HEADER OXIDOREDUCTASE 02-SEP-09 3IVY TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 TITLE 2 CYP125, P212121 CRYSTAL FORM 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 CHOLESTEROL, CYTOCHROME P450, TUBERCULOSIS, MONOOXYGENASE, HEME, KEYWDS 2 IRON, METAL-BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.J.MCLEAN,C.LEVY,A.W.MUNRO,D.LEYS REVDAT 5 06-SEP-23 3IVY 1 REMARK REVDAT 4 23-SEP-15 3IVY 1 REMARK REVDAT 3 13-JUL-11 3IVY 1 VERSN REVDAT 2 29-DEC-09 3IVY 1 JRNL REVDAT 1 03-NOV-09 3IVY 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. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 99798 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 5013 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.2290 - 4.1970 0.74 2558 154 0.1989 0.2192 REMARK 3 2 4.1970 - 3.3330 0.90 2981 161 0.1439 0.1735 REMARK 3 3 3.3330 - 2.9121 0.99 3247 176 0.1319 0.1579 REMARK 3 4 2.9121 - 2.6461 1.00 3236 193 0.1383 0.1725 REMARK 3 5 2.6461 - 2.4566 1.00 3247 163 0.1300 0.1779 REMARK 3 6 2.4566 - 2.3118 1.00 3242 167 0.1367 0.1650 REMARK 3 7 2.3118 - 2.1961 1.00 3272 150 0.1510 0.2327 REMARK 3 8 2.1961 - 2.1005 1.00 3230 162 0.1132 0.1566 REMARK 3 9 2.1005 - 2.0197 1.00 3217 178 0.1030 0.1633 REMARK 3 10 2.0197 - 1.9500 1.00 3217 160 0.1187 0.1729 REMARK 3 11 1.9500 - 1.8890 1.00 3231 156 0.1529 0.2188 REMARK 3 12 1.8890 - 1.8350 1.00 3213 179 0.1172 0.1706 REMARK 3 13 1.8350 - 1.7867 1.00 3202 170 0.1141 0.1979 REMARK 3 14 1.7867 - 1.7432 1.00 3211 172 0.1147 0.1835 REMARK 3 15 1.7432 - 1.7035 1.00 3216 151 0.1081 0.1704 REMARK 3 16 1.7035 - 1.6673 1.00 3196 169 0.1149 0.1749 REMARK 3 17 1.6673 - 1.6339 1.00 3189 190 0.1248 0.2035 REMARK 3 18 1.6339 - 1.6031 1.00 3227 149 0.1375 0.1810 REMARK 3 19 1.6031 - 1.5745 1.00 3151 195 0.1436 0.1982 REMARK 3 20 1.5745 - 1.5478 1.00 3210 153 0.1599 0.2283 REMARK 3 21 1.5478 - 1.5228 1.00 3220 178 0.1857 0.2665 REMARK 3 22 1.5228 - 1.4994 1.00 3153 159 0.1879 0.2328 REMARK 3 23 1.4994 - 1.4773 1.00 3202 160 0.2077 0.2344 REMARK 3 24 1.4773 - 1.4565 1.00 3204 164 0.2342 0.3045 REMARK 3 25 1.4565 - 1.4369 1.00 3156 178 0.2466 0.2690 REMARK 3 26 1.4369 - 1.4182 1.00 3206 178 0.2396 0.2871 REMARK 3 27 1.4182 - 1.4005 1.00 3149 162 0.2672 0.3250 REMARK 3 28 1.4005 - 1.3836 1.00 3196 190 0.2908 0.3248 REMARK 3 29 1.3836 - 1.3675 1.00 3143 161 0.3195 0.3555 REMARK 3 30 1.3675 - 1.3520 0.83 2663 135 0.3456 0.3892 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 72.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.033 3395 REMARK 3 ANGLE : 2.528 4645 REMARK 3 CHIRALITY : 0.189 474 REMARK 3 PLANARITY : 0.017 618 REMARK 3 DIHEDRAL : 17.733 1229 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3IVY 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_1000054932. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) SINGLE CRYSTAL REMARK 200 OPTICS : SINGLE CRYSTAL MONOCHROMATOR AND REMARK 200 TOROIDAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99798 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.38200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 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 1CPT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 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 30.01500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.81500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.01000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.81500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.01500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.01000 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 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 ARG A 142 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 226 CG 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 O ASP A 247 O HOH A 617 1.81 REMARK 500 ND1 HIS A 123 O HOH A 451 1.97 REMARK 500 CA GLY A 371 O HOH A 650 2.00 REMARK 500 SG CYS A 172 O HOH A 562 2.00 REMARK 500 O HOH A 612 O HOH A 959 2.04 REMARK 500 O THR A 372 O HOH A 613 2.04 REMARK 500 O HOH A 650 O HOH A 928 2.05 REMARK 500 O HOH A 462 O HOH A 1095 2.05 REMARK 500 C THR A 372 O HOH A 613 2.05 REMARK 500 O HOH A 614 O HOH A 925 2.05 REMARK 500 N GLY A 250 O HOH A 461 2.06 REMARK 500 O HOH A 637 O HOH A 1073 2.07 REMARK 500 O HOH A 464 O HOH A 1129 2.08 REMARK 500 O GLY A 371 O HOH A 613 2.11 REMARK 500 O HOH A 649 O HOH A 859 2.11 REMARK 500 O HOH A 962 O HOH A 1036 2.12 REMARK 500 CG GLU A 36 O HOH A 615 2.15 REMARK 500 O HOH A 700 O HOH A 1059 2.17 REMARK 500 O HOH A 495 O HOH A 1008 2.19 REMARK 500 O HOH A 663 O HOH A 710 2.19 REMARK 500 OD1 ASN A 55 O HOH A 612 2.19 REMARK 500 O HOH A 450 O HOH A 822 2.19 REMARK 500 N PRO A 20 O HOH A 622 2.19 REMARK 500 O HOH A 471 O HOH A 1017 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 