HEADER OXIDOREDUCTASE 10-FEB-10 2X5L TITLE X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS TITLE 2 CYTOCHROME P450 CYP125, ALTERNATIVE CRYSTAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE CYTOCHROME P450 125; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 17-433; COMPND 5 SYNONYM: CYP125A1; COMPND 6 EC: 1.14.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: HMS174; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCWORI KEYWDS OXIDOREDUCTASE, CHOLESTEROL DEGRADATION, MONOOXYGENASE, METAL-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR H.OUELLET,P.M.KELLS,P.R.ORTIZ DE MONTELLANO,L.M.PODUST REVDAT 5 20-DEC-23 2X5L 1 REMARK REVDAT 4 27-FEB-19 2X5L 1 JRNL REMARK REVDAT 3 07-FEB-18 2X5L 1 SOURCE JRNL REVDAT 2 29-DEC-10 2X5L 1 JRNL REVDAT 1 10-NOV-10 2X5L 0 JRNL AUTH H.OUELLET,P.M.KELLS,P.R.ORTIZ DE MONTELLANO,L.M.PODUST JRNL TITL REVERSE TYPE I INHIBITOR OF MYCOBACTERIUMTUBERCULOSIS JRNL TITL 2 CYP125A1. JRNL REF BIOORG.MED.CHEM.LETT. V. 21 332 2011 JRNL REFN ISSN 0960-894X JRNL PMID 21109436 JRNL DOI 10.1016/J.BMCL.2010.11.007 REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 102.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 63143 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) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3367 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) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3125 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE SET COUNT : 171 REMARK 3 BIN FREE R VALUE : 0.4210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3259 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 714 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : 0.14000 REMARK 3 B33 (A**2) : -0.34000 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): 0.091 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.079 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.786 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3472 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4740 ; 1.970 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 431 ; 5.936 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;32.505 ;23.908 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 546 ;13.093 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;15.069 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 487 ; 0.171 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2767 ; 0.013 ; 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): 2113 ; 2.182 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3405 ; 3.095 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1359 ; 4.542 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1334 ; 6.275 ; 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): 3472 ; 2.703 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 714 ;10.468 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3370 ; 6.721 ; 3.000 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 : 1.40 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 2X5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1290042843. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1159 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66632 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 102.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 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 3IVY REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM ACETATE, 0.1 M BIS REMARK 280 -TRIS, PH 5.5, 17% PEG 10000 AT 4 C, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K 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 27.24000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.11250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.28900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.11250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.24000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.28900 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, VAL 17 TO MET REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 429 TO LEU 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 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 MET A 10 REMARK 465 PRO A 11 REMARK 465 SER A 12 REMARK 465 PRO A 13 REMARK 465 ASN A 14 REMARK 465 LEU A 15 REMARK 465 PRO A 16 REMARK 