HEADER TRANSFERASE 12-FEB-19 6QOX TITLE CRYSTAL STRUCTURE OF TRMD, A TRNA-(N1G37) METHYLTRANSFERASE, FROM TITLE 2 MYCOBACTERIUM ABSCESSUS IN COMPLEX WITH FRAGMENT 27 (METHYL 2- TITLE 3 (HYDROXYMETHYL)-6H-THIENO[2,3-B]PYRROLE-5-CARBOXYLATE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: M1G-METHYLTRANSFERASE,TRNA [GM37] METHYLTRANSFERASE; COMPND 5 EC: 2.1.1.228; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM ABSCESSUS; SOURCE 3 ORGANISM_TAXID: 36809; SOURCE 4 ATCC: 19977; SOURCE 5 GENE: TRMD, MAB_3226C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRMD, TRNA METHYLTRANSFERASE, SPOUT METHYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.E.THOMAS,A.J.WHITEHOUSE,A.G.COYNE,C.ABELL,V.MENDES,T.L.BLUNDELL REVDAT 4 15-MAY-24 6QOX 1 REMARK REVDAT 3 26-AUG-20 6QOX 1 JRNL REVDAT 2 05-AUG-20 6QOX 1 JRNL REVDAT 1 26-FEB-20 6QOX 0 JRNL AUTH S.E.THOMAS,A.J.WHITEHOUSE,K.BROWN,S.BURBAUD, JRNL AUTH 2 J.M.BELARDINELLI,J.SANGEN,R.LAHIRI,M.D.J.LIBARDO,P.GUPTA, JRNL AUTH 3 S.MALHOTRA,H.I.M.BOSHOFF,M.JACKSON,C.ABELL,A.G.COYNE, JRNL AUTH 4 T.L.BLUNDELL,R.A.FLOTO,V.MENDES JRNL TITL FRAGMENT-BASED DISCOVERY OF A NEW CLASS OF INHIBITORS JRNL TITL 2 TARGETING MYCOBACTERIAL TRNA MODIFICATION. JRNL REF NUCLEIC ACIDS RES. V. 48 8099 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32602532 JRNL DOI 10.1093/NAR/GKAA539 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 54299 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 2787 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 58.7383 - 4.7193 1.00 2754 154 0.1773 0.1876 REMARK 3 2 4.7193 - 3.7461 1.00 2640 144 0.1486 0.1933 REMARK 3 3 3.7461 - 3.2726 1.00 2618 142 0.1741 0.1980 REMARK 3 4 3.2726 - 2.9734 1.00 2610 138 0.1964 0.2183 REMARK 3 5 2.9734 - 2.7603 1.00 2589 132 0.2061 0.2311 REMARK 3 6 2.7603 - 2.5975 1.00 2590 129 0.2028 0.2324 REMARK 3 7 2.5975 - 2.4674 1.00 2561 133 0.1909 0.2278 REMARK 3 8 2.4674 - 2.3600 1.00 2573 147 0.1878 0.2271 REMARK 3 9 2.3600 - 2.2692 1.00 2527 160 0.1829 0.2213 REMARK 3 10 2.2692 - 2.1909 1.00 2555 150 0.1834 0.2301 REMARK 3 11 2.1909 - 2.1224 1.00 2541 150 0.1912 0.2113 REMARK 3 12 2.1224 - 2.0617 1.00 2566 140 0.1893 0.2034 REMARK 3 13 2.0617 - 2.0074 1.00 2551 134 0.1929 0.2193 REMARK 3 14 2.0074 - 1.9584 1.00 2561 136 0.1862 0.2436 REMARK 3 15 1.9584 - 1.9139 1.00 2534 127 0.1983 0.2314 REMARK 3 16 1.9139 - 1.8732 1.00 2544 133 0.2056 0.2769 REMARK 3 17 1.8732 - 1.8357 1.00 2559 135 0.2148 0.2570 REMARK 3 18 1.8357 - 1.8011 1.00 2531 151 0.2413 0.2915 REMARK 3 19 1.8011 - 1.7689 1.00 2550 138 0.2556 0.3042 REMARK 3 20 1.7689 - 1.7389 1.00 2558 114 0.2769 0.3080 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.96 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 : 0.009 3363 REMARK 3 ANGLE : 1.020 4611 REMARK 3 CHIRALITY : 0.048 523 REMARK 3 PLANARITY : 0.005 599 REMARK 3 DIHEDRAL : 11.735 1225 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.7396 93.9982 14.8897 REMARK 3 T TENSOR REMARK 3 T11: 0.2095 T22: 