HEADER OXIDOREDUCTASE 13-JUL-09 3I9U TITLE CRYSTAL STRUCTURE OF THE RAT HEME OXYGENASE (HO-1) IN COMPLEX WITH TITLE 2 HEME BINDING DITHIOERYTHRITOL (DTE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEME OXYGENASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-261; COMPND 5 SYNONYM: HO-1, HSP32; COMPND 6 EC: 1.14.99.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: HMOX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMW KEYWDS HEME OXYGENASE, INHIBITOR, ISOZYME, OXIDOREDUCTASE, ENDOPLASMIC KEYWDS 2 RETICULUM, HEME, IRON, METAL-BINDING, MICROSOME, PHOSPHOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.MATSUI,M.UNNO,M.IKEDA-SAITO REVDAT 2 01-NOV-23 3I9U 1 REMARK SEQADV REVDAT 1 19-MAY-10 3I9U 0 JRNL AUTH T.MATSUI,M.IWASAKI,R.SUGIYAMA,M.UNNO,M.IKEDA-SAITO JRNL TITL DIOXYGEN ACTIVATION FOR THE SELF-DEGRADATION OF HEME: JRNL TITL 2 REACTION MECHANISM AND REGULATION OF HEME OXYGENASE. JRNL REF INORG.CHEM. V. 49 3602 2010 JRNL REFN ISSN 0020-1669 JRNL PMID 20380462 JRNL DOI 10.1021/IC901869T REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 14140 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 754 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1017 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1711 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 101 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.76000 REMARK 3 B22 (A**2) : 1.76000 REMARK 3 B33 (A**2) : -2.63000 REMARK 3 B12 (A**2) : 0.88000 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): 0.202 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.185 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.121 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.826 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1812 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2468 ; 1.913 ; 2.034 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 211 ; 5.673 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 87 ;37.719 ;23.793 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 297 ;16.255 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;15.260 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 258 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1394 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1060 ; 1.060 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1701 ; 1.912 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 752 ; 3.170 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 767 ; 5.026 ; 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 : 3 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 11 A 222 REMARK 3 ORIGIN FOR THE GROUP (A): -7.2903 -36.0557-164.0508 REMARK 3 T TENSOR REMARK 3 T11: 0.0039 T22: 0.0368 REMARK 3 T33: 0.0073 T12: 0.0046 REMARK 3 T13: 0.0000 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.1533 L22: 0.3967 REMARK 3 L33: 1.2768 L12: -0.1731 REMARK 3 L13: -0.1906 L23: 0.3535 REMARK 3 S TENSOR REMARK 3 S11: -0.0089 S12: -0.0190 S13: 0.0173 REMARK 3 S21: 0.0023 S22: 0.0026 S23: -0.0079 REMARK 3 S31: 0.0551 S32: -0.0036 S33: 0.0063 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 300 A 300 REMARK 3 ORIGIN FOR THE GROUP (A): -2.2020 -27.3906-168.0463 REMARK 3 T TENSOR REMARK 3 T11: 0.0297 T22: 0.0517 REMARK 3 T33: 0.0526 T12: 0.0021 REMARK 3 T13: -0.0283 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 