PDB Short entry for 3G4Z HEADER OXIDOREDUCTASE 04-FEB-09 3G4Z TITLE CRYSTAL STRUCTURE OF NISOD Y9F MUTANT AT 1.9 A 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 6 21-FEB-24 3G4Z 1 REMARK REVDAT 5 20-OCT-21 3G4Z 1 REMARK SEQADV REVDAT 4 29-NOV-17 3G4Z 1 REMARK REVDAT 3 01-NOV-17 3G4Z 1 REMARK REVDAT 2 13-JUL-11 3G4Z 1 VERSN REVDAT 1 28-APR-09 3G4Z 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. 1.87 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 27302 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1452 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) : 1.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1835 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3090 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.4100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2791 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 458 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) : 30.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.06000 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): 0.171 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.172 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.647 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2873 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3888 ; 1.467 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 348 ; 5.040 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 137 ;35.239 ;24.891 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 501 ;14.663 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;19.750 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 415 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2192 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1554 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1994 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 394 ; 0.212 ; 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): 149 ; 0.315 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 72 ; 0.225 ; 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): 1763 ; 0.906 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2837 ; 1.552 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1110 ; 2.536 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1051 ; 4.179 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 3 A 116 4 REMARK 3 1 C 3 C 116 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 906 ; .28 ; .50 REMARK 3 MEDIUM THERMAL 1 C (A**2): 906 ; 1.09 ; 2.00 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 10 REMARK 3 ORIGIN FOR THE GROUP (A): .0000 .0000 .0000 REMARK 3 T TENSOR REMARK 3 T11: .0000 T22: .0000 REMARK 3 T33: .0000 T12: .0000 REMARK 3 T13: .0000 T23: .0000 REMARK 3 L TENSOR REMARK 3 L11: .0000 L22: .0000 REMARK 3 L33: .0000 L12: .0000 REMARK 3 L13: .0000 L23: .0000 REMARK 3 S TENSOR REMARK 3 S11: .0000 S12: .0000 S13: .0000 REMARK 3 S21: .0000 S22: .0000 S23: .0000 REMARK 3 S31: .0000 S32: .0000 S33: .0000 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 11 A 117 REMARK 3 ORIGIN FOR THE GROUP (A): .0000 .0000 .0000 REMARK 3 T TENSOR REMARK 3 T11: .0000 T22: .0000 REMARK 3 T33: .0000 T12: .0000 REMARK 3 T13: .0000 T23: .0000 REMARK 3 L TENSOR REMARK 3 L11: .0000 L22: .0000 REMARK 3 L33: .0000 L12: .0000 REMARK 3 L13: .0000 L23: .0000 REMARK 3 S TENSOR REMARK 3 S11: .0000 S12: .0000 S13: .0000 REMARK 3 S21: .0000 S22: .0000 S23: .0000 REMARK 3 S31: .0000 S32: .0000 S33: .0000 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 10 REMARK 3 ORIGIN FOR THE GROUP (A): .0000 .0000 .0000 REMARK 3 T TENSOR REMARK 3 T11: .0000 T22: .0000 REMARK 3 T33: .0000 T12: .0000 REMARK 3 T13: .0000 T23: .0000 REMARK 3 L TENSOR REMARK 3 L11: .0000 L22: .0000 REMARK 3 L33: .0000 L12: .0000 REMARK 3 L13: .0000 L23: .0000 REMARK 3 S TENSOR REMARK 3 S11: .0000 S12: .0000 S13: .0000 REMARK 3 S21: .0000 S22: .0000 S23: .0000 REMARK 3 S31: .0000 S32: .0000 S33: .0000 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 11 B 117 REMARK 3 ORIGIN FOR THE GROUP (A): .0000 .0000 .0000 REMARK 3 T TENSOR REMARK 3 T11: .0000 T22: .0000 REMARK 3 T33: .0000 T12: .0000 REMARK 3 T13: .0000 T23: .0000 REMARK 3 L TENSOR REMARK 3 L11: .0000 L22: .0000 REMARK 3 L33: .0000 L12: .0000 REMARK 3 L13: .0000 L23: .0000 REMARK 3 S TENSOR REMARK 3 S11: .0000 S12: .0000 S13: .0000 REMARK 3 S21: .0000 S22: .0000 S23: .0000 REMARK 3 S31: .0000 S32: .0000 S33: .0000 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 10 REMARK 3 ORIGIN FOR THE GROUP (A): .0000 .0000 .0000 REMARK 3 T TENSOR REMARK 3 T11: .0000 T22: .0000 REMARK 3 T33: .0000 T12: .0000 REMARK 3 T13: .0000 T23: .0000 REMARK 3 L TENSOR REMARK 3 L11: .0000 L22: .0000 REMARK 3 L33: .0000 L12: .0000 REMARK 3 L13: .0000 L23: .0000 REMARK 3 S TENSOR REMARK 3 S11: .0000 S12: .0000 S13: .0000 REMARK 3 S21: .0000 S22: .0000 S23: .0000 REMARK 3 S31: .0000 S32: .0000 S33: .0000 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 11 C 117 REMARK 3 ORIGIN FOR THE GROUP (A): .0000 .0000 .0000 REMARK 3 T TENSOR REMARK 3 T11: .0000 T22: .0000 REMARK 3 T33: .0000 T12: .0000 REMARK 3 T13: .0000 T23: .0000 REMARK 3 L TENSOR REMARK 3 L11: .0000 L22: .0000 REMARK 3 L33: .0000 L12: .0000 REMARK 3 L13: .0000 L23: .0000 REMARK 3 S TENSOR REMARK 3 S11: .0000 S12: .0000 S13: .0000 REMARK 3 S21: .0000 S22: .0000 S23: .0000 REMARK 3 S31: .0000 S32: .0000 S33: .0000 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 3G4Z 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_1000051429. