HEADER OXIDOREDUCTASE 12-NOV-19 6TET TITLE THE STRUCTURE OF CYP121 IN COMPLEX WITH INHIBITOR L21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYCOCYCLOSIN SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME P450 121,CYTOCHROME P450 MT2; COMPND 5 EC: 1.14.19.70; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: CYP121, MT2336; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYP121, COMPLEX, INHIBITOR, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.ADAM,J.KOEHNKE REVDAT 3 24-JAN-24 6TET 1 REMARK REVDAT 2 08-DEC-21 6TET 1 JRNL REMARK REVDAT 1 26-MAY-21 6TET 0 JRNL AUTH I.WALTER,S.ADAM,M.V.GENTILINI,A.M.KANY,C.BRENGEL,A.THOMANN, JRNL AUTH 2 T.SPARWASSER,J.KOHNKE,R.W.HARTMANN JRNL TITL STRUCTURE-ACTIVITY RELATIONSHIP AND MODE-OF-ACTION STUDIES JRNL TITL 2 HIGHLIGHT 1-(4-BIPHENYLYLMETHYL)-1H-IMIDAZOLE-DERIVED SMALL JRNL TITL 3 MOLECULES AS POTENT CYP121 INHIBITORS. JRNL REF CHEMMEDCHEM V. 16 2786 2021 JRNL REFN ESSN 1860-7187 JRNL PMID 34010508 JRNL DOI 10.1002/CMDC.202100283 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 67.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.355 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 76688 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.891 REMARK 3 FREE R VALUE TEST SET COUNT : 3751 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 67.3100 - 4.4992 1.00 3061 149 0.1733 0.2105 REMARK 3 2 4.4992 - 3.5712 1.00 2846 134 0.1408 0.1478 REMARK 3 3 3.5712 - 3.1198 1.00 2792 149 0.1596 0.1496 REMARK 3 4 3.1198 - 2.8345 1.00 2792 129 0.1622 0.2055 REMARK 3 5 2.8345 - 2.6313 1.00 2735 146 0.1538 0.1901 REMARK 3 6 2.6313 - 2.4762 1.00 2725 134 0.1507 0.1808 REMARK 3 7 2.4762 - 2.3522 1.00 2710 142 0.1477 0.1638 REMARK 3 8 2.3522 - 2.2498 1.00 2727 132 0.1431 0.1738 REMARK 3 9 2.2498 - 2.1632 1.00 2675 156 0.1495 0.1868 REMARK 3 10 2.1632 - 2.0885 1.00 2715 130 0.1642 0.1908 REMARK 3 11 2.0885 - 2.0232 1.00 2715 123 0.1728 0.1881 REMARK 3 12 2.0232 - 1.9654 1.00 2680 141 0.1850 0.2118 REMARK 3 13 1.9654 - 1.9136 1.00 2678 135 0.1905 0.2174 REMARK 3 14 1.9136 - 1.8669 1.00 2650 147 0.1945 0.2166 REMARK 3 15 1.8669 - 1.8245 1.00 2681 133 0.1994 0.2319 REMARK 3 16 1.8245 - 1.7857 1.00 2655 151 0.2176 0.2342 REMARK 3 17 1.7857 - 1.7499 1.00 2667 153 0.2130 0.2463 REMARK 3 18 1.7499 - 1.7169 1.00 2655 124 0.2362 0.2786 REMARK 3 19 1.7169 - 1.6863 1.00 2627 137 0.2355 0.2719 REMARK 3 20 1.6863 - 1.6577 1.00 2670 128 0.2458 0.2541 REMARK 3 21 1.6577 - 1.6309 1.00 2686 135 0.2617 0.2790 REMARK 3 22 1.6309 - 1.6058 1.00 2629 145 0.2689 0.3060 REMARK 3 23 1.6058 - 1.5822 1.00 2652 118 0.2741 0.3184 REMARK 3 24 1.5822 - 1.5599 1.00 2665 132 0.2716 0.2794 REMARK 3 25 1.5599 - 1.5388 1.00 2662 143 0.2601 0.3020 REMARK 3 26 1.5388 - 1.5189 1.00 2603 145 0.2706 0.2650 REMARK 3 27 1.5189 - 1.4999 0.99 2584 160 0.2613 0.2809 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.152 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.611 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.05 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 : 0.008 3195 REMARK 3 ANGLE : 0.963 4343 REMARK 3 CHIRALITY : 0.072 486 REMARK 3 PLANARITY : 0.007 565 REMARK 3 DIHEDRAL : 24.556 1195 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 5 