465 MET A 17 REMARK 465 PRO A 18 REMARK 465 SER A 19 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 LYS A 233 CE NZ REMARK 470 GLU A 300 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 ND1 HIS A 123 O HOH A 2289 1.73 REMARK 500 O HOH A 2013 O HOH A 2103 1.81 REMARK 500 NZ LYS A 80 O HOH A 2182 1.89 REMARK 500 O HOH A 2479 O HOH A 2489 1.91 REMARK 500 N PRO A 20 O HOH A 2001 1.99 REMARK 500 O HOH A 2534 O HOH A 2535 2.00 REMARK 500 O HOH A 2526 O HOH A 2533 2.03 REMARK 500 O HOH A 2484 O HOH A 2489 2.03 REMARK 500 O HOH A 2096 O HOH A 2207 2.05 REMARK 500 O HOH A 2393 O HOH A 2394 2.07 REMARK 500 CE LYS A 80 O HOH A 2182 2.09 REMARK 500 OD1 ASP A 289 O HOH A 2539 2.10 REMARK 500 O HOH A 2004 O HOH A 2005 2.10 REMARK 500 OE2 GLU A 286 O HOH A 2531 2.11 REMARK 500 O HOH A 2274 O HOH A 2538 2.11 REMARK 500 O GLY A 427 O HOH A 2702 2.16 REMARK 500 O THR A 201 O HOH A 2425 2.18 REMARK 500 O HOH A 2006 O HOH A 2016 2.18 REMARK 500 O HOH A 2565 O HOH A 2574 2.19 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 O HOH A 2232 O HOH A 2576 2654 2.14 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 - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 138 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 150 CD - NE - CZ ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 150 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 256 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 298 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 384 NE - CZ - NH2 ANGL. DEV. = -4.6 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 75.93 -161.00 REMARK 500 ASN A 270 -82.24 -107.42 REMARK 500 THR A 311 71.26 28.43 REMARK 500 PRO A 365 43.13 -87.56 REMARK 500 TRP A 414 -27.82 -142.50 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2024 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A2029 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A2034 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A2047 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A2134 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A2143 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH A2158 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A2163 DISTANCE = 7.28 ANGSTROMS REMARK 525 HOH A2173 DISTANCE = 7.25 ANGSTROMS REMARK 525 HOH A2180 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A2181 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A2377 DISTANCE = 5.92 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 PROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND TO REMARK 600 C377 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 A1434 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 377 SG REMARK 620 2 HEM A1434 NA 100.6 REMARK 620 3 HEM A1434 NB 93.7 90.3 REMARK 620 4 HEM A1434 NC 89.8 169.5 90.0 REMARK 620 5 HEM A1434 ND 100.3 88.3 166.0 88.9 REMARK 620 6 HOH A2517 O 172.3 81.1 78.8 88.7 87.2 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 HEM A 1434 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2X5W RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 REMARK 900 CYP125 IN COMPLEX WITH SUBSTRATE CHOLEST-4-EN-3-ONE REMARK 900 RELATED ID: 2XC3 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYP125 BOUND TO THE REMARK 900 REVERSE TYPE I INHIBITOR REMARK 900 RELATED ID: 2XN8 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE SUBSTRATE-FREE MYCOBACTERIUM TUBERCULOSIS REMARK 900 CYTOCHROME P450 CYP125 REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST 16 RESIDUES UPSTREAM OF V17 ARE TRUNCATED. REMARK 999 MUTATIONS V17M AND C429L WERE ENGINEERED. DBREF 2X5L A 17 433 UNP P63709 CP125_MYCTU 17 433 SEQADV 2X5L MET A 3 UNP P63709 EXPRESSION TAG SEQADV 2X5L HIS A 4 UNP P63709 EXPRESSION TAG SEQADV 2X5L HIS A 5 UNP P63709 EXPRESSION TAG SEQADV 2X5L HIS A 6 UNP P63709 EXPRESSION TAG SEQADV 2X5L HIS A 7 UNP P63709 EXPRESSION TAG SEQADV 2X5L HIS A 8 UNP P63709 EXPRESSION TAG SEQADV 2X5L HIS A 9 UNP P63709 EXPRESSION TAG SEQADV 2X5L MET A 10 UNP P63709 EXPRESSION TAG SEQADV 2X5L PRO A 11 UNP P63709 EXPRESSION TAG SEQADV 2X5L SER A 12 UNP P63709 EXPRESSION TAG SEQADV 2X5L PRO A 13 UNP P63709 EXPRESSION TAG SEQADV 2X5L ASN A 14 UNP P63709 EXPRESSION TAG SEQADV 2X5L LEU A 15 UNP P63709 EXPRESSION TAG SEQADV 2X5L PRO A 16 UNP P63709 EXPRESSION TAG SEQADV 2X5L MET A 