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29628 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 20.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 42.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH WITH ANOMALOUS REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 550 MME, BIS-TRIS, PH 6.5, VAPOR REMARK 280 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 55.77650 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 55.77650 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 29.93800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.78850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.93800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.78850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.77650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.93800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 55.78850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.77650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.93800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 55.78850 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: 14200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 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 55.77650 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 187 LIES ON A SPECIAL POSITION. 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 NH1 ARG A 15 O HOH A 180 1.79 REMARK 500 O HOH B 180 O HOH B 181 1.90 REMARK 500 O HOH B 310 O HOH B 311 1.94 REMARK 500 O HOH C 407 O HOH C 409 1.96 REMARK 500 O HOH B 264 O HOH B 295 1.98 REMARK 500 O HOH A 418 O HOH A 420 2.05 REMARK 500 O HOH B 129 O HOH B 421 2.13 REMARK 500 O HOH B 133 O HOH B 317 2.15 REMARK 500 OE2 GLU B 69 O HOH B 226 2.16 REMARK 500 O HOH A 167 O HOH A 361 2.16 REMARK 500 O HOH A 155 O HOH A 156 2.18 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 C ALA A 117 O HOH B 160 5455 1.51 REMARK 500 O HOH A 468 O HOH B 226 7455 2.16 REMARK 500 O ALA A 117 O HOH B 160 5455 2.16 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 A 3 12.25 88.10 REMARK 500 ASP B 3 40.28 99.15 REMARK 500 ASP C 3 15.60 86.23 REMARK 500 PRO C 11 -6.88 -57.52 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 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 1 N REMARK 620 2 CYS A 2 N 78.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 202 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 1 N REMARK 620 2 CYS B 2 N 81.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI C 203 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 1 N REMARK 620 2 CYS C 2 N 82.2 REMARK 620 N 1 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR C 303 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: 3G4X 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 AT 1.9 A DBREF 3G4Z A 1 117 UNP P80735 SODN_STRCO 15 131 DBREF 3G4Z B 1 117 UNP P80735 SODN_STRCO 15 131 DBREF 3G4Z C 1 117 UNP P80735 SODN_STRCO 15 131 SEQADV 3G4Z PHE A 9 UNP P80735 TYR 23 ENGINEERED MUTATION SEQADV 3G4Z PHE B 9 UNP P80735 TYR 23 ENGINEERED MUTATION SEQADV 3G4Z 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 201 1 HET BR A 301 1 HET BR B 302 1 HET NI B 202 1 HET NI C 203 1 HET BR C 303 1 HETNAM NI NICKEL (II) ION HETNAM BR BROMIDE ION FORMUL 4 NI 3(NI 2+) FORMUL 5 BR 3(BR 1-) FORMUL 10 HOH *458(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 115 1 23 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 ALA C 117 1 25 LINK N HIS A 1 NI NI A 201 1555 1555 2.18 LINK N CYS A 2 NI NI A 201 1555 1555 2.02 LINK N HIS B 1 NI NI B 202 1555 1555 2.08 LINK N CYS B 2 NI NI B 202 1555 1555 2.09 LINK N HIS C 1 NI NI C 203 1555 1555 2.03 LINK N CYS C 2 NI NI C 203 1555 1555 2.06 CISPEP 1 LEU A 4 PRO A 5 0 4.21 CISPEP 2 LEU B 4 PRO B 5 0 -3.33 CISPEP 3 LEU C 4 PRO C 5 0 -2.34 SITE 1 AC1 4 HIS A 1 CYS A 2 ASP A 3 CYS A 6 SITE 1 AC2 5 ASP A 3 PRO A 5 CYS A 6 PHE A 9 SITE 2 AC2 5 HOH A 355 SITE 1 AC3 3 PRO B 5 PHE B 9 ASP B 61 SITE 1 AC4 4 HIS B 1 CYS B 2 ASP B 3 CYS B 6 SITE 1 AC5 3 HIS C 1 CYS C 2 CYS C 6 SITE 1 AC6 4 ASP C 3 PRO C 5 CYS C 6 PHE C 9 CRYST1 59.876 111.577 111.553 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 0.016701 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008964 0.00000