PDB Short entry for 2WIY HEADER ELECTRON TRANSPORT 18-MAY-09 2WIY TITLE CYTOCHROME P450 XPLA HEME DOMAIN P21212 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450-LIKE PROTEIN XPLA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 159-552; COMPND 5 SYNONYM: XPLA-HEME; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOCOCCUS; SOURCE 3 ORGANISM_TAXID: 1827; SOURCE 4 STRAIN: 11Y; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-YSBLIC-3C; SOURCE 9 OTHER_DETAILS: ISOLATION BY SELECTIVE ENRICHMENT KEYWDS CYT-P450, HEME, RDX, BIOREMEDIATION, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR F.SABBADIN,R.JACKSON,N.C.BRUCE,G.GROGAN REVDAT 3 13-OCT-09 2WIY 1 JRNL REVDAT 2 01-SEP-09 2WIY 1 JRNL REVDAT 1 18-AUG-09 2WIY 0 JRNL AUTH F.SABBADIN,R.JACKSON,K.HAIDER,G.TAMPI, JRNL AUTH 2 J.P.TURKENBURG,S.HART,N.C.BRUCE,G.GROGAN JRNL TITL THE 1.5-A STRUCTURE OF XPLA-HEME, AN UNUSUAL JRNL TITL 2 CYTOCHROME P450 HEME DOMAIN THAT CATALYZES JRNL TITL 3 REDUCTIVE BIOTRANSFORMATION OF ROYAL DEMOLITION JRNL TITL 4 EXPLOSIVE. JRNL REF J.BIOL.CHEM. V. 284 28467 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19692330 JRNL DOI 10.1074/JBC.M109.031559 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0082 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 124.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 68213 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) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3634 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) : 1.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4663 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.1510 REMARK 3 BIN FREE R VALUE SET COUNT : 252 REMARK 3 BIN FREE R VALUE : 0.1860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3087 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 698 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 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): 0.060 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.064 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.034 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.854 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3239 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4422 ; 2.330 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 403 ; 5.789 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;31.543 ;23.158 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 494 ;10.946 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;18.818 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 479 ; 0.152 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2535 ; 0.015 ; 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): 1989 ; 1.230 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3211 ; 2.025 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1250 ; 3.487 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1206 ; 5.470 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2WIY COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAY-09. REMARK 100 THE PDBE ID CODE IS EBI-39853. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87260 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68213 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.49 REMARK 200 RESOLUTION RANGE LOW (A) : 124.03 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.4 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.1 REMARK 200 R MERGE FOR SHELL (I) : 0.19 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.00 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 2Z3T REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M BIS-TRIS PROPANE, PH 6.5; REMARK 280 0.2 M MAGNESIUM FORMATE, 20% W/V PEG 3350 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 62.14650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.33850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 62.14650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.33850 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 GENERATING THE BIOMOLECULE 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: PQS 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 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 ARG A 356 CG CD NE CZ NH1 NH2 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 NH1 ARG A 166 - O HOH A 2009 2.12 REMARK 500 NZ LYS A 254 - O HOH A 2208 1.96 REMARK 500 CD ARG A 486 - O HOH A 2605 2.04 REMARK 500 O HOH A 2139 - O HOH A 2484 2.10 REMARK 500 O HOH A 2239 - O HOH A 2358 2.09 REMARK 500 O HOH A 2264 - O HOH A 2271 2.09 REMARK 500 O HOH A 2312 - O HOH A 2496 2.11 REMARK 500 O HOH A 2348 - O HOH A 2556 2.08 REMARK 500 O HOH A 2444 - O HOH A 