17 UNP P63709 VAL 17 ENGINEERED MUTATION SEQADV 2X5L LEU A 429 UNP P63709 CYS 429 ENGINEERED MUTATION SEQRES 1 A 431 MET HIS HIS HIS HIS HIS HIS MET PRO SER PRO ASN LEU SEQRES 2 A 431 PRO MET PRO SER PRO ASN LEU PRO PRO GLY PHE ASP PHE SEQRES 3 A 431 THR ASP PRO ALA ILE TYR ALA GLU ARG LEU PRO VAL ALA SEQRES 4 A 431 GLU PHE ALA GLU LEU ARG SER ALA ALA PRO ILE TRP TRP SEQRES 5 A 431 ASN GLY GLN ASP PRO GLY LYS GLY GLY GLY PHE HIS ASP SEQRES 6 A 431 GLY GLY PHE TRP ALA ILE THR LYS LEU ASN ASP VAL LYS SEQRES 7 A 431 GLU ILE SER ARG HIS SER ASP VAL PHE SER SER TYR GLU SEQRES 8 A 431 ASN GLY VAL ILE PRO ARG PHE LYS ASN ASP ILE ALA ARG SEQRES 9 A 431 GLU ASP ILE GLU VAL GLN ARG PHE VAL MET LEU ASN MET SEQRES 10 A 431 ASP ALA PRO HIS HIS THR ARG LEU ARG LYS ILE ILE SER SEQRES 11 A 431 ARG GLY PHE THR PRO ARG ALA VAL GLY ARG LEU HIS ASP SEQRES 12 A 431 GLU LEU GLN GLU ARG ALA GLN LYS ILE ALA ALA GLU ALA SEQRES 13 A 431 ALA ALA ALA GLY SER GLY ASP PHE VAL GLU GLN VAL SER SEQRES 14 A 431 CYS GLU LEU PRO LEU GLN ALA ILE ALA GLY LEU LEU GLY SEQRES 15 A 431 VAL PRO GLN GLU ASP ARG GLY LYS LEU PHE HIS TRP SER SEQRES 16 A 431 ASN GLU MET THR GLY ASN GLU ASP PRO GLU TYR ALA HIS SEQRES 17 A 431 ILE ASP PRO LYS ALA SER SER ALA GLU LEU ILE GLY TYR SEQRES 18 A 431 ALA MET LYS MET ALA GLU GLU LYS ALA LYS ASN PRO ALA SEQRES 19 A 431 ASP ASP ILE VAL THR GLN LEU ILE GLN ALA ASP ILE ASP SEQRES 20 A 431 GLY GLU LYS LEU SER ASP ASP GLU PHE GLY PHE PHE VAL SEQRES 21 A 431 VAL MET LEU ALA VAL ALA GLY ASN GLU THR THR ARG ASN SEQRES 22 A 431 SER ILE THR GLN GLY MET MET ALA PHE ALA GLU HIS PRO SEQRES 23 A 431 ASP GLN TRP GLU LEU TYR LYS LYS VAL ARG PRO GLU THR SEQRES 24 A 431 ALA ALA ASP GLU ILE VAL ARG TRP ALA THR PRO VAL THR SEQRES 25 A 431 ALA PHE GLN ARG THR ALA LEU ARG ASP TYR GLU LEU SER SEQRES 26 A 431 GLY VAL GLN ILE LYS LYS GLY GLN ARG VAL VAL MET PHE SEQRES 27 A 431 TYR ARG SER ALA ASN PHE ASP GLU GLU VAL PHE GLN ASP SEQRES 28 A 431 PRO PHE THR PHE ASN ILE LEU ARG ASN PRO ASN PRO HIS SEQRES 29 A 431 VAL GLY PHE GLY GLY THR GLY ALA HIS TYR CYS ILE GLY SEQRES 30 A 431 ALA ASN LEU ALA ARG MET THR ILE ASN LEU ILE PHE ASN SEQRES 31 A 431 ALA VAL ALA ASP HIS MET PRO ASP LEU LYS PRO ILE SER SEQRES 32 A 431 ALA PRO GLU ARG LEU ARG SER GLY TRP LEU ASN GLY ILE SEQRES 33 A 431 LYS HIS TRP GLN VAL ASP TYR THR GLY ARG LEU PRO VAL SEQRES 34 A 431 ALA HIS HET HEM A1434 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *714(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 ALA A 105 VAL A 111 1 7 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 GLY A 184 1 13 HELIX 12 12 PRO A 186 GLU A 188 5 3 HELIX 13 13 ASP A 189 GLU A 199 1 11 HELIX 14 14 ASP A 205 ALA A 209 5 5 HELIX 15 15 ASP A 212 ASN A 234 1 23 HELIX 16 16 ASP A 238 GLN A 245 1 8 HELIX 17 17 SER A 254 GLY A 269 1 16 HELIX 18 18 ASN A 270 HIS A 287 1 18 HELIX 19 19 HIS A 287 ARG A 298 1 12 HELIX 20 20 THR A 301 THR A 311 1 11 HELIX 21 21 TYR A 341 ASN A 345 1 5 HELIX 22 22 GLY A 379 MET A 398 1 20 SHEET 1 AA 5 ILE A 52 GLY A 56 0 SHEET 2 AA 5 GLY A 69 ILE A 73 -1 O PHE A 70 N ASN A 55 SHEET 3 AA 5 ARG A 336 PHE A 340 1 O ARG A 336 N TRP A 71 SHEET 4 AA 5 ALA A 315 ALA A 320 -1 O PHE A 316 N MET A 339 SHEET 5 AA 5 PHE A 89 SER A 90 -1 O SER A 90 N THR A 319 SHEET 1 AB 3 SER A 163 ASP A 165 0 SHEET 2 AB 3 GLN A 422 ASP A 424 -1 O VAL A 423 N GLY A 164 SHEET 3 AB 3 LYS A 402 PRO A 403 -1 O LYS A 402 N ASP A 424 SHEET 1 AC 2 TYR A 324 LEU A 326 0 SHEET 2 AC 2 VAL A 329 ILE A 331 -1 O VAL A 329 N LEU A 326 SHEET 1 AD 2 GLU A 408 ARG A 409 0 SHEET 2 AD 2 ILE A 418 HIS A 420 -1 N LYS A 419 O GLU A 408 LINK SG CYS A 377 FE HEM A1434 1555 1555 2.32 LINK FE HEM A1434 O HOH A2517 1555 1555 2.24 CISPEP 1 ALA A 121 PRO A 122 0 2.65 CISPEP 2 ASN A 362 PRO A 363 0 -7.77 SITE 1 AC1 24 MET A 116 LEU A 117 HIS A 124 ARG A 128 SITE 2 AC1 24 MET A 264 ALA A 268 GLY A 269 THR A 272 SITE 3 AC1 24 THR A 273 SER A 276 PRO A 312 PHE A 316 SITE 4 AC1 24 ARG A 318 GLY A 368 PHE A 369 GLY A 370 SITE 5 AC1 24 HIS A 375 TYR A 376 CYS A 377 ILE A 378 SITE 6 AC1 24 HOH A2517 HOH A2593 HOH A2712 HOH A2713 CRYST1 54.480 74.578 102.225 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 0.018355 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013409 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009782 0.00000