HEADER OXIDOREDUCTASE 14-AUG-08 3E5K TITLE CRYSTAL STRUCTURE OF CYP105P1 WILD-TYPE 4-PHENYLIMIDAZOLE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 (CYTOCHROME P450 HYDROXYLASE); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYP105P1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES AVERMITILIS; SOURCE 3 ORGANISM_TAXID: 33903; SOURCE 4 STRAIN: MA-4680; SOURCE 5 GENE: PTEC, SAV413, SAV_413; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 CODONPLUS (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-17B KEYWDS P450, OXIDOREDUCTASE, HEME, IRON, METAL-BINDING, MONOOXYGENASE EXPDTA X-RAY DIFFRACTION AUTHOR L.H.XU,S.FUSHINOBU,H.IKEDA,T.WAKAGI,H.SHOUN REVDAT 5 01-NOV-23 3E5K 1 REMARK REVDAT 4 10-NOV-21 3E5K 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3E5K 1 VERSN REVDAT 2 10-FEB-09 3E5K 1 JRNL REVDAT 1 30-DEC-08 3E5K 0 JRNL AUTH L.H.XU,S.FUSHINOBU,H.IKEDA,T.WAKAGI,H.SHOUN JRNL TITL CRYSTAL STRUCTURES OF CYTOCHROME P450 105P1 FROM JRNL TITL 2 STREPTOMYCES AVERMITILIS: CONFORMATIONAL FLEXIBILITY AND JRNL TITL 3 HISTIDINE LIGATION STATE JRNL REF J.BACTERIOL. V. 191 1211 2009 JRNL REFN ISSN 0021-9193 JRNL PMID 19074393 JRNL DOI 10.1128/JB.01276-08 REMARK 2 REMARK 2 RESOLUTION. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 24928 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1331 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1834 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2967 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 127 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 58.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : -0.02000 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): 0.235 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.145 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.518 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3091 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4212 ; 3.549 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 380 ; 9.383 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 144 ;35.410 ;22.986 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 492 ;23.156 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;26.239 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 467 ; 0.231 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2389 ; 0.016 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1561 ; 0.286 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2158 ; 0.357 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 193 ; 0.172 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.087 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 23 ; 0.275 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.257 ; 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): 1937 ; 2.126 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3064 ; 3.467 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1256 ; 5.716 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1147 ; 8.320 ; 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 9 A 158 REMARK 3 ORIGIN FOR THE GROUP (A): -56.6367 54.6486 -23.8976 REMARK 3 T TENSOR REMARK 3 T11: 0.0771 T22: 0.0809 REMARK 3 T33: 0.0865 T12: -0.0490 REMARK 3 T13: 0.0184 T23: 0.0080 REMARK 3 L TENSOR REMARK 3 L11: 1.5631 L22: 0.6062 REMARK 3 L33: 1.0158 L12: -0.2946 REMARK 3 L13: -0.3009 L23: 0.0235 REMARK 3 S TENSOR REMARK 3 S11: 0.0281 S12: 0.1784 S13: 0.2757 REMARK 3 S21: -0.0656 S22: 0.0092 S23: -0.0432 REMARK 3 S31: -0.3461 S32: 0.0724 S33: -0.0373 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 159 A 236 REMARK 3 ORIGIN FOR THE GROUP (A): -38.2607 49.2995 -24.3100 REMARK 3 T TENSOR REMARK 3 T11: -0.0004 T22: 0.1936 REMARK 3 T33: 0.1105 T12: -0.0866 REMARK 3 T13: 0.0228 T23: 0.0114 REMARK 3 L TENSOR REMARK 3 L11: 3.6814 L22: 2.4797 REMARK 3 L33: 3.5654 L12: 0.8278 REMARK 3 L13: -0.0897 L23: 0.1990 REMARK 3 S TENSOR REMARK 3 S11: 0.1147 S12: -0.0776 S13: 0.0546 REMARK 3 S21: 0.1420 S22: -0.0300 S23: -0.1707 REMARK 3 S31: -0.1038 S32: 0.1452 S33: -0.0847 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 237 A 401 REMARK 3 ORIGIN FOR THE GROUP (A): -64.4425 51.9334 -17.9982 REMARK 3 T TENSOR REMARK 3 T11: 0.0920 T22: 0.0657 REMARK 3 T33: 0.0972 T12: -0.0219 REMARK 3 T13: 0.0141 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 1.5812 L22: 1.1343 REMARK 3 L33: 2.0414 L12: -0.1298 REMARK 3 L13: -0.1284 L23: -0.3197 REMARK 3 S TENSOR REMARK 3 S11: 0.0220 S12: 0.1139 S13: 0.2642 REMARK 3 S21: -0.0179 S22: -0.0196 S23: -0.0994 REMARK 3 S31: -0.3351 S32: 0.1169 S33: -0.0025 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 3E5K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048902. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26300 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 38.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.42900 REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3E5J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.8M SODIUM FORMATE, PH8.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 23.64767 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 47.29533 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 47.29533 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 23.64767 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.5 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -47.29533 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 PRO A 2 REMARK 465 GLU A 3 REMARK 465 PRO A 4 REMARK 465 THR A 5 REMARK 465 ALA A 6 REMARK 465 ASP A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 70 REMARK 465 LEU A 71 REMARK 465 HIS A 72 REMARK 465 THR A 73 REMARK 465 GLN A 74 REMARK 465 ASP A 75 REMARK 465 GLY A 76 REMARK 465 VAL A 77 REMARK 465 VAL A 78 REMARK 465 THR A 79 REMARK 465 GLN A 80 REMARK 465 HIS A 402 REMARK 465 HIS A 403 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 OE1 GLU A 289 NE2 GLN A 308 2.08 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 15 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 15 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG A 29 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 55 NH1 - CZ - NH2 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 55 NE - CZ - NH1 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP A 60 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 PRO A 68 N - CA - C ANGL. DEV. = 17.3 DEGREES REMARK 500 ARG A 84 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 GLU A 94 OE1 - CD - OE2 ANGL. DEV. = 11.1 DEGREES REMARK 500 ASP A 98 CB - CG - OD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 99 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 LEU A 102 CB - CG - CD2 ANGL. DEV. = 10.5 DEGREES REMARK 500 ARG A 109 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 115 NE - CZ - NH1 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 115 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 120 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 120 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 ASP A 127 CB - CG - OD2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ARG A 161 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 200 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 CYS A 244 CA - CB - SG