2446 2.19 REMARK 500 O HOH A 2448 - O HOH A 2450 2.01 REMARK 500 O HOH A 2519 - O HOH A 2597 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 REMARK 500 O HOH A 2091 O HOH A 2332 3556 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 302 CZ ARG A 302 NH1 0.108 REMARK 500 GLU A 320 CD GLU A 320 OE1 0.104 REMARK 500 PHE A 441 CE2 PHE A 441 CZ 0.116 REMARK 500 SER A 491 CA SER A 491 CB 0.118 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 ASP A 165 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 TYR A 184 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 TYR A 184 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 185 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 TYR A 201 CE1 - CZ - CE2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 205 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 205 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 LYS A 259 CD - CE - NZ ANGL. DEV. = 14.1 DEGREES REMARK 500 ARG A 266 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ASP A 274 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG A 288 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 288 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 288 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 302 NE - CZ - NH1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 302 NH1 - CZ - NH2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 309 CB - CG - OD1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ASP A 361 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 PHE A 388 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 PHE A 407 CB - CG - CD1 ANGL. DEV. = 5.2 DEGREES REMARK 500 PHE A 407 CB - CG - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 420 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 448 CB - CG - OD1 ANGL. DEV. = 8.5 DEGREES REMARK 500 ARG A 471 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ASP A 477 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 492 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 PHE A 517 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 GLU A 522 OE1 - CD - OE2 ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 523 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 523 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 526 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 526 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 542 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 543 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 543 NE - CZ - NH2 ANGL. DEV. = -4.7 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 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 HIS A 191 58.94 -141.03 REMARK 500 ASP A 361 44.28 -140.23 REMARK 500 MET A 394 -74.25 -84.92 REMARK 500 ALA A 536 55.44 -146.95 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 393 MET A 394 -148.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP A 198 24.5 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): 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 A1560 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 IMD A1553 N1 REMARK 620 2 HEM A1560 NC 85.0 REMARK 620 3 CYS A 503 SG 170.8 87.5 REMARK 620 4 HEM A1560 NA 89.1 174.1 98.4 REMARK 620 5 HEM A1560 NB 87.1 91.2 87.7 89.2 REMARK 620 6 HEM A1560 ND 88.4 89.5 96.9 89.6 175.4 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 IMD A1553 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1554 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1555 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1556 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1557 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1558 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A1559 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A1560 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WIV RELATED DB: PDB REMARK 900 CYTOCHROME-P450 XPLA HEME DOMAIN P212121 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SUBCLONED HEME DOMAIN - MET159 TO C TERMINUS DBREF 2WIY A 159 552 UNP Q8GPH7 Q8GPH7_RHORH 159 552 SEQRES 1 A 394 MET THR ALA ALA SER ILE ASP ARG GLU LEU VAL PRO TRP SEQRES 2 A 394 SER ASP PRO GLU PHE ARG ASN ASN PRO TYR PRO TRP TYR SEQRES 3 A 394 ARG ARG LEU GLN GLN ASP HIS PRO VAL HIS LYS LEU GLU SEQRES 4 A 394 ASP GLY THR TYR LEU VAL SER ARG TYR ALA ASP VAL SER SEQRES 5 A 394 HIS PHE ALA LYS LEU PRO ILE MET SER VAL GLU PRO GLY SEQRES 6 A 394 TRP ALA ASP ALA GLY PRO TRP ALA VAL ALA SER ASP THR SEQRES 7 A 394 ALA LEU GLY SER ASP PRO PRO HIS HIS THR VAL LEU ARG SEQRES 8 A 394 ARG GLN THR ASN LYS TRP PHE THR PRO LYS LEU VAL ASP SEQRES 9 A 394 GLY TRP