THROUGH 66 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.8505 11.5951 8.5887 REMARK 3 T TENSOR REMARK 3 T11: 0.0953 T22: 0.1196 REMARK 3 T33: 0.1584 T12: -0.0180 REMARK 3 T13: -0.0049 T23: 0.0120 REMARK 3 L TENSOR REMARK 3 L11: 1.8958 L22: 1.4448 REMARK 3 L33: 2.0010 L12: 0.8703 REMARK 3 L13: -0.3806 L23: 0.8952 REMARK 3 S TENSOR REMARK 3 S11: -0.0058 S12: -0.1045 S13: -0.1121 REMARK 3 S21: 0.0332 S22: 0.0538 S23: -0.1798 REMARK 3 S31: -0.0571 S32: 0.2982 S33: -0.0431 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 67 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.7653 22.5544 8.8370 REMARK 3 T TENSOR REMARK 3 T11: 0.1765 T22: 0.0918 REMARK 3 T33: 0.1440 T12: 0.0268 REMARK 3 T13: -0.0105 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.6298 L22: 0.5416 REMARK 3 L33: 0.9929 L12: -0.3746 REMARK 3 L13: 0.0258 L23: -0.0404 REMARK 3 S TENSOR REMARK 3 S11: -0.0106 S12: -0.0006 S13: 0.0916 REMARK 3 S21: -0.0157 S22: -0.0060 S23: 0.0115 REMARK 3 S31: -0.2912 S32: -0.1361 S33: 0.0029 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 328 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.6662 24.7490 10.3349 REMARK 3 T TENSOR REMARK 3 T11: 0.2037 T22: 0.0752 REMARK 3 T33: 0.1237 T12: -0.0436 REMARK 3 T13: -0.0054 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 0.6163 L22: 0.6323 REMARK 3 L33: 0.8551 L12: -0.0454 REMARK 3 L13: -0.1581 L23: -0.0058 REMARK 3 S TENSOR REMARK 3 S11: 0.0270 S12: -0.0087 S13: 0.0385 REMARK 3 S21: 0.0252 S22: -0.0369 S23: 0.0009 REMARK 3 S31: -0.2908 S32: 0.0733 S33: 0.0156 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 329 THROUGH 396 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.2079 23.0655 20.6069 REMARK 3 T TENSOR REMARK 3 T11: 0.2103 T22: 0.0774 REMARK 3 T33: 0.1163 T12: -0.0242 REMARK 3 T13: -0.0130 T23: 0.0021 REMARK 3 L TENSOR REMARK 3 L11: 0.5049 L22: 0.4088 REMARK 3 L33: 1.0663 L12: 0.0433 REMARK 3 L13: -0.1631 L23: -0.2563 REMARK 3 S TENSOR REMARK 3 S11: -0.0013 S12: -0.0046 S13: 0.1009 REMARK 3 S21: 0.0629 S22: -0.0054 S23: -0.0376 REMARK 3 S31: -0.4314 S32: 0.0484 S33: -0.0036 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 6TET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105301. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : POINTLESS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76900 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 87.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1N40 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CALCIUM ACETATE, SODIUM ACETATE, PEG REMARK 280 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 176.48533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 88.24267 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 132.36400 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 44.12133 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 220.60667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 176.48533 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 88.24267 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 44.12133 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 132.36400 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 220.60667 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 941 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 948 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1005 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1060 LIES ON A SPECIAL POSITION. 