0.2884 REMARK 3 T33: 0.2413 T12: 0.0077 REMARK 3 T13: 0.0007 T23: -0.0270 REMARK 3 L TENSOR REMARK 3 L11: 2.2019 L22: 3.2780 REMARK 3 L33: 2.3897 L12: 0.2983 REMARK 3 L13: -0.5631 L23: -0.7164 REMARK 3 S TENSOR REMARK 3 S11: -0.0027 S12: -0.2686 S13: 0.0244 REMARK 3 S21: 0.3246 S22: 0.0951 S23: 0.0168 REMARK 3 S31: -0.1232 S32: 0.1220 S33: -0.1162 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 84 THROUGH 181 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.3311 87.4614 13.2162 REMARK 3 T TENSOR REMARK 3 T11: 0.1926 T22: 0.1828 REMARK 3 T33: 0.2047 T12: 0.0128 REMARK 3 T13: -0.0142 T23: 0.0204 REMARK 3 L TENSOR REMARK 3 L11: 3.5505 L22: 0.0282 REMARK 3 L33: 2.1592 L12: 0.2508 REMARK 3 L13: -1.9653 L23: 0.0558 REMARK 3 S TENSOR REMARK 3 S11: -0.1040 S12: -0.0336 S13: -0.1601 REMARK 3 S21: 0.0146 S22: 0.0729 S23: 0.0288 REMARK 3 S31: 0.1375 S32: -0.0557 S33: 0.0072 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 182 THROUGH 227 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.6877 81.8811 33.0319 REMARK 3 T TENSOR REMARK 3 T11: 0.2342 T22: 0.2699 REMARK 3 T33: 0.2354 T12: 0.0225 REMARK 3 T13: -0.0098 T23: 0.0229 REMARK 3 L TENSOR REMARK 3 L11: 1.0087 L22: 1.9583 REMARK 3 L33: 1.3301 L12: 0.7503 REMARK 3 L13: -0.5012 L23: -1.2586 REMARK 3 S TENSOR REMARK 3 S11: -0.0182 S12: 0.0955 S13: 0.0905 REMARK 3 S21: 0.0254 S22: 0.1534 S23: 0.2419 REMARK 3 S31: -0.0242 S32: -0.4024 S33: -0.1269 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 0 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3892 96.3079 37.1069 REMARK 3 T TENSOR REMARK 3 T11: 0.3361 T22: 0.3391 REMARK 3 T33: 0.2697 T12: -0.0003 REMARK 3 T13: -0.0124 T23: -0.0233 REMARK 3 L TENSOR REMARK 3 L11: 3.4460 L22: 5.0864 REMARK 3 L33: 2.2386 L12: 1.8661 REMARK 3 L13: -0.2850 L23: -1.6473 REMARK 3 S TENSOR REMARK 3 S11: 0.0311 S12: -0.2760 S13: 0.0346 REMARK 3 S21: 0.3587 S22: -0.2941 S23: -0.6831 REMARK 3 S31: -0.3888 S32: 0.3712 S33: 0.2733 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 63 THROUGH 182 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.0977 98.2472 27.1266 REMARK 3 T TENSOR REMARK 3 T11: 0.2555 T22: 0.2115 REMARK 3 T33: 0.2421 T12: 0.0393 REMARK 3 T13: 0.0028 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 1.2577 L22: 0.9669 REMARK 3 L33: 2.2497 L12: 0.2839 REMARK 3 L13: -0.7148 L23: -0.5826 REMARK 3 S TENSOR REMARK 3 S11: -0.0080 S12: -0.0726 S13: 0.1353 REMARK 3 S21: 0.2063 S22: 0.0659 S23: 0.0557 REMARK 3 S31: -0.1904 S32: -0.0415 S33: -0.0436 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 183 THROUGH 231 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.1270 97.6486 -4.9808 REMARK 3 T TENSOR REMARK 3 T11: 0.2802 T22: 0.4378 REMARK 3 T33: 0.2883 T12: -0.0330 REMARK 3 T13: -0.0418 T23: 0.0745 REMARK 3 L TENSOR REMARK 3 L11: 4.0200 L22: 0.4880 REMARK 3 L33: 0.2703 L12: 0.9472 REMARK 3 L13: -1.0619 L23: -0.3042 REMARK 3 S TENSOR REMARK 3 S11: -0.2125 S12: 0.8027 S13: 0.3317 REMARK 3 S21: -0.2644 S22: 0.2487 S23: 0.1858 REMARK 3 S31: 0.0209 S32: -0.1652 S33: -0.0116 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 6QOX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1292100586. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-DEC-15 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 : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9282 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54370 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 REMARK 200 RESOLUTION RANGE LOW (A) : 88.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.79900 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 2.5.7 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08M SODIUM CACODYLATE PH 6.5 -7.0, 1 REMARK 280 -2 M AMMONIUM SULPHATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K 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 37.48150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.24150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.23000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.24150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.48150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.23000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLY A -1 REMARK 465 GLY A 161 REMARK 465 ASN A 162 REMARK 465 ALA A 163 REMARK 465 LEU A 164 REMARK 465 SER A 165 REMARK 465 ALA A 166 REMARK 465 GLN A 167 REMARK 465 GLU A 168 REMARK 465 ASP A 169 REMARK 465 SER A 170 REMARK 465 HIS A 171 REMARK 465 SER A 172 REMARK 465 GLU A 173 REMARK 465 GLY A 174 REMARK 465 MET A 175 REMARK 465 ALA A 176 REMARK 465 GLY A 228 REMARK 465 PHE A 229 REMARK 465 ASP A 230 REMARK 465 SER A 231 REMARK 465 PRO A 232 REMARK 465 THR A 233 REMARK 465 GLY A 234 REMARK 465 GLU A 235 REMARK 465 HIS A 236 REMARK 465 GLY A 237 REMARK 465 GLY A 238 REMARK 465 ASP A 239 REMARK 465 GLY A 240 REMARK 465 LEU A 241 REMARK 465 SER A 242 REMARK 465 GLY B -1 REMARK 465 GLN B 18 REMARK 465 SER B 19 REMARK 465 LEU B 160 REMARK 465 GLY B 161 REMARK 465 ASN B 162 REMARK 465 ALA B 163 REMARK 465 LEU B 164 REMARK 465 SER B 165 REMARK 465 ALA B 166 REMARK 465 GLN B 167 REMARK 465 GLU B 168 REMARK 465 ASP B 169 REMARK 465 SER B 170 REMARK 465 HIS B 171 REMARK 465 SER B 172 REMARK 465 GLU B 173 REMARK 465 GLY B 174 REMARK 465 MET B 175 REMARK 465 ALA B 176 REMARK 465 PRO B 232 REMARK 465 THR B 233 REMARK 465 GLY B 234 REMARK 465 GLU B 235 REMARK 465 HIS B 236 REMARK 465 GLY B 237 REMARK 465 GLY B 238 REMARK 465 ASP B 239 REMARK 465 GLY B 240 REMARK 465 LEU B 241 REMARK 465 SER B 242 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 GLN A 14 CG CD OE1 NE2 REMARK 470 ARG A 17 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 18 CG CD OE1 NE2 REMARK 470 LYS A 23 CG CD CE NZ REMARK 470 ARG A 39 CZ NH1 NH2 REMARK 470 LEU A 160 CG CD1 CD2 REMARK 470 GLU A 180 CD OE1 OE2 REMARK 470 ARG A 216 NE CZ NH1 NH2 REMARK 470 GLN B 14 CD OE1 NE2 REMARK 470 ARG B 17 NE CZ NH1 NH2 REMARK 470 LEU B 20 CG CD1 CD2 REMARK 470 LYS