462 O HOH A 902 2564 2.01 REMARK 500 O HOH A 462 O HOH A 990 2564 2.06 REMARK 500 O HOH A 462 O HOH A 878 2564 2.06 REMARK 500 O HOH A 462 O HOH A 919 2564 2.07 REMARK 500 O HOH A 590 O HOH A 1001 2564 2.11 REMARK 500 O HOH A 583 O HOH A 602 4455 2.13 REMARK 500 O HOH A 654 O HOH A 669 4555 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 36 CD GLU A 36 OE1 0.078 REMARK 500 ASN A 55 CG ASN A 55 OD1 0.145 REMARK 500 TYR A 92 CZ TYR A 92 CE2 0.091 REMARK 500 GLU A 107 CG GLU A 107 CD 0.105 REMARK 500 GLU A 107 CD GLU A 107 OE1 0.155 REMARK 500 LYS A 129 CD LYS A 129 CE 0.274 REMARK 500 LYS A 129 CE LYS A 129 NZ 0.236 REMARK 500 GLU A 168 CG GLU A 168 CD 0.121 REMARK 500 GLU A 168 CD GLU A 168 OE1 0.099 REMARK 500 GLU A 168 CD GLU A 168 OE2 0.068 REMARK 500 GLU A 204 CD GLU A 204 OE2 -0.071 REMARK 500 GLU A 219 CD GLU A 219 OE1 0.086 REMARK 500 ILE A 239 N ILE A 239 CA -0.144 REMARK 500 LYS A 252 CE LYS A 252 NZ 0.229 REMARK 500 GLU A 271 CD GLU A 271 OE2 0.112 REMARK 500 GLU A 286 CG GLU A 286 CD 0.094 REMARK 500 GLU A 286 CD GLU A 286 OE1 0.090 REMARK 500 ARG A 322 CZ ARG A 322 NH1 0.098 REMARK 500 GLU A 348 CD GLU A 348 OE2 0.071 REMARK 500 GLU A 349 CD GLU A 349 OE1 0.069 REMARK 500 GLY A 371 C GLY A 371 O -0.101 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 37 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 VAL A 111 CG1 - CB - CG2 ANGL. DEV. = -13.9 DEGREES REMARK 500 LYS A 129 CD - CE - NZ ANGL. DEV. = 21.0 DEGREES REMARK 500 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 145 CB - CG - OD1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ASP A 205 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 MET A 264 CG - SD - CE ANGL. DEV. = -13.5 DEGREES REMARK 500 GLU A 271 CG - CD - OE2 ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG A 274 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 298 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 308 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 322 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 322 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 342 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 GLY A 371 O - C - N ANGL. DEV. = -10.1 DEGREES REMARK 500 ARG A 384 NH1 - CZ - NH2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 384 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 409 NE - CZ - NH2 ANGL. DEV. = -3.6 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 70.92 -164.36 REMARK 500 ASN A 270 -80.23 -105.27 REMARK 500 THR A 311 70.85 33.18 REMARK 500 PRO A 365 47.32 -84.37 REMARK 500 TRP A 414 -22.16 -143.90 REMARK 500 TRP A 414 -23.45 -143.90 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 ASN A 55 0.07 SIDE CHAIN REMARK 500 GLU A 271 0.07 SIDE CHAIN REMARK 500 ARG A 409 0.08 SIDE CHAIN 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 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 377 SG REMARK 620 2 HEM A 501 NA 99.6 REMARK 620 3 HEM A 501 NB 92.8 89.2 REMARK 620 4 HEM A 501 NC 90.5 169.8 88.9 REMARK 620 5 HEM A 501 ND 99.5 88.2 167.8 91.4 REMARK 620 6 HOH A 610 O 167.9 77.8 75.5 92.0 92.3 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 501 REMARK 900 REMARK 900 RELATED ENTRIES 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: 3IW1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 REMARK 900 CYP125 IN COMPLEX WITH ANDROSTENEDIONE REMARK 900 RELATED ID: 3IW2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYTOCHROME P450 REMARK 900 CYP125 IN COMPLEX WITH ECONAZOLE DBREF 3IVY 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 HEM A 501 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *708(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 ASN A 198 1 10 HELIX 14 14 ASP A 205 ALA A 209 5 5 HELIX 15 15 ASP A 212 LYS A 231 1 20 HELIX 16 16 ILE A 239 GLN A 245 1 7 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 A 5 ILE A 52 GLY A 56 0 SHEET 2 A 5 GLY A 69 ILE A 73 -1 O PHE A 70 N ASN A 55 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 VAL A 329 N LEU A 326 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 501 1555 1555 2.41 LINK FE HEM A 501 O HOH A 610 1555 1555 2.22 CISPEP 1 ALA A 121 PRO A 122 0 3.25 CISPEP 2 ASN A 362 PRO A 363 0 -2.17 SITE 1 AC1 23 LEU A 117 HIS A 124 ARG A 128 MET A 264 SITE 2 AC1 23 ALA A 268 GLY A 269 THR A 272 THR A 273 SITE 3 AC1 23 SER A 276 PHE A 316 ARG A 318 GLY A 368 SITE 4 AC1 23 PHE A 369 GLY A 370 HIS A 375 CYS A 377 SITE 5 AC1 23 ILE A 378 GLY A 379 HOH A 610 HOH A 717 SITE 6 AC1 23 HOH A 721 HOH A 786 HOH A 943 CRYST1 60.030 86.020 89.630 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 0.016658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011625 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011157 0.00000