HEADER OXIDOREDUCTASE 19-DEC-99 1DO6 TITLE CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE IN THE OXIDIZED STATE AT 2.0 TITLE 2 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SOR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NON-HEME IRON PROTEIN, IMMUNOGLOBULIN-LIKE (IG) BETA BARREL FOLD, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.P.YEH,Y.HU,F.E.JENNEY JUNIOR,M.W.ADAMS,D.C.REES REVDAT 6 07-FEB-24 1DO6 1 REMARK LINK REVDAT 5 04-OCT-17 1DO6 1 REMARK REVDAT 4 13-JUL-11 1DO6 1 VERSN REVDAT 3 24-FEB-09 1DO6 1 VERSN REVDAT 2 01-APR-03 1DO6 1 JRNL REVDAT 1 24-MAR-00 1DO6 0 JRNL AUTH A.P.YEH,Y.HU,F.E.JENNEY JR.,M.W.ADAMS,D.C.REES JRNL TITL STRUCTURES OF THE SUPEROXIDE REDUCTASE FROM PYROCOCCUS JRNL TITL 2 FURIOSUS IN THE OXIDIZED AND REDUCED STATES. JRNL REF BIOCHEMISTRY V. 39 2499 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10704199 JRNL DOI 10.1021/BI992428K REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.E.JENNEY JUNIOR,M.F.VERHAGEN,X.CUI,M.W.ADAMS REMARK 1 TITL ANAEROBIC MICROBES: OXYGEN DETOXIFICATION WITHOUT SUPEROXIDE REMARK 1 TITL 2 DISMUTASE REMARK 1 REF SCIENCE V. 286 306 1999 REMARK 1 REFN ISSN 0036-8075 REMARK 1 DOI 10.1126/SCIENCE.286.5438.306 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 16334 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : 6.4% OF 16,334 REFLECTIONS REMARK 3 WERE RANDOMLY SELECTED FOR REMARK 3 THE TEST SET REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1038 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2028 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.20 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 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.490 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010242. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-97 REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 8.0 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XENTRONICS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16334 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.17800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, TRIS-HYDROCHLORIDE, PH 8.0, REMARK 280 GLYCEROL, SODIUM CHLORIDE, ETHANOL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 25.15500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.01000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.15500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.01000 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 12210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 50.31000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 94.02000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 B 267 LIES ON A SPECIAL POSITION. 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 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 14 OE2 REMARK 620 2 HIS A 16 NE2 85.1 REMARK 620 3 HIS A 41 NE2 79.9 96.2 REMARK 620 4 HIS A 47 NE2 87.5 170.4 88.5 REMARK 620 5 CYS A 111 SG 171.1 102.7 94.8 85.2 REMARK 620 6 HIS A 114 ND1 92.0 80.9 171.7 93.3 93.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 205 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 16 NE2 REMARK 620 2 HIS B 41 NE2 90.3 REMARK 620 3 HIS B 47 NE2 153.8 88.1 REMARK 620 4 CYS B 111 SG 115.0 99.5 90.9 REMARK 620 5 HIS B 114 ND1 81.5 162.4 92.5 98.