HEADER OXIDOREDUCTASE 10-FEB-10 2X5W TITLE X-RAY STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 CYP125 TITLE 2 IN COMPLEX WITH SUBSTRATE CHOLEST-4-EN-3-ONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE CYTOCHROME P450 125; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYP125A1; COMPND 5 EC: 1.14.-.-; COMPND 6 ENGINEERED: 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 CHOLESTEROL DEGRADATION, METAL-BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.OUELLET,S.GUAN,J.B.JOHNSTON,E.D.CHOW,P.M.KELLS,A.L.BURLINGAME, AUTHOR 2 J.S.COX,L.M.PODUST,P.R.ORTIZ DE MONTELLANO REVDAT 5 20-DEC-23 2X5W 1 REMARK REVDAT 4 03-APR-19 2X5W 1 REMARK REVDAT 3 07-FEB-18 2X5W 1 SOURCE JRNL REVDAT 2 04-AUG-10 2X5W 1 TITLE JRNL REVDAT 1 16-JUN-10 2X5W 0 JRNL AUTH H.OUELLET,S.GUAN,J.B.JOHNSTON,E.D.CHOW,P.M.KELLS, JRNL AUTH 2 A.L.BURLINGAME,J.S.COX,L.M.PODUST,P.R.ORTIZ DE MONTELLANO JRNL TITL MYCOBACTERIUM TUBERCULOSIS CYP125A1, A STEROID C27 JRNL TITL 2 MONOOXYGENASE THAT DETOXIFIES INTRACELLULARLY GENERATED JRNL TITL 3 CHOLEST-4-EN-3-ONE. JRNL REF MOL.MICROBIOL. V. 77 730 2010 JRNL REFN ISSN 0950-382X JRNL PMID 20545858 JRNL DOI 10.1111/J.1365-2958.2010.07243.X REMARK 2 REMARK 2 RESOLUTION. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 79.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 58287 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) : 0.146 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3098 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) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4003 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : 195 REMARK 3 BIN FREE R VALUE : 0.3840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3196 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 438 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.74000 REMARK 3 B22 (A**2) : -0.18000 REMARK 3 B33 (A**2) : 0.92000 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): 0.095 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.286 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3497 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4784 ; 2.023 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 434 ; 5.952 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 175 ;30.686 ;24.171 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 543 ;14.417 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;17.216 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 490 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2790 ; 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): 2115 ; 2.263 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3410 ; 3.233 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1382 ; 4.890 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1374 ; 6.413 ; 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): 3497 ; 2.658 ; 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. REMARK 4 REMARK 4 2X5W 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_1290042863. 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 : 61386 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 75.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 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 (%): 46.