HEADER OXIDOREDUCTASE 02-SEP-09 3IW2 TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125 TITLE 2 IN COMPLEX WITH ECONAZOLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450 CYP125; COMPND 3 CHAIN: A; COMPND 4 EC: 1.14.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 ATCC: 25618; SOURCE 6 GENE: CYP125, MT3649, MTCY03C7.11, RV3545C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: HMS174(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS ECONAZOLE, CYTOCHROME P450, TUBERCULOSIS, MONOOXYGENASE, CHOLESTEROL, KEYWDS 2 HEME, IRON, METAL-BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.J.MCLEAN,C.LEVY,A.W.MUNRO,D.LEYS REVDAT 6 06-SEP-23 3IW2 1 REMARK REVDAT 5 01-NOV-17 3IW2 1 REMARK REVDAT 4 13-JUL-11 3IW2 1 VERSN REVDAT 3 02-MAR-10 3IW2 1 HETNAM REVDAT 2 29-DEC-09 3IW2 1 JRNL REVDAT 1 03-NOV-09 3IW2 0 JRNL AUTH K.J.MCLEAN,P.LAFITE,C.LEVY,M.R.CHEESMAN,N.MAST,I.A.PIKULEVA, JRNL AUTH 2 D.LEYS,A.W.MUNRO JRNL TITL THE STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYP125: JRNL TITL 2 MOLECULAR BASIS FOR CHOLESTEROL BINDING IN A P450 NEEDED FOR JRNL TITL 3 HOST INFECTION. JRNL REF J.BIOL.CHEM. V. 284 35524 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19846552 JRNL DOI 10.1074/JBC.M109.032706 REMARK 2 REMARK 2 RESOLUTION. 2.19 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 21805 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) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1179 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) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1306 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.1630 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3126 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 329 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : 0.03000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.218 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.139 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.008 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3312 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2234 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4512 ; 1.866 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5406 ; 1.237 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 405 ; 8.818 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;30.945 ;24.024 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 517 ;14.456 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;15.704 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 464 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3745 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 690 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 775 ; 0.265 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2426 ; 0.215 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1578 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1605 ; 0.092 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 311 ; 0.229 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.397 ; 0.200 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): 5 ; 0.143 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 21 ; 0.214 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.334 ; 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): 2212 ; 1.620 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 811 ; 0.608 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3202 ; 2.195 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1486 ; 3.875 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1303 ; 5.382 ; 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 : 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3IW2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000054936. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21805 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 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 (%) : 94.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.2.0019 REMARK 200 STARTING MODEL: PDB ENTRY 3IVY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION WAS REFINED TO TWO REMARK 280 DIFFERENT CONDITIONS, BOTH CONSISTING OF MGCL2 WITH 0.1 M HEPES REMARK 280 (EITHER PH 7.0 OR 7.5) AND 20% PEG 6000 OR 25% PEG 3350, REMARK 280 RESPECTIVELY., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K, REMARK 280 PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 29.81600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.72750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.00800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.72750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.81600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.00800 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: 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 SER A 2 REMARK 465 TRP A 3 REMARK 465 ASN A 4 REMARK 465 HIS A 5 REMARK 465 GLN A 6 REMARK 465 SER A 7 REMARK 465 VAL A 8 REMARK 465 GLU A 9 REMARK 465 ILE A 10 REMARK 465 ALA A 11 REMARK 465 VAL A 12 REMARK 465 ARG A 13 REMARK 465 ARG A 14 REMARK 465 THR A 15 REMARK 465 THR A 16 REMARK 465 VAL A 17 REMARK 465 PRO A 18 REMARK 465 SER A 19 REMARK 465 ALA A 232 REMARK 465 LYS A 233 REMARK 465 ASN A 234 REMARK 465 PRO A 235 REMARK 465 ALA A 236 REMARK 465 ASP A 237 REMARK 465 ASP A 238 REMARK 465 ILE A 248 REMARK 465 ASP A 249 REMARK 465 GLY A 427 REMARK 465 ARG A 428 REMARK 465 CYS A 429 REMARK 465 PRO A 430 REMARK 465 VAL A 431 REMARK 465 ALA A 432 REMARK 465 HIS A 433 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 ASN A 21 CG OD1 ND2 REMARK 470 ARG A 138 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 226 CG CD CE NZ REMARK 470 GLU A 229 CG CD OE1 OE2 REMARK 470 GLU A 230 CG CD OE1 OE2 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 OD1 ASP A 247 O HOH A 724 1.78 REMARK 500 N ASP A 247 O HOH A 724 1.81 REMARK 500 CG ASP A 247 O HOH A 724 1.85 REMARK 500 CB ASP A 247 O HOH A 724 1.93 REMARK 500 O HOH A 441 O HOH A 641 1.96 REMARK 500 CG2 THR A 241 O HOH A 546 2.05 REMARK 500 C THR A 426 O HOH A 670 2.08 REMARK 500 CB ASN A 21 O HOH A 523 2.10 REMARK 500 OE1 GLU A 251 O HOH A 727 2.11 REMARK 500 CA ASP A 247 O HOH A 724 2.11 REMARK 500 O HOH A 523 O HOH A 697 2.12 REMARK 500 O HOH A 521 O HOH A 705 2.14 REMARK 500 O HOH A 610 O HOH A 738 2.15 REMARK 500 O HOH A 578 O HOH A 583 2.15 REMARK 500 O HOH A 598 O HOH A 704 2.18 REMARK 500 NE ARG A 84 O HOH A 582 2.18 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 OD2 ASP A 256 O HOH A 757 2564 1.90 REMARK 500 O HOH A 598 O HOH A 701 4555 2.02 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 