HEADER OXIDOREDUCTASE 16-APR-10 2XC3 TITLE X-RAY STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYP125 BOUND TO THE TITLE 2 REVERSE TYPE I INHIBITOR 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, 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 2XC3 1 REMARK REVDAT 4 03-APR-19 2XC3 1 REMARK REVDAT 3 07-FEB-18 2XC3 1 SOURCE JRNL REVDAT 2 29-DEC-10 2XC3 1 JRNL REVDAT 1 10-NOV-10 2XC3 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. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 3 NUMBER OF REFLECTIONS : 53185 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) : 0.125 REMARK 3 R VALUE (WORKING SET) : 0.122 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2840 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2448 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 57.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.2550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3193 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 73 REMARK 3 SOLVENT ATOMS : 584 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24000 REMARK 3 B22 (A**2) : 0.21000 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): 0.090 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.076 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.113 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3446 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 28 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4705 ; 1.926 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 64 ; 1.387 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 427 ; 5.880 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;30.742 ;24.024 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 536 ;12.130 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;13.827 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 486 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2735 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 15 ; 0.012 ; 0.020 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): 2095 ; 2.280 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3372 ; 3.320 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1351 ; 4.966 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1333 ; 6.848 ; 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): 3474 ; 2.643 ; 3.000 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 : 1.40 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. RESIDUES 233-237 ARE DISORDERED. REMARK 4 REMARK 4 2XC3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-10. REMARK 100 THE DEPOSITION ID IS D_1290043665. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-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) : 1.11588 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56093 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.14000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2X5L REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS, REMARK 280 PH 5.5, 0.5 M NACL, 4 DEG. CELSIUS, 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 27.17800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.20350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.19950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.20350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.17800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.19950 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 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 HIS A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 MET A 17 REMARK 465 PRO A 18 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 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 SER A 19 OG REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 ARG A 133 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 138 CD NE CZ NH1 NH2 REMARK 470 ARG A 142 NE CZ NH1 NH2 REMARK 470 GLU A 230 CG CD OE1 OE2 REMARK 470 ASP A 238 CG OD1 OD2 REMARK 470 GLN A 242 CG CD OE1 NE2 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 CB GLU A 168 O HOH A 2304 1.78 REMARK 500 O HOH A 2234 O HOH A 2252 2.00 REMARK 500 O HOH A 2317 O HOH A 2318 2.07 REMARK 500 O HOH A 2440 O HOH A 2441 2.08 REMARK 500 O THR A 201 O HOH A 2340 2.11 REMARK 500 O HOH A 2414 O HOH A 2415 2.13 REMARK 500 OD1 ASN A 21 O HOH A 2003 2.14 REMARK 500 O HOH A 2330 O HOH A 2332 2.14 REMARK 500 O HOH A 2222 O HOH A 2421 2.14 REMARK 500 O HOH A 2529 O HOH A 2533 2.15 REMARK 500 NZ LYS A 129 O HOH A 2237 2.16 REMARK 500 O HOH A 2215 O HOH A 2415 2.17 REMARK 500 CG LEU A 401 O HOH A 2535 2.19 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 SER A 48 CB SER A 48 OG -0.086 REMARK 500 GLU A 349 CD GLU A 349 OE2 0.077 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 99 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 LYS A 129 CD - CE - NZ ANGL. DEV. = 16.7 DEGREES REMARK 500 MET A 200 CB - CG - SD ANGL. DEV. = -21.3 DEGREES REMARK 500 MET A 200 CG - SD - CE ANGL. DEV. = -9.6 DEGREES REMARK 500 LYS A 333 CD - CE - NZ ANGL. DEV. = 19.0 DEGREES REMARK 500 ARG A 384 NE - CZ - NH2 ANGL. DEV. = -4.8 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 ALA A 50 74.30 -160.33 REMARK 500 ASN A 270 -79.41 -98.38 REMARK 500 THR A 311 68.68 29.80 REMARK 500 SER A 327 52.68 39.94 REMARK 500 PRO A 365 41.34 -87.48 REMARK 500 MET A 398 53.32 -143.57 REMARK 500 TRP A 414 -22.54 -146.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 409 0.08 SIDE CHAIN 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 A2035 DISTANCE = 6.90 ANGSTROMS REMARK 525 HOH A2040 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2233 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A2292 DISTANCE = 6.98 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 A-[(4-METHYLCYCLOHEXYL)CARBONYL REMARK 600 AMINO]-N-4-PYRIDINYL-1H-INDOLE-3-PROPANAMIDE (RT8): REMARK 600 REVERSE TYPE I INHIBITOR REMARK 600 PROTOPORPHYRIN IX CONTAINING FE (HEM): THIOLATE BOND TO CYS REMARK 600 377 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 A1433 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 377 SG REMARK 620 2 HEM A1433 NA 98.4 REMARK 620 3 HEM A1433 NB 90.5 89.0 REMARK 620 4 HEM A1433 NC 87.1 174.4 89.8 REMARK 620 5 HEM A1433 ND 96.5 91.0 173.0 89.6 REMARK 620 6 HOH A2401 O 174.1 81.9 83.6 92.6 89.4 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 HEM A 1433 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RT8 A 1434 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2X5W RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF CYP125A1 FROM M. TUBERCULOSIS BOUND TO THE REMARK 900 SUBSTRATE CHOLEST- 4-EN-3-ONE REMARK 900 RELATED ID: 2X5L RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE TRUNCATED FORM OF CYP125A1 FROM M. REMARK 900 TUBERCULOSIS REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIRST 16 RESIDUES UPSTREAM OF V17 ARE TRUNCATED. MUTATIONS REMARK 999 V17M AND C429L ARE ENGINEERED. 