PDB Short entry for 3G50 HEADER OXIDOREDUCTASE 04-FEB-09 3G50 TITLE CRYSTAL STRUCTURE OF NISOD D3A 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 5 21-FEB-24 3G50 1 REMARK REVDAT 4 20-OCT-21 3G50 1 REMARK SEQADV REVDAT 3 01-NOV-17 3G50 1 REMARK REVDAT 2 13-JUL-11 3G50 1 VERSN REVDAT 1 28-APR-09 3G50 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 28277 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1519 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1990 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2753 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 291 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) : 37.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.00000 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): 0.158 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.493 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2849 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3858 ; 1.564 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 347 ; 4.652 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;34.846 ;24.701 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 502 ;14.027 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.921 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 412 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2166 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1470 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1983 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 273 ; 0.189 ; 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): 118 ; 0.249 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 29 ; 0.180 ; 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): 1743 ; 0.977 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2807 ; 1.717 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1106 ; 2.778 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1049 ; 4.568 ; 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): -13.9398 21.0401 28.9185 REMARK 3 T TENSOR REMARK 3 T11: .0825 T22: .0574 REMARK 3 T33: .2727 T12: .0492 REMARK 3 T13: -.0246 T23: -.0012 REMARK 3 L TENSOR REMARK 3 L11: 3.3065 L22: 1.5926 REMARK 3 L33: 2.5717 L12: -2.2944 REMARK 3 L13: -2.8964 L23: 2.0068 REMARK 3 S TENSOR REMARK 3 S11: .0459 S12: -.1587 S13: .3548 REMARK 3 S21: -.0031 S22: .1477 S23: -.2509 REMARK 3 S31: -.0386 S32: .1305 S33: -.1936 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): 1.0432 24.3022 16.2586 REMARK 3 T TENSOR REMARK 3 T11: .0503 T22: .0051 REMARK 3 T33: .0143 T12: -.0058 REMARK 3 T13: .0110 T23: .0046 REMARK 3 L TENSOR REMARK 3 L11: 1.6644 L22: .8542 REMARK 3 L33: .3175 L12: -.5339 REMARK 3 L13: -.0506 L23: .0537 REMARK 3 S TENSOR REMARK 3 S11: .0201 S12: .0428 S13: .1308 REMARK 3 S21: -.0765 S22: .0088 S23: -.0306 REMARK 3 S31: -.1192 S32: .0151 S33: -.0289 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 4 B 7 REMARK 3 ORIGIN FOR THE GROUP (A): -16.9011 -4.6629 28.5532 REMARK 3 T TENSOR REMARK 3 T11: .0648 T22: .0590 REMARK 3 T33: .0515 T12: -.0255 REMARK 3 T13: -.0121 T23: .0018 REMARK 3 L TENSOR REMARK 3 L11: .7131 L22: 9.8514 REMARK 3 L33: 2.3657 L12: 2.6481 REMARK 3 L13: 1.2976 L23: 4.8275 REMARK 3 S TENSOR REMARK 3 S11: .0949 S12: -.0398 S13: .0599 REMARK 3 S21: .4109 S22: -.1876 S23: .2132 REMARK 3 S31: .2028 S32: -.0863 S33: .0927 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): 1.0589 -7.5989 16.3177 REMARK 3 T TENSOR REMARK 3 T11: .0224 T22: .0147 REMARK 3 T33: .0107 T12: .0046 REMARK 3 T13: -.0035 T23: -.0093 REMARK 3 L TENSOR REMARK 3 L11: 1.3180 L22: .8044 REMARK 3 L33: .9177 L12: .7141 REMARK 3 L13: -.5392 L23: -.3243 REMARK 3 S TENSOR REMARK 3 S11: -.0403 S12: .1058 S13: -.0337 REMARK 3 S21: -.0814 S22: .0085 S23: .0415 REMARK 3 S31: .0856 S32: -.0218 S33: .0318 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): -2.5129 7.7102 46.6597 REMARK 3 T TENSOR REMARK 3 T11: .3560 T22: .1979 REMARK 3 T33: .2055 T12: .0658 REMARK 3 T13: .0268 T23: .0326 REMARK 3 L TENSOR REMARK 3 L11: .0017 L22: .0007 REMARK 3 L33: .0081 L12: -.0009 REMARK 3 L13: -.0027 L23: .0022 REMARK 3 S TENSOR REMARK 3 S11: -.0187 S12: -.0054 S13: .0087 REMARK 3 S21: .0143 S22: .0088 S23: .0016 REMARK 3 S31: .0533 S32: .0124 S33: .0100 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): 15.9710 8.5866 39.9301 REMARK 3 T TENSOR REMARK 3 T11: .0152 T22: .0196 REMARK 3 T33: .0186 T12: -.0045 REMARK 3 T13: -.0148 T23: .0018 REMARK 3 L TENSOR REMARK 3 L11: .6370 L22: .6094 REMARK 3 L33: 1.3846 L12: -.1622 REMARK 3 L13: -.4775 L23: .3497 REMARK 3 S TENSOR REMARK 3 S11: .0071 S12: -.0667 S13: .0225 REMARK 3 S21: .0899 S22: .0034 S23: -.1002 REMARK 3 S31: .0346 S32: .0967 S33: -.0105 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 3G50 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_1000051430. 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 : 29881 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 21.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 41.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.92900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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 (%): 48.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 550 MME, MGCL2, HEPES, 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 55.84750 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 55.84750 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 29.99400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.13700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.99400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.13700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 55.84750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.99400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.13700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 55.84750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.99400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.13700 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: 13630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 55.84750 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 121 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 182 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 HIS B 1 REMARK 465 CYS B 2 REMARK 465 ALA B 3 REMARK 465 ALA B 117 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 NZ LYS C 92 O HOH C 260 2.03 REMARK 500 O HOH A 261 O HOH A 262 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 39 NE - CZ - NH2 ANGL. DEV. = -3.8 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 CYS C 2 31.90 -179.57 REMARK 500 ALA C 3 77.56 39.92 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 69.7 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 NI C 203 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 AT 2.01 A REMARK 900 RELATED ID: 3G4Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NISOD Y9F MUTANT AT 1.9 A DBREF 3G50 A 1 117 UNP P80735 SODN_STRCO 15 131 DBREF 3G50 B 1 117 UNP P80735 SODN_STRCO 15 131 DBREF 3G50 C 1 117 UNP P80735 SODN_STRCO 15 131 SEQADV 3G50 ALA A 3 UNP P80735 ASP 17 ENGINEERED MUTATION SEQADV 3G50 ALA B 3 UNP P80735 ASP 17 ENGINEERED MUTATION SEQADV 3G50 ALA C 3 UNP P80735 ASP 17 ENGINEERED MUTATION SEQRES 1 A 117 HIS CYS ALA LEU PRO CYS GLY VAL TYR 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 ALA LEU PRO CYS GLY VAL TYR 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 ALA LEU PRO CYS GLY VAL TYR 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 NI C 203 1 HETNAM NI NICKEL (II) ION FORMUL 4 NI 2(NI 2+) FORMUL 6 HOH *291(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 LYS A 115 1 23 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 ASN C 31 1 21 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 HIS A 1 NI NI A 201 1555 1555 2.33 LINK N CYS A 2 NI NI A 201 1555 1555 2.46 LINK N HIS C 1 NI NI C 203 1555 1555 2.14 CISPEP 1 LEU A 4 PRO A 5 0 -0.30 CISPEP 2 LEU B 4 PRO B 5 0 -7.03 CISPEP 3 LEU C 4 PRO C 5 0 4.42 SITE 1 AC1 3 HIS A 1 CYS A 2 CYS A 6 SITE 1 AC2 3 HIS C 1 CYS C 2 CYS C 6 CRYST1 59.988 112.274 111.695 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 0.016670 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008907 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008953 0.00000