HEADER TRANSFERASE 12-FEB-19 6QOE TITLE CRYSTAL STRUCTURE OF TRMD, A TRNA-(N1G37) METHYLTRANSFERASE, FROM TITLE 2 MYCOBACTERIUM ABSCESSUS IN COMPLEX WITH FRAGMENT 8 (3-[(2- TITLE 3 THIENYLTHIO)METHYL]BENZOIC ACID) 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 6QOE 1 REMARK REVDAT 3 26-AUG-20 6QOE 1 JRNL REVDAT 2 05-AUG-20 6QOE 1 JRNL REVDAT 1 04-MAR-20 6QOE 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. 3.06 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) : 3.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10225 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 508 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 58.7196 - 4.8523 0.99 2515 137 0.1789 0.2670 REMARK 3 2 4.8523 - 3.8517 1.00 2395 151 0.1674 0.2158 REMARK 3 3 3.8517 - 3.3649 1.00 2427 88 0.1918 0.3444 REMARK 3 4 3.3649 - 3.0572 1.00 2380 132 0.2494 0.3760 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) : 0.570 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.77 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 : 0.010 3336 REMARK 3 ANGLE : 1.303 4577 REMARK 3 CHIRALITY : 0.053 520 REMARK 3 PLANARITY : 0.007 598 REMARK 3 DIHEDRAL : 13.596 1209 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 15 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.6451 -13.4780 22.0363 REMARK 3 T TENSOR REMARK 3 T11: 0.4259 T22: 0.6923 REMARK 3 T33: 0.5264 T12: -0.0721 REMARK 3 T13: -0.0410 T23: 0.0206 REMARK 3 L TENSOR REMARK 3 L11: 3.7196 L22: 6.4878 REMARK 3 L33: 3.9184 L12: -1.6575 REMARK 3 L13: 0.2878 L23: -1.0050 REMARK 3 S TENSOR REMARK 3 S11: -0.0681 S12: -1.5691 S13: -0.2085 REMARK 3 S21: 1.4611 S22: 0.1707 S23: -0.3377 REMARK 3 S31: -0.0674 S32: -0.9424 S33: 0.0024 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 29 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.8563 -2.9390 31.8766 REMARK 3 T TENSOR REMARK 3 T11: 0.9758 T22: 1.2450 REMARK 3 T33: 1.4437 T12: 0.1589 REMARK 3 T13: 0.2619 T23: -0.3505 REMARK 3 L TENSOR REMARK 3 L11: 3.1418 L22: 8.1289 REMARK 3 L33: 3.0389 L12: -1.1621 REMARK 3 L13: 1.0508 L23: -0.5802 REMARK 3 S TENSOR REMARK 3 S11: 0.2390 S12: -0.4256 S13: 0.3396 REMARK 3 S21: 0.2401 S22: -0.7198 S23: -0.0013 REMARK 3 S31: -0.1777 S32: -1.1036 S33: 0.0613 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 30 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): -40.8183 -20.7520 15.2815 REMARK 3 T TENSOR REMARK 3 T11: 0.4666 T22: 0.5604 REMARK 3 T33: 0.5152 T12: -0.0669 REMARK 3 T13: 0.0387 T23: 0.1668 REMARK 3 L TENSOR REMARK 3 L11: 3.6868 L22: 1.7879 REMARK 3 L33: 3.0615 L12: 2.2770 REMARK 3 L13: 1.7795 L23: 1.1500 REMARK 3 S TENSOR REMARK 3 S11: 0.0998 S12: -0.1413 S13: -0.0248 REMARK 3 S21: 0.2261 S22: -0.0641 S23: 0.7952 REMARK 3 S31: 0.1575 S32: -0.3583 S33: 0.0635 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.7467 -17.7787 6.6262 REMARK 3 T TENSOR REMARK 3 T11: 0.2751 T22: 0.3420 REMARK 3 T33: 0.4382 T12: 0.0161 REMARK 3 T13: -0.0218 T23: 0.0448 REMARK 3 L TENSOR REMARK 3 L11: 2.9205 L22: 1.5519 REMARK 3 L33: 3.3693 L12: 0.8792 REMARK 3 L13: 0.4197 L23: 1.4628 REMARK 3 S TENSOR REMARK 3 S11: 0.0457 S12: -0.1736 S13: -0.1577 REMARK 3 S21: -0.2664 S22: -0.3023 S23: 0.6679 REMARK 3 S31: -0.1500 S32: -0.2760 S33: 0.1428 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 84 THROUGH 115 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.5877 -8.3523 12.5115 REMARK 3 T TENSOR REMARK 3 T11: 0.3367 T22: 0.4179 REMARK 3 T33: 0.3872 T12: 0.0724 REMARK 3 T13: -0.0553 T23: 0.0497 