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULPHATE, 0.1 M BIS- REMARK 280 TRIS, PH 5.5, 25% PEG 3350, 4 DEGREE C., 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 36.83300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.79600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.98850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.79600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.83300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.98850 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 -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 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 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 SER A 19 OG REMARK 470 GLU A 107 CG CD OE1 OE2 REMARK 470 ARG A 142 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 168 CD OE1 OE2 REMARK 470 GLU A 229 CD OE1 OE2 REMARK 470 GLU A 286 CD OE1 OE2 REMARK 470 GLN A 352 CG CD OE1 NE2 REMARK 470 LYS A 402 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLN A 177 OE1 GLN A 187 1.18 REMARK 500 O GLN A 352 OD1 ASP A 353 1.35 REMARK 500 O GLU A 300 O HOH A 2311 1.95 REMARK 500 O HOH A 2349 O HOH A 2356 1.98 REMARK 500 O HOH A 2061 O HOH A 2164 2.09 REMARK 500 CB CYS A 172 O HOH A 2205 2.10 REMARK 500 NH2 ARG A 133 O HOH A 2159 2.12 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 GLU A 257 CD GLU A 257 OE1 0.075 REMARK 500 GLU A 257 CD GLU A 257 OE2 -0.082 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 30 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 99 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 106 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 MET A 398 CG - SD - CE ANGL. DEV. = -14.4 DEGREES REMARK 500 ARG A 409 NE - CZ - NH2 ANGL. DEV. = -3.5 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 72.57 -161.62 REMARK 500 VAL A 170 -59.09 -121.58 REMARK 500 THR A 272 -69.16 -121.11 REMARK 500 THR A 311 68.37 29.61 REMARK 500 PRO A 365 44.69 -85.88 REMARK 500 THR A 372 -174.32 69.76 REMARK 500 MET A 398 59.25 -147.75 REMARK 500 TRP A 414 -23.44 -142.23 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 A2043 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A2180 DISTANCE = 6.05 ANGSTROMS 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 A1431 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 377 SG REMARK 620 2 HEM A1431 NA 102.6 REMARK 620 3 HEM A1431 NB 96.3 89.9 REMARK 620 4 HEM A1431 NC 91.3 166.1 87.5 REMARK 620 5 HEM A1431 ND 103.2 88.1 160.4 89.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1428 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K2B A 1429 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1430 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 1431 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2X5L RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE TRUNCATED FORM OF CYP125A1 FROM M. REMARK 900 TUBERCULOSIS DBREF 2X5W A -6 0 PDB 2X5W 2X5W -6 0 DBREF 2X5W A 1 433 UNP P63709 CP125_MYCTU 1 433 SEQRES 1 A 440 MET HIS HIS HIS HIS HIS HIS MET SER TRP ASN HIS GLN SEQRES 2 A 440 SER VAL GLU ILE ALA VAL ARG ARG THR THR VAL PRO SER SEQRES 3 A 440 PRO ASN LEU PRO PRO GLY PHE ASP PHE THR ASP PRO ALA SEQRES 4 A 440 ILE TYR ALA GLU ARG LEU PRO VAL ALA GLU PHE ALA GLU SEQRES 5 A 440 LEU ARG SER ALA ALA PRO ILE TRP TRP ASN GLY GLN ASP SEQRES 6 A 440 PRO GLY LYS GLY GLY GLY PHE HIS ASP GLY GLY PHE TRP SEQRES 7 A 440 ALA ILE THR LYS LEU ASN ASP VAL LYS GLU ILE SER ARG SEQRES 8 A 440 HIS SER ASP VAL PHE SER SER TYR GLU ASN GLY VAL ILE SEQRES 9 A 440 PRO ARG PHE LYS ASN ASP ILE ALA ARG GLU ASP ILE GLU SEQRES 10 A 440 VAL GLN ARG PHE VAL MET LEU ASN MET ASP ALA PRO HIS SEQRES 11 A 440 HIS THR ARG LEU ARG LYS ILE ILE SER ARG GLY PHE THR SEQRES 12 A 440 PRO ARG ALA VAL GLY ARG LEU HIS ASP GLU LEU GLN GLU SEQRES 13 A 440 ARG ALA GLN LYS ILE ALA ALA GLU ALA ALA ALA ALA GLY SEQRES 14 A 440 SER GLY ASP PHE VAL GLU GLN VAL SER CYS GLU LEU PRO SEQRES 15 A 440 LEU GLN ALA ILE ALA GLY