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 THR A 2 REMARK 465 ALA A 3 REMARK 465 THR A 4 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ILE A 357 CD1 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 HOH A 918 O HOH A 939 1.98 REMARK 500 O1 EDO A 503 O HOH A 601 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 603 O HOH A 603 10665 1.91 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 PHE A 137 -69.51 -143.69 REMARK 500 ARG A 340 143.87 -171.76 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 A1063 DISTANCE = 6.10 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 A 509 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 345 SG REMARK 620 2 HEM A 509 NA 97.6 REMARK 620 3 HEM A 509 NB 89.3 90.7 REMARK 620 4 HEM A 509 NC 87.7 174.6 88.6 REMARK 620 5 HEM A 509 ND 94.8 88.5 175.9 91.8 REMARK 620 6 HOH A 692 O 174.7 87.0 88.0 87.6 87.9 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 EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue N5Z A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 509 DBREF 6TET A 1 396 UNP P9WPP6 CP121_MYCTO 1 396 SEQRES 1 A 396 MET THR ALA THR VAL LEU LEU GLU VAL PRO PHE SER ALA SEQRES 2 A 396 ARG GLY ASP ARG ILE PRO ASP ALA VAL ALA GLU LEU ARG SEQRES 3 A 396 THR ARG GLU PRO ILE ARG LYS VAL ARG THR ILE THR GLY SEQRES 4 A 396 ALA GLU ALA TRP LEU VAL SER SER TYR ALA LEU CYS THR SEQRES 5 A 396 GLN VAL LEU GLU ASP ARG ARG PHE SER MET LYS GLU THR SEQRES 6 A 396 ALA ALA ALA GLY ALA PRO ARG LEU ASN ALA LEU THR VAL SEQRES 7 A 396 PRO PRO GLU VAL VAL ASN ASN MET GLY ASN ILE ALA ASP SEQRES 8 A 396 ALA GLY LEU ARG LYS ALA VAL MET LYS ALA ILE THR PRO SEQRES 9 A 396 LYS ALA PRO GLY LEU GLU GLN PHE LEU ARG ASP THR ALA SEQRES 10 A 396 ASN SER LEU LEU ASP ASN LEU ILE THR GLU GLY ALA PRO SEQRES 11 A 396 ALA ASP LEU ARG ASN ASP PHE ALA ASP PRO LEU ALA THR SEQRES 12 A 396 ALA LEU HIS CYS LYS VAL LEU GLY ILE PRO GLN GLU ASP SEQRES 13 A 396 GLY PRO LYS LEU PHE ARG SER LEU SER ILE ALA PHE MET SEQRES 14 A 396 SER SER ALA ASP PRO ILE PRO ALA ALA LYS ILE ASN TRP SEQRES 15 A 396 ASP ARG ASP ILE GLU TYR MET ALA GLY ILE LEU GLU ASN SEQRES 16 A 396 PRO ASN ILE THR THR GLY LEU MET GLY GLU LEU SER ARG SEQRES 17 A 396 LEU ARG LYS ASP PRO ALA TYR SER HIS VAL SER ASP GLU SEQRES 18 A 396 LEU PHE ALA THR ILE GLY VAL THR PHE PHE GLY ALA GLY SEQRES 19 A 396 VAL ILE SER THR GLY SER PHE LEU THR THR ALA LEU ILE SEQRES 20 A 396 SER LEU ILE GLN ARG PRO GLN LEU ARG ASN LEU LEU HIS SEQRES 21 A 396 GLU LYS PRO GLU LEU ILE PRO ALA GLY VAL GLU GLU LEU SEQRES 22 A 396 LEU ARG ILE ASN LEU SER PHE ALA ASP GLY LEU PRO ARG SEQRES 23 A 396 LEU ALA THR ALA ASP ILE GLN VAL GLY ASP VAL LEU VAL SEQRES 24 A 396 ARG LYS GLY GLU LEU VAL LEU VAL LEU LEU GLU GLY ALA SEQRES 25 A 396 ASN PHE ASP PRO GLU HIS PHE PRO ASN PRO GLY SER ILE SEQRES 26 A 396 GLU LEU ASP ARG PRO ASN PRO THR SER HIS LEU ALA PHE SEQRES 27 A 396 GLY ARG GLY GLN HIS PHE CYS PRO GLY SER ALA LEU GLY SEQRES 28 A 396 ARG ARG HIS ALA GLN ILE GLY ILE GLU ALA LEU LEU LYS SEQRES 29 A 396 LYS MET PRO GLY VAL ASP LEU ALA VAL PRO