PDB Short entry for 1P3T HEADER OXIDOREDUCTASE 18-APR-03 1P3T TITLE CRYSTAL STRUCTURES OF THE NO-AND CO-BOUND HEME OXYGENASE FROM TITLE 2 NEISSERIA MENINGITIDIS: IMPLICATIONS FOR OXYGEN ACTIVATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEME OXYGENASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HO-1; HEME OXYGENASE (DECYCLIZING) 1; COMPND 5 EC: 1.14.99.3; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: HEME-COMPLEXED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 487; SOURCE 4 GENE: HEMO; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PWMZ1651 KEYWDS HEME OXYGENASE, HEME DEGRADATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.FRIEDMAN,L.LAD,R.DESHMUKH,H.LI,A.WILKS,T.L.POULOS REVDAT 3 16-AUG-23 1P3T 1 REMARK REVDAT 2 24-FEB-09 1P3T 1 VERSN REVDAT 1 09-DEC-03 1P3T 0 JRNL AUTH J.FRIEDMAN,L.LAD,R.DESHMUKH,H.LI,A.WILKS,T.L.POULOS JRNL TITL CRYSTAL STRUCTURES OF THE NO- AND CO-BOUND HEME OXYGENASE JRNL TITL 2 FROM NEISSERIAE MENINGITIDIS. IMPLICATIONS FOR O2 ACTIVATION JRNL REF J.BIOL.CHEM. V. 278 34654 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12819228 JRNL DOI 10.1074/JBC.M302985200 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 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) (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 12602 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 SET) : 0.254 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 609 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 : 1578 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.44 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.370 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1P3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000018972. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 119 REMARK 200 PH : 8.5 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) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12602 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : 0.06700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 38.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.67 REMARK 200 R MERGE FOR SHELL (I) : 0.61100 REMARK 200 R SYM FOR SHELL (I) : 0.55500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.370 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1J77 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, SODIUM ACETATE, PEG 3350, PH REMARK 280 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 51.07100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.62250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.62250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 76.60650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.62250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.62250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.53550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.62250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.62250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 76.60650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.62250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.62250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.53550 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.07100 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A 1 REMARK 465 SER A 2 REMARK 465 GLU A 3 REMARK 465 THR A 4 REMARK 465 GLU A 5 REMARK 465 ASN A 6 REMARK 465 GLN A 7 REMARK 465 HIS A 207 REMARK 465 ARG A 208 REMARK 465 HIS A 209 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 GLU A 71 15.45 58.07 REMARK 500 LYS A 97 -164.96 -68.89 REMARK 500 HIS A 137 114.15 -163.48 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 HEM A 300 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 23 NE2 REMARK 620 2 HEM A 300 NA 97.2 REMARK 620 3 HEM A 300 NB 107.5 88.9 REMARK 620 4 HEM A 300 NC 96.9 165.8 88.6 REMARK 620 5 HEM A 300 ND 86.8 89.3 165.7 89.6 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 HEM A 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OYK RELATED DB: PDB REMARK 900 RELATED ID: 1OYL RELATED DB: PDB REMARK 900 RELATED ID: 1OZE RELATED DB: PDB REMARK 900 RELATED ID: 1OZL RELATED DB: PDB REMARK 900 RELATED ID: 1OZR RELATED DB: PDB REMARK 900 RELATED ID: 1OZW RELATED DB: PDB REMARK 900 RELATED ID: 1P3U RELATED DB: PDB REMARK 900 RELATED ID: 1P3V RELATED DB: PDB DBREF 1P3T A 1 209 UNP Q9RGD9 Q9RGD9_NEIME 22 230 SEQRES 1 A 209 MET SER GLU THR GLU ASN GLN ALA LEU THR PHE ALA LYS SEQRES 2 A 209 ARG LEU LYS ALA ASP THR THR ALA VAL HIS ASP SER VAL SEQRES 3 A 209 ASP ASN LEU VAL MET SER VAL GLN PRO PHE VAL SER LYS SEQRES 4 A 209 GLU ASN TYR ILE LYS PHE LEU LYS LEU GLN SER VAL PHE SEQRES 5 A 209 HIS LYS ALA VAL ASP HIS ILE TYR LYS ASP ALA GLU LEU SEQRES 6 A 209 ASN LYS ALA ILE PRO GLU LEU GLU TYR MET ALA ARG TYR SEQRES 7 A 209 ASP ALA VAL THR GLN ASP LEU LYS ASP LEU GLY GLU GLU SEQRES 8 A 209 PRO TYR LYS PHE ASP LYS GLU LEU PRO TYR GLU ALA GLY SEQRES 9 A 209 ASN LYS ALA ILE GLY TRP LEU TYR CYS ALA GLU GLY SER SEQRES 10 A 209 ASN LEU GLY ALA ALA PHE LEU PHE LYS HIS ALA GLN LYS SEQRES 11 A 209 LEU ASP TYR ASN GLY GLU HIS GLY ALA ARG HIS LEU ALA SEQRES 12 A 209 PRO HIS PRO ASP GLY ARG GLY LYS HIS TRP ARG ALA PHE SEQRES 13 A 209 VAL GLU HIS LEU ASN ALA LEU ASN LEU THR PRO GLU ALA SEQRES 14 A 209 GLU ALA GLU ALA ILE GLN GLY ALA ARG GLU ALA PHE ALA SEQRES 15 A 209 PHE TYR LYS VAL VAL LEU ARG GLU THR PHE GLY LEU ALA SEQRES 16 A 209 ALA ASP ALA GLU ALA PRO GLU GLY MET MET PRO HIS ARG SEQRES 17 A 209 HIS HET HEM A 300 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *62(H2 O) HELIX 1 1 THR A 10 VAL A 33 1 24 HELIX 2 2 SER A 38 VAL A 56 1 19 HELIX 3 3 VAL A 56 LYS A 61 1 6 HELIX 4 4 GLU A 64 ILE A 69 1 6 HELIX 5 5 GLU A 71 ALA A 76 5 6 HELIX 6 6 ARG A 77 LEU A 88 1 12 HELIX 7 7 ALA A 103 GLY A 120 1 18 HELIX 8 8 GLY A 120 GLN A 129 1 10 HELIX 9 9 LYS A 130 ASP A 132 5 3 HELIX 10 10 ALA A 139 ALA A 143 5 5 HELIX 11 11 GLY A 148 LEU A 163 1 16 HELIX 12 12 THR A 166 PHE A 192 1 27 LINK NE2 HIS A 23 FE HEM A 300 1555 1555 2.12 SITE 1 AC1 16 LYS A 16 HIS A 23 ASP A 27 MET A 31 SITE 2 AC1 16 TYR A 112 CYS A 113 GLY A 116 SER A 117 SITE 3 AC1 16 LEU A 119 GLY A 120 PHE A 123 LEU A 124 SITE 4 AC1 16 PHE A 181 TYR A 184 HOH A 332 HOH A 355 CRYST1 63.245 63.245 102.142 90.00 90.00 90.00 P 43 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 0.015812 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015812 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009790 0.00000