B 23 CG CD CE NZ REMARK 470 ASP B 26 CG OD1 OD2 REMARK 470 LEU B 29 CG CD1 CD2 REMARK 470 VAL B 44 CG1 CG2 REMARK 470 HIS B 45 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 46 CE NZ REMARK 470 GLU B 77 CD OE1 OE2 REMARK 470 VAL B 159 CG1 CG2 REMARK 470 LYS B 206 CE NZ 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 TYR A 111 -121.44 53.99 REMARK 500 PRO A 157 107.47 -51.07 REMARK 500 TYR B 111 -132.08 52.14 REMARK 500 ASP B 135 67.30 -102.20 REMARK 500 PRO B 157 107.15 -55.58 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 B 542 DISTANCE = 6.20 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JA5 B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6NVR RELATED DB: PDB DBREF 6QOX A 1 242 UNP B1MDI3 B1MDI3_MYCA9 1 242 DBREF 6QOX B 1 242 UNP B1MDI3 B1MDI3_MYCA9 1 242 SEQADV 6QOX GLY A -1 UNP B1MDI3 EXPRESSION TAG SEQADV 6QOX SER A 0 UNP B1MDI3 EXPRESSION TAG SEQADV 6QOX GLY B -1 UNP B1MDI3 EXPRESSION TAG SEQADV 6QOX SER B 0 UNP B1MDI3 EXPRESSION TAG SEQRES 1 A 244 GLY SER MET LYS ILE ASP VAL VAL THR ILE PHE PRO GLU SEQRES 2 A 244 TYR LEU GLN PRO VAL ARG GLN SER LEU PRO GLY LYS ALA SEQRES 3 A 244 ILE ASP ALA GLY LEU VAL ASP VAL ALA VAL HIS ASP LEU SEQRES 4 A 244 ARG ARG TRP THR HIS ASP VAL HIS LYS SER VAL ASP ASP SEQRES 5 A 244 SER PRO TYR GLY GLY GLY PRO GLY MET VAL MET LYS PRO SEQRES 6 A 244 THR VAL TRP GLY ASP ALA LEU ASP GLU ILE CYS THR SER SEQRES 7 A 244 GLU THR LEU LEU VAL VAL PRO THR PRO ALA GLY TYR PRO SEQRES 8 A 244 PHE THR GLN GLU THR ALA TRP GLN TRP SER THR GLU ASP SEQRES 9 A 244 HIS LEU VAL ILE ALA CYS GLY ARG TYR GLU GLY ILE ASP SEQRES 10 A 244 GLN ARG VAL ALA ASP ASP ALA ALA THR ARG MET ARG VAL SEQRES 11 A 244 ARG GLU VAL SER ILE GLY ASP TYR VAL LEU ASN GLY GLY SEQRES 12 A 244 GLU ALA ALA ALA LEU VAL ILE ILE GLU ALA VAL LEU ARG SEQRES 13 A 244 LEU VAL PRO GLY VAL LEU GLY ASN ALA LEU SER ALA GLN SEQRES 14 A 244 GLU ASP SER HIS SER GLU GLY MET ALA SER LEU LEU GLU SEQRES 15 A 244 GLY PRO SER TYR THR ARG PRO PRO SER TRP ARG GLY MET SEQRES 16 A 244 ASP VAL PRO PRO VAL LEU LEU SER GLY ASP HIS ALA LYS SEQRES 17 A 244 ILE ALA ALA TRP ARG ALA GLU GLN SER ARG GLN ARG THR SEQRES 18 A 244 ILE GLU ARG ARG PRO ASP LEU LEU GLY PHE ASP SER PRO SEQRES 19 A 244 THR GLY GLU HIS GLY GLY ASP GLY LEU SER SEQRES 1 B 244 GLY SER MET LYS ILE ASP VAL VAL THR ILE PHE PRO GLU SEQRES 2 B 244 TYR LEU GLN PRO VAL ARG GLN SER LEU PRO GLY LYS ALA SEQRES 3 B 244 ILE ASP ALA GLY LEU VAL ASP VAL ALA VAL HIS ASP LEU SEQRES 4 B 244 ARG ARG TRP THR HIS ASP VAL HIS LYS SER VAL ASP ASP SEQRES 5 B 244 SER PRO TYR GLY GLY GLY PRO GLY MET VAL MET LYS PRO SEQRES 6 B 244 THR VAL TRP GLY ASP ALA LEU ASP GLU ILE CYS THR SER SEQRES 7 B 244 GLU THR LEU LEU VAL VAL PRO THR PRO ALA GLY TYR PRO SEQRES 8 B 244 PHE THR GLN GLU THR ALA TRP GLN TRP SER THR GLU ASP SEQRES 9 B 244 HIS LEU VAL ILE ALA CYS GLY ARG TYR GLU GLY ILE ASP SEQRES 10 B 244 GLN ARG VAL ALA ASP ASP ALA ALA THR ARG MET ARG VAL SEQRES 11 B 244 ARG GLU VAL SER ILE GLY ASP