HEADER OXIDOREDUCTASE (SUPEROXIDE ACCEPTOR) 06-MAY-91 3SDP TITLE THE 2.1 ANGSTROMS RESOLUTION STRUCTURE OF IRON SUPEROXIDE DISMUTASE TITLE 2 FROM PSEUDOMONAS OVALIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRON SUPEROXIDE DISMUTASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.15.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303 KEYWDS OXIDOREDUCTASE (SUPEROXIDE ACCEPTOR) EXPDTA X-RAY DIFFRACTION AUTHOR B.L.STODDARD,D.RINGE,G.A.PETSKO REVDAT 4 28-FEB-24 3SDP 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 3SDP 1 VERSN REVDAT 2 01-APR-03 3SDP 1 JRNL REVDAT 1 15-APR-93 3SDP 0 JRNL AUTH B.L.STODDARD,P.L.HOWELL,D.RINGE,G.A.PETSKO JRNL TITL THE 2.1-A RESOLUTION STRUCTURE OF IRON SUPEROXIDE DISMUTASE JRNL TITL 2 FROM PSEUDOMONAS OVALIS. JRNL REF BIOCHEMISTRY V. 29 8885 1990 JRNL REFN ISSN 0006-2960 JRNL PMID 2271564 JRNL DOI 10.1021/BI00490A002 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.L.STODDARD,D.RINGE,G.A.PETSKO REMARK 1 TITL THE STRUCTURE OF IRON SUPEROXIDE DISMUTASE FROM PSEUDOMONAS REMARK 1 TITL 2 OVALIS BOUND TO THE INHIBITOR AZIDE: COORDINATION CHANGES REMARK 1 TITL 3 AND DYNAMICS DURING CATALYSIS REMARK 1 REF PROTEIN ENG. V. 4 113 1990 REMARK 1 REFN ISSN 0269-2139 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2908 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.033 ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3SDP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000179147. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.55000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 A 1 REMARK 465 PHE A 2 REMARK 465 GLU A 3 REMARK 465 LEU A 4 REMARK 465 LYS A 191 REMARK 465 THR A 192 REMARK 465 PHE A 193 REMARK 465 LYS A 194 REMARK 465 ALA A 195 REMARK 465 ALA B 1 REMARK 465 PHE B 2 REMARK 465 GLU B 3 REMARK 465 LEU B 4 REMARK 465 LYS B 191 REMARK 465 THR B 192 REMARK 465 PHE B 193 REMARK 465 LYS B 194 REMARK 465 ALA B 195 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 FE A 196 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 26 NE2 REMARK 620 2 HIS A 74 NE2 99.6 REMARK 620 3 ASP A 156 OD2 97.8 120.0 REMARK 620 4 HIS A 160 NE2 93.7 128.1 107.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 196 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 26 NE2 REMARK 620 2 HIS B 74 NE2 104.3 REMARK 620 3 ASP B 156 OD2 118.0 102.7 REMARK 620 4 HIS B 160 NE2 90.7 136.3 105.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: FEA REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: FEB REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 196 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 196 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE 85 OF EACH CHAIN IS IDENTIFIED AS ALA IN THIS REMARK 999 ENTRY. NOTE THAT THIS RESIDUE IS IDENTIFIED AS GLY IN REMARK 999 SWISSPROT ENTRY SODF_PSEOV. DBREF 3SDP A 1 195 UNP P09223 SODF_PSEPU 1 195 DBREF 3SDP B 1 195 UNP P09223 SODF_PSEPU 1 195 SEQADV 3SDP ALA A 85 UNP P09223 GLY 85 CONFLICT SEQADV 3SDP ALA B 85 UNP P09223 GLY 85 CONFLICT SEQRES 1 A 195 ALA PHE GLU LEU PRO PRO LEU PRO TYR ALA HIS ASP ALA SEQRES 2 A 195 LEU GLN PRO HIS ILE SER LYS GLU THR LEU GLU TYR HIS SEQRES 3 A 195 HIS ASP LYS HIS HIS ASN THR TYR VAL VAL ASN LEU ASN SEQRES 4 A 195 ASN LEU VAL PRO GLY THR PRO GLU PHE GLU GLY LYS THR SEQRES 5 A 195 LEU GLU GLU ILE VAL LYS SER SER SER GLY GLY ILE PHE SEQRES 6 A 195 ASN ASN ALA ALA GLN VAL TRP ASN HIS THR