3.0471 L22: 3.7442 REMARK 3 L33: 2.6891 L12: 0.0059 REMARK 3 L13: -0.0667 L23: 1.5219 REMARK 3 S TENSOR REMARK 3 S11: -0.1336 S12: 0.2367 S13: 0.0109 REMARK 3 S21: 0.0446 S22: 0.0446 S23: -0.3173 REMARK 3 S31: -0.1965 S32: -0.1305 S33: 0.0889 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 : A 2001 A 2001 REMARK 3 ORIGIN FOR THE GROUP (A): -3.2904 -33.0346-168.9029 REMARK 3 T TENSOR REMARK 3 T11: 0.0215 T22: 0.0753 REMARK 3 T33: 0.1052 T12: -0.0370 REMARK 3 T13: -0.0209 T23: 0.0186 REMARK 3 L TENSOR REMARK 3 L11: 2.6720 L22: 8.2743 REMARK 3 L33: 20.5210 L12: 4.7020 REMARK 3 L13: -7.4048 L23: -13.0305 REMARK 3 S TENSOR REMARK 3 S11: -0.0861 S12: 0.2748 S13: 0.1445 REMARK 3 S21: -0.1558 S22: 0.4859 S23: 0.2564 REMARK 3 S31: 0.2428 S32: -0.7579 S33: -0.3998 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 3I9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054145. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14964 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 32.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.32900 REMARK 200 FOR SHELL : 7.040 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: PDB ENTRY 3I9T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2M SODIUM FORMATE, 10MM SODIUM REMARK 280 AZIDE, 5MM DTV, PH7.4, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 80.16267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 40.08133 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 40.08133 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 80.16267 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLU A 2 REMARK 465 ARG A 3 REMARK 465 PRO A 4 REMARK 465 GLN A 5 REMARK 465 LEU A 6 REMARK 465 ASP A 7 REMARK 465 SER A 8 REMARK 465 MET A 9 REMARK 465 SER A 10 REMARK 465 GLU A 223 REMARK 465 GLU A 224 REMARK 465 HIS A 225 REMARK 465 LYS A 226 REMARK 465 ASP A 227 REMARK 465 GLN A 228 REMARK 465 SER A 229 REMARK 465 PRO A 230 REMARK 465 SER A 231 REMARK 465 GLN A 232 REMARK 465 THR A 233 REMARK 465 GLU A 234 REMARK 465 PHE A 235 REMARK 465 LEU A 236 REMARK 465 ARG A 237 REMARK 465 GLN A 238 REMARK 465 ARG A 239 REMARK 465 PRO A 240 REMARK 465 ALA A 241 REMARK 465 SER A 242 REMARK 465 LEU A 243 REMARK 465 VAL A 244 REMARK 465 GLN A 245 REMARK 465 ASP A 246 REMARK 465 THR A 247 REMARK 465 THR A 248 REMARK 465 SER A 249 REMARK 465 ALA A 250 REMARK 465 GLU A 251 REMARK 465 THR A 252 REMARK 465 PRO A 253 REMARK 465 ARG A 254 REMARK 465 GLY A 255 REMARK 465 LYS A 256 REMARK 465 SER A 257 REMARK 465 GLN A 258 REMARK 465 ILE A 259 REMARK 465 SER A 260 REMARK 465 THR A 261 REMARK 465 ARG A 262 REMARK 465 LEU A 263 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 11 CG CD OE1 NE2 REMARK 470 GLN A 91 CG CD OE1 NE2 REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 LYS A 177 CG CD CE NZ 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 OH TYR A 74 O HOH A 352 2.06 REMARK 500 O HOH A 314 O HOH A 317 2.19 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 35 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 185 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 198 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 198 NE - CZ - NH2 ANGL. DEV. = -3.9 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 TYR A 74 -31.55 -130.94 REMARK 500 SER A 142 -103.73 -119.89 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 