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 205 DBREF 1DO6 A 1 124 UNP P82385 SOR_PYRFU 1 124 DBREF 1DO6 B 1 124 UNP P82385 SOR_PYRFU 1 124 SEQRES 1 A 124 MET ILE SER GLU THR ILE ARG SER GLY ASP TRP LYS GLY SEQRES 2 A 124 GLU LYS HIS VAL PRO VAL ILE GLU TYR GLU ARG GLU GLY SEQRES 3 A 124 GLU LEU VAL LYS VAL LYS VAL GLN VAL GLY LYS GLU ILE SEQRES 4 A 124 PRO HIS PRO ASN THR THR GLU HIS HIS ILE ARG TYR ILE SEQRES 5 A 124 GLU LEU TYR PHE LEU PRO GLU GLY GLU ASN PHE VAL TYR SEQRES 6 A 124 GLN VAL GLY ARG VAL GLU PHE THR ALA HIS GLY GLU SER SEQRES 7 A 124 VAL ASN GLY PRO ASN THR SER ASP VAL TYR THR GLU PRO SEQRES 8 A 124 ILE ALA TYR PHE VAL LEU LYS THR LYS LYS LYS GLY LYS SEQRES 9 A 124 LEU TYR ALA LEU SER TYR CYS ASN ILE HIS GLY LEU TRP SEQRES 10 A 124 GLU ASN GLU VAL THR LEU GLU SEQRES 1 B 124 MET ILE SER GLU THR ILE ARG SER GLY ASP TRP LYS GLY SEQRES 2 B 124 GLU LYS HIS VAL PRO VAL ILE GLU TYR GLU ARG GLU GLY SEQRES 3 B 124 GLU LEU VAL LYS VAL LYS VAL GLN VAL GLY LYS GLU ILE SEQRES 4 B 124 PRO HIS PRO ASN THR THR GLU HIS HIS ILE ARG TYR ILE SEQRES 5 B 124 GLU LEU TYR PHE LEU PRO GLU GLY GLU ASN PHE VAL TYR SEQRES 6 B 124 GLN VAL GLY ARG VAL GLU PHE THR ALA HIS GLY GLU SER SEQRES 7 B 124 VAL ASN GLY PRO ASN THR SER ASP VAL TYR THR GLU PRO SEQRES 8 B 124 ILE ALA TYR PHE VAL LEU LYS THR LYS LYS LYS GLY LYS SEQRES 9 B 124 LEU TYR ALA LEU SER TYR CYS ASN ILE HIS GLY LEU TRP SEQRES 10 B 124 GLU ASN GLU VAL THR LEU GLU HET FE A 200 1 HET FE B 205 1 HETNAM FE FE (III) ION FORMUL 3 FE 2(FE 3+) FORMUL 5 HOH *128(H2 O) HELIX 1 1 MET A 1 GLU A 4 5 4 HELIX 2 2 MET B 1 GLU B 4 5 4 SHEET 1 A 5 ILE A 6 ARG A 7 0 SHEET 2 A 5 GLY A 115 LEU A 123 1 O LEU A 116 N ARG A 7 SHEET 3 A 5 GLY A 103 CYS A 111 -1 O GLY A 103 N LEU A 123 SHEET 4 A 5 ILE A 49 PRO A 58 -1 N ARG A 50 O TYR A 110 SHEET 5 A 5 TYR A 65 GLU A 71 -1 O TYR A 65 N PHE A 56 SHEET 1 B 3 VAL A 19 GLU A 25 0 SHEET 2 B 3 LEU A 28 GLN A 34 -1 O LEU A 28 N GLU A 25 SHEET 3 B 3 ILE A 92 LYS A 98 -1 N ALA A 93 O VAL A 33 SHEET 1 C 5 ILE B 6 ARG B 7 0 SHEET 2 C 5 GLY B 115 LEU B 123 1 O LEU B 116 N ARG B 7 SHEET 3 C 5 GLY B 103 CYS B 111 -1 O GLY B 103 N LEU B 123 SHEET 4 C 5 ILE B 49 PRO B 58 -1 N ARG B 50 O TYR B 110 SHEET 5 C 5 TYR B 65 GLU B 71 -1 N TYR B 65 O PHE B 56 SHEET 1 D 3 VAL B 19 GLU B 25 0 SHEET 2 D 3 LEU B 28 GLN B 34 -1 O LEU B 28 N GLU B 25 SHEET 3 D 3 ILE B 92 LYS B 98 -1 N ALA B 93 O VAL B 33 LINK OE2 GLU A 14 FE FE A 200 1555 1555 2.01 LINK NE2 HIS A 16 FE FE A 200 1555 1555 2.14 LINK NE2 HIS A 41 FE FE A 200 1555 1555 2.15 LINK NE2 HIS A 47 FE FE A 200 1555 1555 2.20 LINK SG CYS A 111 FE FE A 200 1555 1555 2.42 LINK ND1 HIS A 114 FE FE A 200 1555 1555 2.09 LINK NE2 HIS B 16 FE FE B 205 1555 1555 2.15 LINK NE2 HIS B 41 FE FE B 205 1555 1555 2.21 LINK NE2 HIS B 47 FE FE B 205 1555 1555 2.20 LINK SG CYS B 111 FE FE B 205 1555 1555 2.34 LINK ND1 HIS B 114 FE FE B 205 1555 1555 2.05 SITE 1 AC1 6 GLU A 14 HIS A 16 HIS A 41 HIS A 47 SITE 2 AC1 6 CYS A 111 HIS A 114 SITE 1 AC2 6 LYS B 15 HIS B 16 HIS B 41 HIS B 47 SITE 2 AC2 6 CYS B 111 HIS B 114 CRYST1 50.310 94.020 52.900 90.00 90.00 90.00 P 21 21 2 8 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 0.019877 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010636 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018904 0.00000