CYS A 172 CB CYS A 172 SG -0.106 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 133 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 MET A 200 CG - SD - CE ANGL. DEV. = 12.6 DEGREES REMARK 500 PRO A 213 C - N - CA ANGL. DEV. = 19.3 DEGREES REMARK 500 PRO A 213 C - N - CD ANGL. DEV. = -15.8 DEGREES REMARK 500 ARG A 322 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 LEU A 401 CA - CB - CG ANGL. DEV. = 14.7 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 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 ALA A 50 70.65 -165.32 REMARK 500 HIS A 85 59.55 -91.08 REMARK 500 PRO A 213 -55.90 -6.84 REMARK 500 ASN A 270 -89.84 -92.76 REMARK 500 ARG A 298 56.98 39.52 REMARK 500 THR A 311 65.36 29.42 REMARK 500 LYS A 333 123.63 -30.33 REMARK 500 PRO A 365 46.69 -80.83 REMARK 500 MET A 398 59.36 -147.78 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 ASP A 212 PRO A 213 121.91 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 434 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 377 SG REMARK 620 2 HEM A 434 NA 101.4 REMARK 620 3 HEM A 434 NB 92.7 90.3 REMARK 620 4 HEM A 434 NC 85.9 172.3 87.3 REMARK 620 5 HEM A 434 ND 96.1 89.1 171.1 92.2 REMARK 620 6 HOH A 439 O 175.6 78.1 83.0 94.4 88.2 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 EKO A 665 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 434 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IVY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 REMARK 900 CYP125, P212121 CRYSTAL FORM REMARK 900 RELATED ID: 3IW0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 REMARK 900 CYP125, C2221 CRYSTAL FORM REMARK 900 RELATED ID: 2IW1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 REMARK 900 CYP125 IN COMPLEX WITH ANDROSTENEDIONE DBREF 3IW2 A 1 433 UNP P63709 CP125_MYCTU 1 433 SEQRES 1 A 433 MET SER TRP ASN HIS GLN SER VAL GLU ILE ALA VAL ARG SEQRES 2 A 433 ARG THR THR VAL PRO SER PRO ASN LEU PRO PRO GLY PHE SEQRES 3 A 433 ASP PHE THR ASP PRO ALA ILE TYR ALA GLU ARG LEU PRO SEQRES 4 A 433 VAL ALA GLU PHE ALA GLU LEU ARG SER ALA ALA PRO ILE SEQRES 5 A 433 TRP TRP ASN GLY GLN ASP PRO GLY LYS GLY GLY GLY PHE SEQRES 6 A 433 HIS ASP GLY GLY PHE TRP ALA ILE THR LYS LEU ASN ASP SEQRES 7 A 433 VAL LYS GLU ILE SER ARG HIS SER ASP VAL PHE SER SER SEQRES 8 A 433 TYR GLU ASN GLY VAL ILE PRO ARG PHE LYS ASN ASP ILE SEQRES 9 A 433 ALA ARG GLU ASP ILE GLU VAL GLN ARG PHE VAL MET LEU SEQRES 10 A 433 ASN MET ASP ALA PRO HIS HIS THR ARG LEU ARG LYS ILE SEQRES 11 A 433 ILE SER ARG GLY PHE THR PRO ARG ALA VAL GLY ARG LEU SEQRES 12 A 433 HIS ASP GLU LEU GLN GLU ARG ALA GLN LYS ILE ALA ALA SEQRES 13 A 433 GLU ALA ALA ALA ALA GLY SER GLY ASP PHE VAL GLU GLN SEQRES 14 A 433 VAL SER CYS GLU LEU PRO LEU GLN ALA ILE ALA GLY LEU SEQRES 15 A 433 LEU GLY VAL PRO GLN GLU ASP ARG GLY LYS LEU PHE HIS SEQRES 16 A 433 TRP SER ASN GLU MET THR GLY ASN GLU ASP PRO GLU TYR SEQRES 17 A 433 ALA HIS ILE ASP PRO LYS ALA SER SER ALA GLU LEU ILE SEQRES 18 A 433 GLY TYR ALA MET LYS MET ALA GLU GLU LYS ALA LYS ASN SEQRES 19 A 433 PRO ALA ASP ASP ILE VAL THR GLN LEU ILE GLN ALA ASP SEQRES 20 A 433 ILE ASP GLY GLU LYS LEU SER ASP ASP GLU PHE GLY PHE SEQRES 21 A 433 PHE VAL VAL MET LEU ALA VAL ALA GLY ASN GLU THR THR SEQRES 22 A 433 ARG ASN SER ILE THR GLN GLY MET