VAL ARG THR THR ARG GLU LEU VAL GLY ASP LEU SEQRES 10 A 394 LEU ASP GLY VAL GLU ALA GLY GLN VAL ILE GLU ALA ARG SEQRES 11 A 394 ARG ASP LEU ALA VAL VAL PRO THR HIS VAL THR MET ALA SEQRES 12 A 394 ARG VAL LEU GLN LEU PRO GLU ASP ASP ALA ASP ALA VAL SEQRES 13 A 394 MET GLU ALA MET PHE GLU ALA MET LEU MET GLN SER ALA SEQRES 14 A 394 GLU PRO ALA ASP GLY ASP VAL ASP ARG ALA ALA VAL ALA SEQRES 15 A 394 PHE GLY TYR LEU SER ALA ARG VAL ALA GLU MET LEU GLU SEQRES 16 A 394 ASP LYS ARG VAL ASN PRO GLY ASP GLY LEU ALA ASP SER SEQRES 17 A 394 LEU LEU ASP ALA ALA ARG ALA GLY GLU ILE THR GLU SER SEQRES 18 A 394 GLU ALA ILE ALA THR ILE LEU VAL PHE TYR ALA VAL GLY SEQRES 19 A 394 HIS MET ALA ILE GLY TYR LEU ILE ALA SER GLY ILE GLU SEQRES 20 A 394 LEU PHE ALA ARG ARG PRO GLU VAL PHE THR ALA PHE ARG SEQRES 21 A 394 ASN ASP GLU SER ALA ARG ALA ALA ILE ILE ASN GLU MET SEQRES 22 A 394 VAL ARG MET ASP PRO PRO GLN LEU SER PHE LEU ARG PHE SEQRES 23 A 394 PRO THR GLU ASP VAL GLU ILE GLY GLY VAL LEU ILE GLU SEQRES 24 A 394 ALA GLY SER PRO ILE ARG PHE MET ILE GLY ALA ALA ASN SEQRES 25 A 394 ARG ASP PRO GLU VAL PHE ASP ASP PRO ASP VAL PHE ASP SEQRES 26 A 394 HIS THR ARG PRO PRO ALA ALA SER ARG ASN LEU SER PHE SEQRES 27 A 394 GLY LEU GLY PRO HIS SER CYS ALA GLY GLN ILE ILE SER SEQRES 28 A 394 ARG ALA GLU ALA THR THR VAL PHE ALA VAL LEU ALA GLU SEQRES 29 A 394 ARG TYR GLU ARG ILE GLU LEU ALA GLU GLU PRO THR VAL SEQRES 30 A 394 ALA HIS ASN ASP PHE ALA ARG ARG TYR ARG LYS LEU PRO SEQRES 31 A 394 ILE VAL LEU SER HET IMD A1553 5 HET EDO A1554 4 HET EDO A1555 4 HET EDO A1556 4 HET EDO A1557 4 HET EDO A1558 4 HET EDO A1559 4 HET HEM A1560 43 HETNAM EDO 1,2-ETHANEDIOL HETNAM IMD IMIDAZOLE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE FORMUL 2 EDO 6(C2 H6 O2) FORMUL 3 IMD C3 H5 N2 1+ FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 5 HOH *698(H2 O1) HELIX 1 1 THR A 160 VAL A 169 1 10 HELIX 2 2 ASP A 173 ASN A 179 1 7 HELIX 3 3 PRO A 180 HIS A 191 1 12 HELIX 4 4 ARG A 205 ALA A 213 1 9 HELIX 5 5 VAL A 220 ASP A 226 1 7 HELIX 6 6 ALA A 227 THR A 236 5 10 HELIX 7 7 THR A 236 SER A 240 5 5 HELIX 8 8 PRO A 243 LYS A 254 1 12 HELIX 9 9 THR A 257 VAL A 265 1 9 HELIX 10 10 VAL A 265 GLY A 278 1 14 HELIX 11 11 ALA A 287 ALA A 292 1 6 HELIX 12 12 ALA A 292 GLN A 305 1 14 HELIX 13 13 ASP A 310 LEU A 323 1 14 HELIX 14 14 MET A 324 SER A 326 5 3 HELIX 15 15 GLY A 332 ASN A 358 1 27 HELIX 16 16 GLY A 362 ALA A 373 1 12 HELIX 17 17 THR A 377 GLY A 392 1 16 HELIX 18 18 MET A 394 ARG A 410 1 17 HELIX 19 19 ARG A 410 ASP A 420 1 11 HELIX 20 20 ALA A 423 ASP A 435 1 13 HELIX 21 21 ILE A 466 ASN A 470 1 5 HELIX 22 22 PRO A 487 SER A 491 5 5 HELIX 23 23 LEU A 498 SER A 502 5 5 HELIX 24 24 GLY A 505 TYR A 524 1 20 SHEET 1 AA 5 VAL A 193 LYS A 195 0 SHEET 2 AA 5 TYR A 201 VAL A 203 -1 O LEU A 202 N HIS A 194 SHEET 3 AA 5 ILE A 462 MET A 465 1 O ARG A 463 N VAL A 203 SHEET 4 AA 5 SER A 440 PRO A 445 -1 O PHE A 441 N PHE A 464 SHEET 5 AA 5 MET A 218 SER A 219 -1 O SER A 219 N PHE A 444 SHEET 1 AB 3 ILE A 285 GLU A 286 0 SHEET 2 AB 3 PRO A 548 SER A 552 -1 O ILE A 549 N ILE A 285 SHEET 3 AB 3 ARG A 526 LEU A 529 -1 O ARG A 526 N SER A 552 SHEET 1 AC 2 VAL A 449 ILE A 451 0 SHEET 2 AC 2 VAL A 454 ILE A 456 -1 O VAL A 454 N ILE A 451 SHEET 1 AD 2 THR A 534 VAL A 535 0 SHEET 2 AD 2 TYR A 544 LYS A 546 -1 N ARG A 545 O THR A 534 LINK FE HEM A1560 N1 IMD A1553 1555 1555 2.16 LINK FE HEM A1560 SG CYS A 503 1555 1555 2.38 CISPEP 1 PRO A 242 PRO A 243 0 11.04 SITE 1 AC1 3 GLN A 438 HEM A1560 HOH A2538 SITE 1 AC2 10 TYR A 206 ARG A 266 GLU A 270 VAL A 475 SITE 2 AC2 10 ALA A 489 ALA A 490 SER A 491 ARG A 492 SITE 3 AC2 10 HOH A2689 HOH A2690 SITE 1 AC3 7 PHE A 256 CYS A 503 ALA A 504 GLN A 506 SITE 2 AC3 7 ILE A 507 HOH A2691 HOH A2692 SITE 1 AC4 5 PRO A 174 ASN A 178 VAL A 535 ALA A 536 SITE 2 AC4 5 HIS A 537 SITE 1 AC5 5 ALA A 207 ASP A 208 HIS A 211 LYS A 259 SITE 2 AC5 5 ASP A 262 SITE 1 AC6 5 GLY A 282 GLN A 283 VAL A 550 LEU A 551 SITE 2 AC6 5 HOH A2694 SITE 1 AC7 4 LYS A 254 TRP A 255 HOH A2695 HOH A2696 SITE 1 AC8 26 ALA A 237 LEU A 238 HIS A 245 ARG A 249 SITE 2 AC8 26 MET A 300 PHE A 388 ALA A 395 ILE A 396 SITE 3 AC8 26 PRO A 437 PHE A 441 ARG A 443 ILE A 466 SITE 4 AC8 26 SER A 495 PHE A 496 GLY A 497 PRO A 500 SITE 5 AC8 26 HIS A 501 CYS A 503 ALA A 504 ILE A 508 SITE 6 AC8 26 SER A 509 IMD A1553 HOH A2154 HOH A2533 SITE 7 AC8 26 HOH A2697 HOH A2698 CRYST1 124.293 64.677 54.048 90.00 90.00 90.00 P 21 21 2 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 0.008046 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015461 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018502 0.00000