ILE ASP GLN SEQRES 30 A 396 LEU VAL TRP ARG THR ARG PHE GLN ARG ARG ILE PRO GLU SEQRES 31 A 396 ARG LEU PRO VAL LEU TRP HET EDO A 501 10 HET N5Z A 502 36 HET EDO A 503 10 HET PGE A 504 24 HET EDO A 505 10 HET EDO A 506 10 HET EDO A 507 10 HET EDO A 508 10 HET HEM A 509 73 HETNAM EDO 1,2-ETHANEDIOL HETNAM N5Z 1-[(~{E})-3-[4-(4-FLUOROPHENYL)PHENYL]PROP-2- HETNAM 2 N5Z ENYL]IMIDAZOLE HETNAM PGE TRIETHYLENE GLYCOL HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN EDO ETHYLENE GLYCOL HETSYN HEM HEME FORMUL 2 EDO 6(C2 H6 O2) FORMUL 3 N5Z C18 H15 F N2 FORMUL 5 PGE C6 H14 O4 FORMUL 10 HEM C34 H32 FE N4 O4 FORMUL 11 HOH *463(H2 O) HELIX 1 AA1 ASP A 20 GLU A 29 1 10 HELIX 2 AA2 SER A 47 ASP A 57 1 11 HELIX 3 AA3 MET A 62 ALA A 67 5 6 HELIX 4 AA4 PRO A 79 VAL A 83 5 5 HELIX 5 AA5 ASN A 84 ALA A 92 1 9 HELIX 6 AA6 LEU A 94 ILE A 102 1 9 HELIX 7 AA7 GLY A 108 GLY A 128 1 21 HELIX 8 AA8 PHE A 137 GLY A 151 1 15 HELIX 9 AA9 PRO A 153 GLU A 155 5 3 HELIX 10 AB1 ASP A 156 SER A 163 1 8 HELIX 11 AB2 SER A 163 PHE A 168 1 6 HELIX 12 AB3 ILE A 175 GLU A 194 1 20 HELIX 13 AB4 THR A 200 LYS A 211 1 12 HELIX 14 AB5 ASP A 212 SER A 216 5 5 HELIX 15 AB6 SER A 219 GLN A 251 1 33 HELIX 16 AB7 ARG A 252 LYS A 262 1 11 HELIX 17 AB8 LEU A 265 ILE A 276 1 12 HELIX 18 AB9 LEU A 308 PHE A 314 1 7 HELIX 19 AC1 ARG A 340 PHE A 344 5 5 HELIX 20 AC2 GLY A 347 MET A 366 1 20 HELIX 21 AC3 PRO A 374 LEU A 378 5 5 SHEET 1 AA1 5 ILE A 31 ARG A 35 0 SHEET 2 AA1 5 GLU A 41 VAL A 45 -1 O LEU A 44 N ARG A 32 SHEET 3 AA1 5 LEU A 304 VAL A 307 1 O LEU A 306 N TRP A 43 SHEET 4 AA1 5 LEU A 284 ALA A 288 -1 N ARG A 286 O VAL A 305 SHEET 5 AA1 5 PHE A 60 SER A 61 -1 N SER A 61 O LEU A 287 SHEET 1 AA2 3 ALA A 131 ASP A 132 0 SHEET 2 AA2 3 PRO A 393 LEU A 395 -1 O VAL A 394 N ALA A 131 SHEET 3 AA2 3 ASP A 370 LEU A 371 -1 N ASP A 370 O LEU A 395 SHEET 1 AA3 2 ILE A 292 VAL A 294 0 SHEET 2 AA3 2 VAL A 297 VAL A 299 -1 O VAL A 297 N VAL A 294 LINK SG CYS A 345 FE HEM A 509 1555 1555 2.31 LINK FE HEM A 509 O HOH A 692 1555 1555 2.25 CISPEP 1 VAL A 9 PRO A 10 0 -3.78 CISPEP 2 ALA A 129 PRO A 130 0 0.98 SITE 1 AC1 5 SER A 216 ASP A 220 ASP A 328 PRO A 330 SITE 2 AC1 5 HOH A 647 SITE 1 AC2 13 THR A 77 VAL A 78 ALA A 167 PHE A 168 SITE 2 AC2 13 ALA A 178 ASN A 181 TRP A 182 THR A 229 SITE 3 AC2 13 PHE A 280 ARG A 386 EDO A 503 HEM A 509 SITE 4 AC2 13 HOH A 692 SITE 1 AC3 6 VAL A 83 N5Z A 502 HEM A 509 HOH A 601 SITE 2 AC3 6 HOH A 875 HOH A 957 SITE 1 AC4 6 VAL A 5 ALA A 288 THR A 289 LYS A 301 SITE 2 AC4 6 GLY A 302 HOH A1003 SITE 1 AC5 3 THR A 27 ASP A 296 HOH A 960 SITE 1 AC6 5 SER A 248 GLN A 251 ARG A 252 ILE A 276 SITE 2 AC6 5 HOH A 640 SITE 1 AC7 2 LYS A 63 GLU A 64 SITE 1 AC8 3 LEU A 160 ARG A 184 ASP A 185 SITE 1 AC9 22 MET A 62 MET A 86 HIS A 146 GLY A 234 SITE 2 AC9 22 SER A 237 PHE A 241 PHE A 280 LEU A 284 SITE 3 AC9 22 ARG A 286 ALA A 337 PHE A 338 GLY A 339 SITE 4 AC9 22 HIS A 343 CYS A 345 PRO A 346 N5Z A 502 SITE 5 AC9 22 EDO A 503 HOH A 646 HOH A 692 HOH A 701 SITE 6 AC9 22 HOH A 713 HOH A 786 CRYST1 77.726 77.726 264.728 90.00 90.00 120.00 P 65 2 2 12 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 0.012866 0.007428 0.000000 0.00000 SCALE2 0.000000 0.014856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003777 0.00000