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 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 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