MET ALA PHE ALA GLU SEQRES 23 A 433 HIS PRO ASP GLN TRP GLU LEU TYR LYS LYS VAL ARG PRO SEQRES 24 A 433 GLU THR ALA ALA ASP GLU ILE VAL ARG TRP ALA THR PRO SEQRES 25 A 433 VAL THR ALA PHE GLN ARG THR ALA LEU ARG ASP TYR GLU SEQRES 26 A 433 LEU SER GLY VAL GLN ILE LYS LYS GLY GLN ARG VAL VAL SEQRES 27 A 433 MET PHE TYR ARG SER ALA ASN PHE ASP GLU GLU VAL PHE SEQRES 28 A 433 GLN ASP PRO PHE THR PHE ASN ILE LEU ARG ASN PRO ASN SEQRES 29 A 433 PRO HIS VAL GLY PHE GLY GLY THR GLY ALA HIS TYR CYS SEQRES 30 A 433 ILE GLY ALA ASN LEU ALA ARG MET THR ILE ASN LEU ILE SEQRES 31 A 433 PHE ASN ALA VAL ALA ASP HIS MET PRO ASP LEU LYS PRO SEQRES 32 A 433 ILE SER ALA PRO GLU ARG LEU ARG SER GLY TRP LEU ASN SEQRES 33 A 433 GLY ILE LYS HIS TRP GLN VAL ASP TYR THR GLY ARG CYS SEQRES 34 A 433 PRO VAL ALA HIS HET EKO A 665 24 HET HEM A 434 43 HETNAM EKO 4-[(2R)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL) HETNAM 2 EKO ETHYL]-1H-IMIDAZOLE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 EKO C18 H15 CL3 N2 O FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 HOH *329(H2 O) HELIX 1 1 ASP A 30 ALA A 35 1 6 HELIX 2 2 PRO A 39 ALA A 50 1 12 HELIX 3 3 LYS A 75 HIS A 85 1 11 HELIX 4 4 ARG A 106 VAL A 111 1 6 HELIX 5 5 GLN A 112 MET A 119 5 8 HELIX 6 6 PRO A 122 SER A 132 1 11 HELIX 7 7 ARG A 133 PHE A 135 5 3 HELIX 8 8 THR A 136 ARG A 142 1 7 HELIX 9 9 LEU A 143 GLY A 162 1 20 HELIX 10 10 PHE A 166 VAL A 170 1 5 HELIX 11 11 CYS A 172 LEU A 183 1 12 HELIX 12 12 PRO A 186 MET A 200 1 15 HELIX 13 13 ASP A 205 ALA A 209 5 5 HELIX 14 14 ASP A 212 LYS A 231 1 20 HELIX 15 15 ILE A 239 GLN A 245 1 7 HELIX 16 16 SER A 254 GLY A 269 1 16 HELIX 17 17 ASN A 270 HIS A 287 1 18 HELIX 18 18 HIS A 287 ARG A 298 1 12 HELIX 19 19 THR A 301 THR A 311 1 11 HELIX 20 20 TYR A 341 ASN A 345 1 5 HELIX 21 21 GLY A 379 MET A 398 1 20 SHEET 1 A 5 ILE A 52 GLY A 56 0 SHEET 2 A 5 GLY A 69 ILE A 73 -1 O ALA A 72 N TRP A 53 SHEET 3 A 5 ARG A 336 PHE A 340 1 O VAL A 338 N TRP A 71 SHEET 4 A 5 ALA A 315 ALA A 320 -1 N PHE A 316 O MET A 339 SHEET 5 A 5 PHE A 89 SER A 90 -1 N SER A 90 O THR A 319 SHEET 1 B 3 SER A 163 ASP A 165 0 SHEET 2 B 3 GLN A 422 ASP A 424 -1 O VAL A 423 N GLY A 164 SHEET 3 B 3 LYS A 402 PRO A 403 -1 N LYS A 402 O ASP A 424 SHEET 1 C 2 TYR A 324 LEU A 326 0 SHEET 2 C 2 VAL A 329 ILE A 331 -1 O ILE A 331 N TYR A 324 SHEET 1 D 2 GLU A 408 ARG A 409 0 SHEET 2 D 2 ILE A 418 HIS A 420 -1 O LYS A 419 N GLU A 408 LINK SG CYS A 377 FE HEM A 434 1555 1555 2.27 LINK FE HEM A 434 O HOH A 439 1555 1555 2.40 CISPEP 1 ALA A 121 PRO A 122 0 1.19 CISPEP 2 ASN A 362 PRO A 363 0 -6.42 SITE 1 AC1 8 ASP A 108 VAL A 111 GLN A 112 SER A 217 SITE 2 AC1 8 ALA A 218 VAL A 263 VAL A 267 HOH A 597 SITE 1 AC2 25 LEU A 117 HIS A 124 ARG A 128 PHE A 135 SITE 2 AC2 25 MET A 264 ALA A 268 GLY A 269 THR A 272 SITE 3 AC2 25 THR A 273 PHE A 316 ARG A 318 TYR A 341 SITE 4 AC2 25 GLY A 368 PHE A 369 GLY A 370 ALA A 374 SITE 5 AC2 25 HIS A 375 CYS A 377 ILE A 378 GLY A 379 SITE 6 AC2 25 ALA A 383 HOH A 439 HOH A 459 HOH A 473 SITE 7 AC2 25 HOH A 628 CRYST1 59.632 86.016 89.455 90.00 90.00 90.00 P 21 21 21 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 0.016770 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011626 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011179 0.00000