PHE TYR TRP SEQRES 7 A 195 ASN CYS LEU SER PRO ASP ALA GLY GLY GLN PRO THR GLY SEQRES 8 A 195 ALA LEU ALA ASP ALA ILE ASN ALA ALA PHE GLY SER PHE SEQRES 9 A 195 ASP LYS PHE LYS GLU GLU PHE THR LYS THR SER VAL GLY SEQRES 10 A 195 THR PHE GLY SER GLY TRP ALA TRP LEU VAL LYS ALA ASP SEQRES 11 A 195 GLY SER LEU ALA LEU CYS SER THR ILE GLY ALA GLY ALA SEQRES 12 A 195 PRO LEU THR SER GLY ASP THR PRO LEU LEU THR CYS ASP SEQRES 13 A 195 VAL TRP GLU HIS ALA TYR TYR ILE ASP TYR ARG ASN LEU SEQRES 14 A 195 ARG PRO LYS TYR VAL GLU ALA PHE TRP ASN LEU VAL ASN SEQRES 15 A 195 TRP ALA PHE VAL ALA GLU GLU GLY LYS THR PHE LYS ALA SEQRES 1 B 195 ALA PHE GLU LEU PRO PRO LEU PRO TYR ALA HIS ASP ALA SEQRES 2 B 195 LEU GLN PRO HIS ILE SER LYS GLU THR LEU GLU TYR HIS SEQRES 3 B 195 HIS ASP LYS HIS HIS ASN THR TYR VAL VAL ASN LEU ASN SEQRES 4 B 195 ASN LEU VAL PRO GLY THR PRO GLU PHE GLU GLY LYS THR SEQRES 5 B 195 LEU GLU GLU ILE VAL LYS SER SER SER GLY GLY ILE PHE SEQRES 6 B 195 ASN ASN ALA ALA GLN VAL TRP ASN HIS THR PHE TYR TRP SEQRES 7 B 195 ASN CYS LEU SER PRO ASP ALA GLY GLY GLN PRO THR GLY SEQRES 8 B 195 ALA LEU ALA ASP ALA ILE ASN ALA ALA PHE GLY SER PHE SEQRES 9 B 195 ASP LYS PHE LYS GLU GLU PHE THR LYS THR SER VAL GLY SEQRES 10 B 195 THR PHE GLY SER GLY TRP ALA TRP LEU VAL LYS ALA ASP SEQRES 11 B 195 GLY SER LEU ALA LEU CYS SER THR ILE GLY ALA GLY ALA SEQRES 12 B 195 PRO LEU THR SER GLY ASP THR PRO LEU LEU THR CYS ASP SEQRES 13 B 195 VAL TRP GLU HIS ALA TYR TYR ILE ASP TYR ARG ASN LEU SEQRES 14 B 195 ARG PRO LYS TYR VAL GLU ALA PHE TRP ASN LEU VAL ASN SEQRES 15 B 195 TRP ALA PHE VAL ALA GLU GLU GLY LYS THR PHE LYS ALA HET FE A 196 1 HET FE B 196 1 HETNAM FE FE (III) ION FORMUL 3 FE 2(FE 3+) FORMUL 5 HOH *180(H2 O) HELIX 1 AA LYS A 20 ASN A 40 1HIS 26 IS A LIGAND TO FE 21 HELIX 2 BA ILE A 64 ASN A 79 1HIS 74 IS A LIGAND TO FE 16 HELIX 3 CA GLY A 91 PHE A 101 1 11 HELIX 4 DA SER A 103 THR A 112 1 10 HELIX 5 EA ARG A 167 ASN A 179 1 13 HELIX 6 FA TRP A 183 GLY A 190 1 8 HELIX 7 AB LYS B 20 ASN B 40 1HIS 26 IS A LIGAND TO FE 21 HELIX 8 BB ILE B 64 ASN B 79 1HIS 74 IS A LIGAND TO FE 16 HELIX 9 CB GLY B 91 PHE B 101 1 11 HELIX 10 DB SER B 103 THR B 112 1 10 HELIX 11 EB ARG B 167 ASN B 179 1 13 HELIX 12 FB TRP B 183 GLY B 190 1 8 SHEET 1 AA 3 SER A 132 ILE A 139 0 SHEET 2 AA 3 TRP A 123 ASP A 130 -1 N VAL A 127 O LEU A 133 SHEET 3 AA 3 ASP A 149 VAL A 157 -1 N THR A 150 O LYS A 128 SHEET 1 AB 3 SER B 132 ILE B 139 0 SHEET 2 AB 3 TRP B 123 ASP B 130 -1 N VAL B 127 O LEU B 133 SHEET 3 AB 3 ASP B 149 VAL B 157 -1 N THR B 150 O LYS B 128 LINK NE2 HIS A 26 FE FE A 196 1555 1555 2.57 LINK NE2 HIS A 74 FE FE A 196 1555 1555 2.29 LINK OD2 ASP A 156 FE FE A 196 1555 1555 2.37 LINK NE2 HIS A 160 FE FE A 196 1555 1555 2.39 LINK NE2 HIS B 26 FE FE B 196 1555 1555 2.58 LINK NE2 HIS B 74 FE FE B 196 1555 1555 2.30 LINK OD2 ASP B 156 FE FE B 196 1555 1555 2.25 LINK NE2 HIS B 160 FE FE B 196 1555 1555 2.58 SITE 1 FEA 5 HIS A 26 HIS A 74 ASP A 156 HIS A 160 SITE 2 FEA 5 FE A 196 SITE 1 FEB 5 HIS B 26 HIS B 74 ASP B 156 HIS B 160 SITE 2 FEB 5 FE B 196 SITE 1 AC1 4 HIS A 26 HIS A 74 ASP A 156 HIS A 160 SITE 1 AC2 4 HIS B 26 HIS B 74 ASP B 156 HIS B 160 CRYST1 81.900 49.100 61.700 90.00 106.80 90.00 P 1 21 1 4 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 0.012210 0.000000 0.003686 0.00000 SCALE2 0.000000 0.020367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016930 0.00000