 117 HIS HIS VAL SER VAL LEU TRP SER ASP TYR PHE LYS PRO
SEQRES 6 B 117 PRO HIS PHE GLU LYS TYR PRO GLU LEU HIS GLN LEU VAL
SEQRES 7 B 117 ASN ASP THR LEU LYS ALA LEU SER ALA ALA LYS GLY SER
SEQRES 8 B 117 LYS ASP PRO ALA THR GLY GLN LYS ALA LEU ASP TYR ILE
SEQRES 9 B 117 ALA GLN ILE ASP LYS ILE PHE TRP GLU THR LYS LYS ALA
SEQRES 1 C 117 HIS CYS ASP LEU PRO CYS GLY VAL PHE ASP PRO ALA GLN
SEQRES 2 C 117 ALA ARG ILE GLU ALA GLU SER VAL LYS ALA VAL GLN GLU
SEQRES 3 C 117 LYS MET ALA GLY ASN ASP ASP PRO HIS PHE GLN THR ARG
SEQRES 4 C 117 ALA THR VAL ILE LYS GLU GLN ARG ALA GLU LEU ALA LYS
SEQRES 5 C 117 HIS HIS VAL SER VAL LEU TRP SER ASP TYR PHE LYS PRO
SEQRES 6 C 117 PRO HIS PHE GLU LYS TYR PRO GLU LEU HIS GLN LEU VAL
SEQRES 7 C 117 ASN ASP THR LEU LYS ALA LEU SER ALA ALA LYS GLY SER
SEQRES 8 C 117 LYS ASP PRO ALA THR GLY GLN LYS ALA LEU ASP TYR ILE
SEQRES 9 C 117 ALA GLN ILE ASP LYS ILE PHE TRP GLU THR LYS LYS ALA
HET NI A 201N 1
HET CL A 301C 1
HET NI B 202N 1
HET CL B 302C 1
HET NI C 203N 1
HET CL C 303C 1
HETNAM NI NICKEL (II) ION
HETNAM CL CHLORIDE ION
FORMUL 4 NI 3(NI 2+)
FORMUL 5 CL 3(CL 1-)
FORMUL 10 HOH *389(H2 O)
HELIX 1 1 PRO A 11 ALA A 29 1 19
HELIX 2 2 ASP A 33 TYR A 62 1 30
HELIX 3 3 LYS A 64 TYR A 71 1 8
HELIX 4 4 GLU A 73 GLY A 90 1 18
HELIX 5 5 ASP A 93 ALA A 117 1 25
HELIX 6 6 PRO B 11 ALA B 29 1 19
HELIX 7 7 ASP B 33 TYR B 62 1 30
HELIX 8 8 LYS B 64 TYR B 71 1 8
HELIX 9 9 GLU B 73 GLY B 90 1 18
HELIX 10 10 ASP B 93 LYS B 116 1 24
HELIX 11 11 PRO C 11 ALA C 29 1 19
HELIX 12 12 ASP C 33 TYR C 62 1 30
HELIX 13 13 LYS C 64 TYR C 71 1 8
HELIX 14 14 GLU C 73 GLY C 90 1 18
HELIX 15 15 ASP C 93 LYS C 116 1 24
LINK N AHIS A 1 NI NI A 201N 1555 1555 2.04
LINK N BHIS A 1 NI NI A 201N 1555 1555 2.12
LINK ND1BHIS A 1 NI NI A 201N 1555 1555 2.23
LINK N CYS A 2 NI NI A 201N 1555 1555 2.02
LINK N AHIS B 1 NI NI B 202N 1555 1555 2.01
LINK N BHIS B 1 NI NI B 202N 1555 1555 2.03
LINK N CYS B 2 NI NI B 202N 1555 1555 2.06
LINK N AHIS C 1 NI NI C 203N 1555 1555 1.91
LINK N BHIS C 1 NI NI C 203N 1555 1555 2.01
LINK ND1BHIS C 1 NI NI C 203N 1555 1555 2.58
LINK N CYS C 2 NI NI C 203N 1555 1555 2.08
CISPEP 1 LEU A 4 PRO A 5 0 2.65
CISPEP 2 LEU B 4 PRO B 5 0 -0.29
CISPEP 3 LEU C 4 PRO C 5 0 7.60
SITE 1 AC1 4 HIS A 1 CYS A 2 CYS A 6 CL A 301C
SITE 1 AC2 7 HIS A 1 ASP A 3 PRO A 5 CYS A 6
SITE 2 AC2 7 PHE A 9 HOH A 123 NI A 201N
SITE 1 AC3 5 HIS B 1 CYS B 2 ASP B 3 CYS B 6
SITE 2 AC3 5 CL B 302C
SITE 1 AC4 7 HIS B 1 ASP B 3 PRO B 5 CYS B 6
SITE 2 AC4 7 PHE B 9 NI B 202N HOH B 349
SITE 1 AC5 4 HIS C 1 CYS C 2 CYS C 6 CL C 303C
SITE 1 AC6 8 HIS C 1 ASP C 3 PRO C 5 CYS C 6
SITE 2 AC6 8 PHE C 9 NI C 203N HOH C 340 HOH C 393
CRYST1 60.089 112.568 111.866 90.00 90.00 90.00 C 2 2 21 24
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 0.016642 0.000000 0.000000 0.00000
SCALE2 0.000000 0.008884 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008939 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