REMARK 3 L TENSOR REMARK 3 L11: 2.9395 L22: 1.0219 REMARK 3 L33: 3.4904 L12: -0.2126 REMARK 3 L13: -0.5073 L23: 1.6004 REMARK 3 S TENSOR REMARK 3 S11: -0.2949 S12: 0.0421 S13: 0.4637 REMARK 3 S21: 0.1353 S22: 0.1967 S23: -0.2165 REMARK 3 S31: -0.2460 S32: 0.2435 S33: 0.2011 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 116 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.5476 -11.4978 11.8298 REMARK 3 T TENSOR REMARK 3 T11: 0.3657 T22: 0.2807 REMARK 3 T33: 0.3252 T12: -0.0085 REMARK 3 T13: 0.0016 T23: -0.0506 REMARK 3 L TENSOR REMARK 3 L11: 2.0336 L22: 0.2049 REMARK 3 L33: 1.3146 L12: 0.2257 REMARK 3 L13: 0.3929 L23: 0.6517 REMARK 3 S TENSOR REMARK 3 S11: 0.0443 S12: 0.1215 S13: -0.0274 REMARK 3 S21: 0.0425 S22: -0.0658 S23: -0.1599 REMARK 3 S31: 0.0052 S32: 0.1495 S33: 0.0389 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 181 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.6309 -0.6660 25.4366 REMARK 3 T TENSOR REMARK 3 T11: 0.4274 T22: 0.4539 REMARK 3 T33: 0.8863 T12: -0.0581 REMARK 3 T13: 0.2554 T23: -0.1397 REMARK 3 L TENSOR REMARK 3 L11: 6.5976 L22: 0.6102 REMARK 3 L33: 0.5882 L12: -1.6687 REMARK 3 L13: -0.0228 L23: -0.1370 REMARK 3 S TENSOR REMARK 3 S11: -0.1033 S12: -0.2202 S13: 0.3665 REMARK 3 S21: 0.4234 S22: -0.3395 S23: 1.0598 REMARK 3 S31: -0.1503 S32: -0.3273 S33: -0.2021 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 182 THROUGH 227 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.9554 -3.1720 32.0923 REMARK 3 T TENSOR REMARK 3 T11: 0.3566 T22: 0.4179 REMARK 3 T33: 0.4229 T12: -0.0030 REMARK 3 T13: -0.0562 T23: -0.0491 REMARK 3 L TENSOR REMARK 3 L11: 1.4250 L22: 1.9738 REMARK 3 L33: 1.2067 L12: 0.8300 REMARK 3 L13: 0.5358 L23: 0.9550 REMARK 3 S TENSOR REMARK 3 S11: 0.0193 S12: 0.1039 S13: -0.2443 REMARK 3 S21: 0.1311 S22: 0.2814 S23: -0.1582 REMARK 3 S31: 0.1790 S32: 0.3795 S33: -0.3038 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 0 THROUGH 22 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.4424 -22.6613 32.5360 REMARK 3 T TENSOR REMARK 3 T11: 0.4932 T22: 0.6033 REMARK 3 T33: 0.4340 T12: -0.0371 REMARK 3 T13: 0.0284 T23: -0.0672 REMARK 3 L TENSOR REMARK 3 L11: 0.5478 L22: 4.6054 REMARK 3 L33: 2.3098 L12: 1.3656 REMARK 3 L13: 1.0758 L23: 2.3426 REMARK 3 S TENSOR REMARK 3 S11: -0.0389 S12: 0.1015 S13: -0.1267 REMARK 3 S21: -0.0857 S22: -0.2266 S23: 1.8864 REMARK 3 S31: 0.0677 S32: -0.4441 S33: 0.0953 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 23 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.3584 -26.0369 35.4220 REMARK 3 T TENSOR REMARK 3 T11: 0.3788 T22: 0.6361 REMARK 3 T33: 0.2707 T12: 0.0210 REMARK 3 T13: -0.0144 T23: 0.0221 REMARK 3 L TENSOR REMARK 3 L11: 2.6018 L22: 2.2011 REMARK 3 L33: 2.2398 L12: -0.8936 REMARK 3 L13: 0.3887 L23: -1.4860 REMARK 3 S TENSOR REMARK 3 S11: 0.0493 S12: -0.3126 S13: 0.1802 REMARK 3 S21: 0.7332 S22: -0.2846 S23: 0.6284 REMARK 3 S31: 0.1391 S32: -1.0273 S33: 0.1640 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 41 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.7278 -16.0355 34.0066 REMARK 3 T TENSOR REMARK 3 T11: 0.5300 T22: 0.3487 REMARK 3 T33: 0.3600 T12: 0.0487 REMARK 3 T13: -0.0409 T23: 0.0231 REMARK 3 L TENSOR REMARK 3 L11: 2.5237 L22: 1.3438 REMARK 3 L33: 2.1669 L12: 0.4718 REMARK 3 L13: 2.0733 L23: 1.5881 REMARK 3 S TENSOR REMARK 3 S11: 0.0306 S12: -0.2581 S13: -0.0972 REMARK 3 S21: 0.4148 S22: 0.0200 S23: -0.1249 REMARK 3 S31: 0.3783 S32: -0.1374 S33: -0.0635 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 