25 NE2 REMARK 620 2 HEM A 300 NA 89.3 REMARK 620 3 HEM A 300 NB 87.3 90.4 REMARK 620 4 HEM A 300 NC 90.8 175.9 85.5 REMARK 620 5 HEM A 300 ND 93.5 89.0 179.0 95.0 REMARK 620 6 DTU A2001 S1 178.7 90.9 91.4 88.9 87.8 REMARK 620 N 1 2 3 4 5 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 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTU A 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I9T RELATED DB: PDB REMARK 900 SAME PROTEIN WITH SIMILAR LIGAND DBREF 3I9U A 1 261 UNP P06762 HMOX1_RAT 1 261 SEQADV 3I9U ARG A 262 UNP P06762 EXPRESSION TAG SEQADV 3I9U LEU A 263 UNP P06762 EXPRESSION TAG SEQRES 1 A 263 MET GLU ARG PRO GLN LEU ASP SER MET SER GLN ASP LEU SEQRES 2 A 263 SER GLU ALA LEU LYS GLU ALA THR LYS GLU VAL HIS ILE SEQRES 3 A 263 ARG ALA GLU ASN SER GLU PHE MET ARG ASN PHE GLN LYS SEQRES 4 A 263 GLY GLN VAL SER ARG GLU GLY PHE LYS LEU VAL MET ALA SEQRES 5 A 263 SER LEU TYR HIS ILE TYR THR ALA LEU GLU GLU GLU ILE SEQRES 6 A 263 GLU ARG ASN LYS GLN ASN PRO VAL TYR ALA PRO LEU TYR SEQRES 7 A 263 PHE PRO GLU GLU LEU HIS ARG ARG ALA ALA LEU GLU GLN SEQRES 8 A 263 ASP MET ALA PHE TRP TYR GLY PRO HIS TRP GLN GLU ALA SEQRES 9 A 263 ILE PRO TYR THR PRO ALA THR GLN HIS TYR VAL LYS ARG SEQRES 10 A 263 LEU HIS GLU VAL GLY GLY THR HIS PRO GLU LEU LEU VAL SEQRES 11 A 263 ALA HIS ALA TYR THR ARG TYR LEU GLY ASP LEU SER GLY SEQRES 12 A 263 GLY GLN VAL LEU LYS LYS ILE ALA GLN LYS ALA MET ALA SEQRES 13 A 263 LEU PRO SER SER GLY GLU GLY LEU ALA PHE PHE THR PHE SEQRES 14 A 263 PRO SER ILE ASP ASN PRO THR LYS PHE LYS GLN LEU TYR SEQRES 15 A 263 ARG ALA ARG MET ASN THR LEU GLU MET THR PRO GLU VAL SEQRES 16 A 263 LYS HIS ARG VAL THR GLU GLU ALA LYS THR ALA PHE LEU SEQRES 17 A 263 LEU ASN ILE GLU LEU PHE GLU GLU LEU GLN ALA LEU LEU SEQRES 18 A 263 THR GLU GLU HIS LYS ASP GLN SER PRO SER GLN THR GLU SEQRES 19 A 263 PHE LEU ARG GLN ARG PRO ALA SER LEU VAL GLN ASP THR SEQRES 20 A 263 THR SER ALA GLU THR PRO ARG GLY LYS SER GLN ILE SER SEQRES 21 A 263 THR ARG LEU HET HEM A 300 43 HET DTU A2001 8 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM DTU (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 DTU C4 H10 O2 S2 FORMUL 4 HOH *101(H2 O) HELIX 1 1 ASP A 12 ASN A 30 1 19 HELIX 2 2 SER A 31 LYS A 39 1 9 HELIX 3 3 SER A 43 ASN A 68 1 26 HELIX 4 4 TYR A 74 TYR A 78 5 5 HELIX 5 5 PHE A 79 HIS A 84 1 6 HELIX 6 6 ARG A 85 GLY A 98 1 14 HELIX 7 7 HIS A 100 ILE A 105 1 6 HELIX 8 8 THR A 108 HIS A 125 1 18 HELIX 9 9 LEU A 128 LEU A 141 1 14 HELIX 10 10 SER A 142 ALA A 156 1 15 HELIX 11 11 LEU A 164 THR A 168 5 5 HELIX 12 12 ASN A 174 ASN A 187 1 14 HELIX 13 13 THR A 192 THR A 222 1 31 LINK NE2 HIS A 25 FE HEM A 300 1555 1555 2.06 LINK FE HEM A 300 S1 DTU A2001 1555 1555 2.23 SITE 1 AC1 17 LYS A 18 HIS A 25 GLU A 29 MET A 34 SITE 2 AC1 17 GLN A 38 TYR A 134 THR A 135 GLY A 139 SITE 3 AC1 17 SER A 142 GLY A 143 ARG A 183 PHE A 207 SITE 4 AC1 17 ASN A 210 PHE A 214 HOH A 287 HOH A 354 SITE 5 AC1 17 DTU A2001 SITE 1 AC2 10 ARG A 136 GLY A 139 ASP A 140 GLY A 143 SITE 2 AC2 10 GLY A 144 LEU A 147 HOH A 267 HOH A 268 SITE 3 AC2 10 HEM A 300 HOH A 365 CRYST1 65.882 65.882 120.244 90.00 90.00 120.00 P 32 2 1 6 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 0.015179 0.008763 0.000000 0.00000 SCALE2 0.000000 0.017527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008316 0.00000