ANGL. DEV. = -12.0 DEGREES REMARK 500 MET A 245 CG - SD - CE ANGL. DEV. = -18.2 DEGREES REMARK 500 LEU A 252 CB - CG - CD2 ANGL. DEV. = 19.2 DEGREES REMARK 500 LEU A 262 CB - CG - CD1 ANGL. DEV. = 15.6 DEGREES REMARK 500 ARG A 264 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 GLU A 265 OE1 - CD - OE2 ANGL. DEV. = 12.7 DEGREES REMARK 500 GLU A 265 CG - CD - OE1 ANGL. DEV. = -17.3 DEGREES REMARK 500 VAL A 270 CG1 - CB - CG2 ANGL. DEV. = -15.3 DEGREES REMARK 500 ARG A 290 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 LEU A 314 CB - CG - CD2 ANGL. DEV. = 11.6 DEGREES REMARK 500 ASP A 330 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 330 CB - CG - OD2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ARG A 333 CG - CD - NE ANGL. DEV. = -12.6 DEGREES REMARK 500 ARG A 333 NE - CZ - NH1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 333 NE - CZ - NH2 ANGL. DEV. = -9.4 DEGREES REMARK 500 ARG A 334 CB - CG - CD ANGL. DEV. = -16.3 DEGREES REMARK 500 LEU A 365 CB - CA - C ANGL. DEV. = -16.4 DEGREES REMARK 500 ARG A 367 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 368 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 368 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 VAL A 378 CB - CA - C ANGL. DEV. = -11.7 DEGREES REMARK 500 GLU A 379 OE1 - CD - OE2 ANGL. DEV. = -7.4 DEGREES REMARK 500 ARG A 384 NE - CZ - NH1 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 PHE A 39 -152.35 -92.31 REMARK 500 HIS A 43 125.44 57.89 REMARK 500 GLU A 44 77.79 170.59 REMARK 500 PRO A 82 -116.10 -3.24 REMARK 500 LEU A 87 -55.65 81.05 REMARK 500 ARG A 132 -14.71 -47.45 REMARK 500 PHE A 142 -57.89 -152.60 REMARK 500 ASP A 176 54.83 -105.09 REMARK 500 ALA A 180 -74.31 -34.08 REMARK 500 THR A 293 -16.99 57.99 REMARK 500 ARG A 294 166.90 132.06 REMARK 500 ILE A 331 2.07 -66.78 REMARK 500 ASP A 386 -164.72 -103.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS A 43 GLU A 44 -65.75 REMARK 500 ALA A 292 THR A 293 58.41 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 A1408 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 348 SG REMARK 620 2 HEM A1408 NA 100.4 REMARK 620 3 HEM A1408 NB 87.9 87.7 REMARK 620 4 HEM A1408 NC 79.2 176.6 88.9 REMARK 620 5 HEM A1408 ND 91.7 88.7 176.2 94.7 REMARK 620 6 PIM A 501 N3 172.4 87.2 92.0 93.2 88.8 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 1408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PIM A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3E5J RELATED DB: PDB REMARK 900 RELATED ID: 3E5L RELATED DB: PDB DBREF 3E5K A 1 399 UNP Q93H81 Q93H81_STRAW 1 399 SEQADV 3E5K ILE A 387 UNP Q93H81 MET 387 ENGINEERED MUTATION SEQADV 3E5K HIS A 400 UNP Q93H81 EXPRESSION TAG SEQADV 3E5K HIS A 401 UNP Q93H81 EXPRESSION TAG SEQADV 3E5K HIS A 402 UNP Q93H81 EXPRESSION TAG SEQADV 3E5K HIS A 403 UNP Q93H81 EXPRESSION TAG SEQRES 1 A 403 MET PRO GLU PRO THR ALA ASP ALA PRO THR VAL PRO LYS SEQRES 2 A 403 ALA ARG SER CYS PRO PHE LEU PRO PRO ASP GLY ILE ALA SEQRES 3 A 403 ASP ILE ARG ALA ALA ALA PRO VAL THR ARG ALA THR PHE SEQRES 4 A 403 THR SER GLY HIS GLU ALA TRP LEU VAL THR GLY TYR GLU SEQRES 5 A 403 GLU VAL ARG ALA LEU LEU ARG ASP SER SER PHE SER VAL SEQRES 6 A 403 GLN VAL PRO HIS ALA LEU HIS THR GLN ASP GLY VAL VAL SEQRES 7 A 403 THR GLN LYS PRO GLY ARG GLY SER LEU LEU TRP GLN ASP SEQRES 8 A 403 GLU PRO GLU HIS THR SER ASP ARG LYS LEU LEU ALA LYS SEQRES 9 A 403 GLU PHE THR VAL ARG ARG MET GLN ALA LEU ARG PRO ASN SEQRES 10 A 403 ILE GLN ARG ILE VAL ASP GLU HIS LEU ASP ALA ILE GLU SEQRES 11 A 403 ALA ARG GLY GLY PRO VAL ASP LEU VAL LYS THR PHE ALA SEQRES 12 A 403 ASN ALA VAL PRO SER