TYR VAL LEU ASN GLY GLY SEQRES 12 B 244 GLU ALA ALA ALA LEU VAL ILE ILE GLU ALA VAL LEU ARG SEQRES 13 B 244 LEU VAL PRO GLY VAL LEU GLY ASN ALA LEU SER ALA GLN SEQRES 14 B 244 GLU ASP SER HIS SER GLU GLY MET ALA SER LEU LEU GLU SEQRES 15 B 244 GLY PRO SER TYR THR ARG PRO PRO SER TRP ARG GLY MET SEQRES 16 B 244 ASP VAL PRO PRO VAL LEU LEU SER GLY ASP HIS ALA LYS SEQRES 17 B 244 ILE ALA ALA TRP ARG ALA GLU GLN SER ARG GLN ARG THR SEQRES 18 B 244 ILE GLU ARG ARG PRO ASP LEU LEU GLY PHE ASP SER PRO SEQRES 19 B 244 THR GLY GLU HIS GLY GLY ASP GLY LEU SER HET JA5 B 301 14 HETNAM JA5 METHYL 2-(HYDROXYMETHYL)-6~{H}-THIENO[2,3-B]PYRROLE-5- HETNAM 2 JA5 CARBOXYLATE FORMUL 3 JA5 C9 H9 N O3 S FORMUL 4 HOH *287(H2 O) HELIX 1 AA1 PHE A 9 TYR A 12 5 4 HELIX 2 AA2 LEU A 13 LEU A 20 1 8 HELIX 3 AA3 PRO A 21 ALA A 27 1 7 HELIX 4 AA4 ARG A 38 THR A 41 5 4 HELIX 5 AA5 LYS A 62 CYS A 74 1 13 HELIX 6 AA6 THR A 91 SER A 99 1 9 HELIX 7 AA7 GLN A 116 ALA A 123 1 8 HELIX 8 AA8 GLY A 141 ARG A 154 1 14 HELIX 9 AA9 PRO A 196 SER A 201 5 6 HELIX 10 AB1 ASP A 203 ARG A 223 1 21 HELIX 11 AB2 PRO A 224 LEU A 227 5 4 HELIX 12 AB3 PHE B 9 ARG B 17 5 9 HELIX 13 AB4 PRO B 21 ALA B 27 1 7 HELIX 14 AB5 ARG B 38 THR B 41 5 4 HELIX 15 AB6 LYS B 62 CYS B 74 1 13 HELIX 16 AB7 THR B 91 SER B 99 1 9 HELIX 17 AB8 GLN B 116 ALA B 123 1 8 HELIX 18 AB9 GLY B 141 ARG B 154 1 14 HELIX 19 AC1 PRO B 196 SER B 201 5 6 HELIX 20 AC2 ASP B 203 ARG B 223 1 21 HELIX 21 AC3 PRO B 224 GLY B 228 5 5 SHEET 1 AA1 6 VAL A 30 ASP A 36 0 SHEET 2 AA1 6 MET A 1 THR A 7 1 N VAL A 5 O HIS A 35 SHEET 3 AA1 6 HIS A 103 ALA A 107 1 O ILE A 106 N ASP A 4 SHEET 4 AA1 6 LEU A 79 PRO A 83 1 N VAL A 81 O VAL A 105 SHEET 5 AA1 6 ARG A 127 SER A 132 1 O ARG A 129 N LEU A 80 SHEET 6 AA1 6 TYR A 88 PRO A 89 1 N TYR A 88 O SER A 132 SHEET 1 AA2 2 ASP A 49 ASP A 50 0 SHEET 2 AA2 2 VAL A 60 MET A 61 -1 O VAL A 60 N ASP A 50 SHEET 1 AA3 2 SER A 189 TRP A 190 0 SHEET 2 AA3 2 MET A 193 ASP A 194 -1 O MET A 193 N TRP A 190 SHEET 1 AA4 6 VAL B 30 ASP B 36 0 SHEET 2 AA4 6 MET B 1 THR B 7 1 N VAL B 5 O HIS B 35 SHEET 3 AA4 6 HIS B 103 ALA B 107 1 O ILE B 106 N ASP B 4 SHEET 4 AA4 6 LEU B 79 PRO B 83 1 N VAL B 81 O VAL B 105 SHEET 5 AA4 6 ARG B 127 SER B 132 1 O ARG B 129 N LEU B 80 SHEET 6 AA4 6 TYR B 88 PRO B 89 1 N TYR B 88 O GLU B 130 SHEET 1 AA5 2 ASP B 49 ASP B 50 0 SHEET 2 AA5 2 VAL B 60 MET B 61 -1 O VAL B 60 N ASP B 50 SHEET 1 AA6 2 SER B 189 TRP B 190 0 SHEET 2 AA6 2 MET B 193 ASP B 194 -1 O MET B 193 N TRP B 190 CISPEP 1 ARG A 186 PRO A 187 0 4.13 CISPEP 2 ARG A 186 PRO A 187 0 3.64 CISPEP 3 ARG B 186 PRO B 187 0 1.17 SITE 1 AC1 10 PRO B 83 PRO B 85 GLY B 109 ARG B 110 SITE 2 AC1 10 SER B 132 ILE B 133 GLY B 134 ASN B 139 SITE 3 AC1 10 GLY B 140 HOH B 510 CRYST1 74.963 78.460 88.483 90.00 90.00 90.00 P 21 21 21 8 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 0.013340 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012745 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011302 0.00000