LEU LEU GLY VAL PRO GLN GLU SEQRES 16 A 440 ASP ARG GLY LYS LEU PHE HIS TRP SER ASN GLU MET THR SEQRES 17 A 440 GLY ASN GLU ASP PRO GLU TYR ALA HIS ILE ASP PRO LYS SEQRES 18 A 440 ALA SER SER ALA GLU LEU ILE GLY TYR ALA MET LYS MET SEQRES 19 A 440 ALA GLU GLU LYS ALA LYS ASN PRO ALA ASP ASP ILE VAL SEQRES 20 A 440 THR GLN LEU ILE GLN ALA ASP ILE ASP GLY GLU LYS LEU SEQRES 21 A 440 SER ASP ASP GLU PHE GLY PHE PHE VAL VAL MET LEU ALA SEQRES 22 A 440 VAL ALA GLY ASN GLU THR THR ARG ASN SER ILE THR GLN SEQRES 23 A 440 GLY MET MET ALA PHE ALA GLU HIS PRO ASP GLN TRP GLU SEQRES 24 A 440 LEU TYR LYS LYS VAL ARG PRO GLU THR ALA ALA ASP GLU SEQRES 25 A 440 ILE VAL ARG TRP ALA THR PRO VAL THR ALA PHE GLN ARG SEQRES 26 A 440 THR ALA LEU ARG ASP TYR GLU LEU SER GLY VAL GLN ILE SEQRES 27 A 440 LYS LYS GLY GLN ARG VAL VAL MET PHE TYR ARG SER ALA SEQRES 28 A 440 ASN PHE ASP GLU GLU VAL PHE GLN ASP PRO PHE THR PHE SEQRES 29 A 440 ASN ILE LEU ARG ASN PRO ASN PRO HIS VAL GLY PHE GLY SEQRES 30 A 440 GLY THR GLY ALA HIS TYR CYS ILE GLY ALA ASN LEU ALA SEQRES 31 A 440 ARG MET THR ILE ASN LEU ILE PHE ASN ALA VAL ALA ASP SEQRES 32 A 440 HIS MET PRO ASP LEU LYS PRO ILE SER ALA PRO GLU ARG SEQRES 33 A 440 LEU ARG SER GLY TRP LEU ASN GLY ILE LYS HIS TRP GLN SEQRES 34 A 440 VAL ASP TYR THR GLY ARG CYS PRO VAL ALA HIS HET SO4 A1428 5 HET K2B A1429 28 HET EDO A1430 4 HET HEM A1431 43 HETNAM SO4 SULFATE ION HETNAM K2B (8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE HETNAM EDO 1,2-ETHANEDIOL HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN EDO ETHYLENE GLYCOL HETSYN HEM HEME FORMUL 2 SO4 O4 S 2- FORMUL 3 K2B C27 H44 O FORMUL 4 EDO C2 H6 O2 FORMUL 5 HEM C34 H32 FE N4 O4 FORMUL 6 HOH *438(H2 O) HELIX 1 1 ASP A 30 ARG A 37 1 8 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 ARG A 133 1 12 HELIX 7 7 THR A 136 LEU A 143 1 8 HELIX 8 8 LEU A 143 ALA A 161 1 19 HELIX 9 9 PHE A 166 VAL A 170 1 5 HELIX 10 10 CYS A 172 GLY A 184 1 13 HELIX 11 11 PRO A 186 GLU A 188 5 3 HELIX 12 12 ASP A 189 GLY A 202 1 14 HELIX 13 13 ASP A 205 ALA A 209 5 5 HELIX 14 14 ASP A 212 ASN A 234 1 23 HELIX 15 15 ASP A 238 ALA A 246 1 9 HELIX 16 16 SER A 254 THR A 272 1 19 HELIX 17 17 THR A 272 HIS A 287 1 16 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 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 ASP A 247 ILE A 248 0 SHEET 2 AC 2 GLU A 251 LYS A 252 -1 O GLU A 251 N ILE A 248 SHEET 1 AD 2 TYR A 324 LEU A 326 0 SHEET 2 AD 2 VAL A 329 ILE A 331 -1 O VAL A 329 N LEU A 326 SHEET 1 AE 2 GLU A 408 ARG A 409 0 SHEET 2 AE 2 ILE A 418 HIS A 420 -1 N LYS A 419 O GLU A 408 LINK SG CYS A 377 FE HEM A1431 1555 1555 2.36 CISPEP 1 ALA A 121 PRO A 122 0 4.72 CISPEP 2 ASN A 362 PRO A 363 0 -3.18 SITE 1 AC1 8 ARG A 84 HIS A 85 HIS A 195 ASN A 198 SITE 2 AC1 8 TYR A 208 HOH A2226 HOH A2239 HOH A2432 SITE 1 AC2 10 ASP A 108 GLN A 112 MET A 200 PRO A 213 SITE 2 AC2 10 LYS A 214 VAL A 267 ALA A 268 TRP A 414 SITE 3 AC2 10 HEM A1431 HOH A2434 SITE 1 AC3 6 HIS A 210 TYR A 376 ALA A 380 ASN A 381 SITE 2 AC3 6 ARG A 384 HOH A2388 SITE 1 AC4 25 MET A 116 LEU A 117 HIS A 124 ARG A 128 SITE 2 AC4 25 ILE A 179 MET A 264 ALA A 268 THR A 272 SITE 3 AC4 25 THR A 273 PRO A 312 PHE A 316 ARG A 318 SITE 4 AC4 25 GLY A 368 PHE A 369 GLY A 370 HIS A 375 SITE 5 AC4 25 CYS A 377 ILE A 378 GLY A 379 ALA A 383 SITE 6 AC4 25 K2B A1429 HOH A2344 HOH A2436 HOH A2437 SITE 7 AC4 25 HOH A2438 CRYST1 73.666 75.977 79.592 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 0.013575 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013162 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012564 0.00000