MET VAL ILE SER ASP LEU PHE GLY SEQRES 13 A 403 VAL PRO VAL GLU ARG ARG ALA GLU PHE GLN ASP ILE ALA SEQRES 14 A 403 GLU ALA MET MET ARG VAL ASP GLN ASP ALA ALA ALA THR SEQRES 15 A 403 GLU ALA ALA GLY MET ARG LEU GLY GLY LEU LEU TYR GLN SEQRES 16 A 403 LEU VAL GLN GLU ARG ARG ALA ASN PRO GLY ASP ASP LEU SEQRES 17 A 403 ILE SER ALA LEU ILE THR THR GLU ASP PRO ASP GLY VAL SEQRES 18 A 403 VAL ASP ASP MET PHE LEU MET ASN ALA ALA GLY THR LEU SEQRES 19 A 403 LEU ILE ALA ALA HIS ASP THR THR ALA CYS MET ILE GLY SEQRES 20 A 403 LEU GLY THR ALA LEU LEU LEU ASP SER PRO ASP GLN LEU SEQRES 21 A 403 ALA LEU LEU ARG GLU ASP PRO SER LEU VAL GLY ASN ALA SEQRES 22 A 403 VAL GLU GLU LEU LEU ARG TYR LEU THR ILE GLY GLN PHE SEQRES 23 A 403 GLY GLY GLU ARG VAL ALA THR ARG ASP VAL GLU LEU GLY SEQRES 24 A 403 GLY VAL ARG ILE ALA LYS GLY GLU GLN VAL VAL ALA HIS SEQRES 25 A 403 VAL LEU ALA ALA ASP PHE ASP PRO ALA PHE VAL GLU GLU SEQRES 26 A 403 PRO GLU ARG PHE ASP ILE THR ARG ARG PRO ALA PRO HIS SEQRES 27 A 403 LEU ALA PHE GLY PHE GLY ALA HIS GLN CYS ILE GLY GLN SEQRES 28 A 403 GLN LEU ALA ARG ILE GLU LEU GLN ILE VAL PHE GLU THR SEQRES 29 A 403 LEU PHE ARG ARG LEU PRO GLY LEU ARG LEU ALA LYS PRO SEQRES 30 A 403 VAL GLU GLU LEU ARG PHE ARG HIS ASP ILE VAL PHE TYR SEQRES 31 A 403 GLY VAL HIS GLU LEU PRO VAL THR TRP HIS HIS HIS HIS HET HEM A1408 43 HET PIM A 501 11 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM PIM 4-PHENYL-1H-IMIDAZOLE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 PIM C9 H8 N2 FORMUL 4 HOH *127(H2 O) HELIX 1 1 GLY A 24 ALA A 32 1 9 HELIX 2 2 GLY A 50 ASP A 60 1 11 HELIX 3 3 PRO A 93 ALA A 103 1 11 HELIX 4 4 THR A 107 LEU A 114 1 8 HELIX 5 5 LEU A 114 GLY A 133 1 20 HELIX 6 6 LEU A 138 PHE A 142 1 5 HELIX 7 7 ASN A 144 PHE A 155 1 12 HELIX 8 8 PRO A 158 GLU A 160 5 3 HELIX 9 9 ARG A 161 ARG A 174 1 14 HELIX 10 10 ASP A 178 ASN A 203 1 26 HELIX 11 11 ASP A 207 THR A 214 1 8 HELIX 12 12 ASP A 223 ASP A 240 1 18 HELIX 13 13 ASP A 240 LEU A 254 1 15 HELIX 14 14 SER A 256 ASP A 266 1 11 HELIX 15 15 LEU A 269 THR A 282 1 14 HELIX 16 16 HIS A 312 PHE A 318 1 7 HELIX 17 17 PHE A 343 GLN A 347 5 5 HELIX 18 18 GLY A 350 LEU A 369 1 20 HELIX 19 19 PRO A 377 LEU A 381 5 5 SHEET 1 A 5 VAL A 34 THR A 38 0 SHEET 2 A 5 GLU A 44 VAL A 48 -1 O LEU A 47 N THR A 35 SHEET 3 A 5 GLN A 308 ALA A 311 1 O VAL A 310 N VAL A 48 SHEET 4 A 5 GLU A 289 ALA A 292 -1 N ARG A 290 O VAL A 309 SHEET 5 A 5 PHE A 63 GLN A 66 -1 N SER A 64 O VAL A 291 SHEET 1 B 3 VAL A 136 ASP A 137 0 SHEET 2 B 3 PRO A 396 THR A 398 -1 O VAL A 397 N VAL A 136 SHEET 3 B 3 ARG A 373 LEU A 374 -1 N ARG A 373 O THR A 398 SHEET 1 C 2 VAL A 296 LEU A 298 0 SHEET 2 C 2 VAL A 301 ILE A 303 -1 O ILE A 303 N VAL A 296 SHEET 1 D 2 PHE A 383 HIS A 385 0 SHEET 2 D 2 TYR A 390 VAL A 392 -1 O GLY A 391 N ARG A 384 LINK SG CYS A 348 FE HEM A1408 1555 1555 2.20 LINK N3 PIM A 501 FE HEM A1408 1555 1555 1.91 CISPEP 1 GLY A 42 HIS A 43 0 2.43 CISPEP 2 PRO A 82 GLY A 83 0 -16.00 CISPEP 3 GLU A 92 PRO A 93 0 17.78 CISPEP 4 GLY A 134 PRO A 135 0 -4.99 CISPEP 5 LYS A 305 GLY A 306 0 -9.18 SITE 1 AC1 20 LEU A 87 LEU A 88 HIS A 95 ARG A 99 SITE 2 AC1 20 ALA A 237 THR A 241 THR A 242 THR A 282 SITE 3 AC1 20 PHE A 286 GLY A 287 GLY A 288 ARG A 290 SITE 4 AC1 20 ALA A 340 PHE A 341 GLY A 342 HIS A 346 SITE 5 AC1 20 CYS A 348 GLY A 350 ALA A 354 HOH A1411 SITE 1 AC2 3 LEU A 88 THR A 241 PHE A 286 CRYST1 143.725 143.725 70.943 90.00 90.00 120.00 P 31 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 0.006958 0.004017 0.000000 0.00000 SCALE2 0.000000 0.008034 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014096 0.00000