6XHIS TAG IS ENGINEERED AT REMARK 999 THE N-TERMINUS DBREF 2XC3 A 17 433 UNP P63709 CP125_MYCTU 17 433 SEQADV 2XC3 MET A 10 UNP P63709 EXPRESSION TAG SEQADV 2XC3 HIS A 11 UNP P63709 EXPRESSION TAG SEQADV 2XC3 HIS A 12 UNP P63709 EXPRESSION TAG SEQADV 2XC3 HIS A 13 UNP P63709 EXPRESSION TAG SEQADV 2XC3 HIS A 14 UNP P63709 EXPRESSION TAG SEQADV 2XC3 HIS A 15 UNP P63709 EXPRESSION TAG SEQADV 2XC3 HIS A 16 UNP P63709 EXPRESSION TAG SEQADV 2XC3 MET A 17 UNP P63709 VAL 17 ENGINEERED MUTATION SEQADV 2XC3 LEU A 429 UNP P63709 CYS 429 ENGINEERED MUTATION SEQRES 1 A 424 MET HIS HIS HIS HIS HIS HIS MET PRO SER PRO ASN LEU SEQRES 2 A 424 PRO PRO GLY PHE ASP PHE THR ASP PRO ALA ILE TYR ALA SEQRES 3 A 424 GLU ARG LEU PRO VAL ALA GLU PHE ALA GLU LEU ARG SER SEQRES 4 A 424 ALA ALA PRO ILE TRP TRP ASN GLY GLN ASP PRO GLY LYS SEQRES 5 A 424 GLY GLY GLY PHE HIS ASP GLY GLY PHE TRP ALA ILE THR SEQRES 6 A 424 LYS LEU ASN ASP VAL LYS GLU ILE SER ARG HIS SER ASP SEQRES 7 A 424 VAL PHE SER SER TYR GLU ASN GLY VAL ILE PRO ARG PHE SEQRES 8 A 424 LYS ASN ASP ILE ALA ARG GLU ASP ILE GLU VAL GLN ARG SEQRES 9 A 424 PHE VAL MET LEU ASN MET ASP ALA PRO HIS HIS THR ARG SEQRES 10 A 424 LEU ARG LYS ILE ILE SER ARG GLY PHE THR PRO ARG ALA SEQRES 11 A 424 VAL GLY ARG LEU HIS ASP GLU LEU GLN GLU ARG ALA GLN SEQRES 12 A 424 LYS ILE ALA ALA GLU ALA ALA ALA ALA GLY SER GLY ASP SEQRES 13 A 424 PHE VAL GLU GLN VAL SER CYS GLU LEU PRO LEU GLN ALA SEQRES 14 A 424 ILE ALA GLY LEU LEU GLY VAL PRO GLN GLU ASP ARG GLY SEQRES 15 A 424 LYS LEU PHE HIS TRP SER ASN GLU MET THR GLY ASN GLU SEQRES 16 A 424 ASP PRO GLU TYR ALA HIS ILE ASP PRO LYS ALA SER SER SEQRES 17 A 424 ALA GLU LEU ILE GLY TYR ALA MET LYS MET ALA GLU GLU SEQRES 18 A 424 LYS ALA LYS ASN PRO ALA ASP ASP ILE VAL THR GLN LEU SEQRES 19 A 424 ILE GLN ALA ASP ILE ASP GLY GLU LYS LEU SER ASP ASP SEQRES 20 A 424 GLU PHE GLY PHE PHE VAL VAL MET LEU ALA VAL ALA GLY SEQRES 21 A 424 ASN GLU THR THR ARG ASN SER ILE THR GLN GLY MET MET SEQRES 22 A 424 ALA PHE ALA GLU HIS PRO ASP GLN TRP GLU LEU TYR LYS SEQRES 23 A 424 LYS VAL ARG PRO GLU THR ALA ALA ASP GLU ILE VAL ARG SEQRES 24 A 424 TRP ALA THR PRO VAL THR ALA PHE GLN ARG THR ALA LEU SEQRES 25 A 424 ARG ASP TYR GLU LEU SER GLY VAL GLN ILE LYS LYS GLY SEQRES 26 A 424 GLN ARG VAL VAL MET PHE TYR ARG SER ALA ASN PHE ASP SEQRES 27 A 424 GLU GLU VAL PHE GLN ASP PRO PHE THR PHE ASN ILE LEU SEQRES 28 A 424 ARG ASN PRO ASN PRO HIS VAL GLY PHE GLY GLY THR GLY SEQRES 29 A 424 ALA HIS TYR CYS ILE GLY ALA ASN LEU ALA ARG MET THR SEQRES 30 A 424 ILE ASN LEU ILE PHE ASN ALA VAL ALA ASP HIS MET PRO SEQRES 31 A 424 ASP LEU LYS PRO ILE SER ALA PRO GLU ARG LEU ARG SER SEQRES 32 A 424 GLY TRP LEU ASN GLY ILE LYS HIS TRP GLN VAL ASP TYR SEQRES 33 A 424 THR GLY ARG LEU PRO VAL ALA HIS HET HEM A1433 43 HET RT8 A1434 30 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM RT8 NALPHA-[(TRANS-4-METHYLCYCLOHEXYL)CARBONYL]-N-PYRIDIN- HETNAM 2 RT8 4-YL-D-TRYPTOPHANAMIDE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 RT8 C24 H28 N4 O2 FORMUL 4 HOH *584(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 ALA A 161 1 19 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 THR A 201 1 13 HELIX 14 14 ASP A 205 ALA A 209 5 5 HELIX 15 15 ASP A 212 ALA A 232 1 21 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 A1433 1555 1555 2.31 LINK FE HEM A1433 O HOH A2401 1555 1555 2.17 CISPEP 1 ALA A 121 PRO A 122 0 5.00 CISPEP 2 ASN A 362 PRO A 363 0 -2.43 SITE 1 AC1 24 LEU A 117 HIS A 124 ARG A 128 MET A 264 SITE 2 AC1 24 ALA A 268 GLY A 269 THR A 272 THR A 273 SITE 3 AC1 24 SER A 276 PRO A 312 PHE A 316 ARG A 318 SITE 4 AC1 24 GLY A 368 PHE A 369 GLY A 371 ALA A 374 SITE 5 AC1 24 HIS A 375 CYS A 377 ILE A 378 GLY A 379 SITE 6 AC1 24 HOH A2401 HOH A2580 HOH A2581 HOH A2582 SITE 1 AC2 16 ILE A 97 PHE A 100 ASP A 108 GLN A 112 SITE 2 AC2 16 VAL A 115 LEU A 117 THR A 201 LYS A 214 SITE 3 AC2 16 PHE A 260 VAL A 263 VAL A 267 TRP A 414 SITE 4 AC2 16 HOH A2205 HOH A2339 HOH A2583 HOH A2584 CRYST1 54.356 76.399 90.407 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 0.018397 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013089 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011061 0.00000