101 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.8699 -17.8627 33.0051 REMARK 3 T TENSOR REMARK 3 T11: 0.4364 T22: 0.2527 REMARK 3 T33: 0.3931 T12: 0.0162 REMARK 3 T13: -0.0992 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 2.3822 L22: 3.1260 REMARK 3 L33: 4.1927 L12: 2.0891 REMARK 3 L13: 1.3958 L23: 0.5122 REMARK 3 S TENSOR REMARK 3 S11: 0.2855 S12: -0.0749 S13: 0.1471 REMARK 3 S21: 0.3569 S22: 0.0214 S23: -0.3546 REMARK 3 S31: 0.2803 S32: 0.1835 S33: -0.2535 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 132 THROUGH 182 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.8990 -19.7710 18.2910 REMARK 3 T TENSOR REMARK 3 T11: 0.3508 T22: 0.3018 REMARK 3 T33: 0.3539 T12: -0.0173 REMARK 3 T13: 0.0203 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 1.4332 L22: 0.5950 REMARK 3 L33: 1.6395 L12: -0.6779 REMARK 3 L13: 0.0921 L23: -0.9923 REMARK 3 S TENSOR REMARK 3 S11: -0.0499 S12: 0.2091 S13: -0.2469 REMARK 3 S21: -0.0418 S22: -0.0212 S23: -0.1773 REMARK 3 S31: 0.0857 S32: 0.1383 S33: 0.1161 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 183 THROUGH 222 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.0273 -21.8902 -6.2007 REMARK 3 T TENSOR REMARK 3 T11: 0.4610 T22: 0.5714 REMARK 3 T33: 0.5290 T12: 0.0097 REMARK 3 T13: 0.0538 T23: -0.1693 REMARK 3 L TENSOR REMARK 3 L11: 2.3679 L22: 1.4509 REMARK 3 L33: 1.5964 L12: -0.0520 REMARK 3 L13: 0.3948 L23: 0.2300 REMARK 3 S TENSOR REMARK 3 S11: -0.4756 S12: 0.5889 S13: -0.5854 REMARK 3 S21: -0.3146 S22: 0.3468 S23: 0.0449 REMARK 3 S31: 0.0052 S32: 0.1151 S33: 0.1261 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 223 THROUGH 232 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2148 -9.8664 1.6276 REMARK 3 T TENSOR REMARK 3 T11: 0.3253 T22: 0.3723 REMARK 3 T33: 0.3389 T12: 0.0120 REMARK 3 T13: 0.0033 T23: -0.0497 REMARK 3 L TENSOR REMARK 3 L11: 7.1338 L22: 6.6482 REMARK 3 L33: 8.1570 L12: 3.2910 REMARK 3 L13: -1.5055 L23: -3.2176 REMARK 3 S TENSOR REMARK 3 S11: 0.2677 S12: -0.7018 S13: 1.0449 REMARK 3 S21: 0.3717 S22: -0.2700 S23: -0.9984 REMARK 3 S31: -0.5728 S32: -0.2362 S33: 0.1416 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 6QOE 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_1292100517. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-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 : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10264 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.060 REMARK 200 RESOLUTION RANGE LOW (A) : 58.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.15900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.78800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 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 37.29800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.37900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.86950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.37900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.29800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.86950 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 ARG B 17 REMARK 465 GLN B 18 REMARK 465 SER B 19 REMARK 465 LEU B 20 REMARK 465 PRO B 21 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 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 LYS A 23 CG CD CE NZ REMARK 470 LEU A 29 CG CD1 CD2 REMARK 470 ARG A 39 NE CZ NH1 NH2 REMARK 470 TYR A 111 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU A 112 CG CD OE1 OE2 REMARK 470 GLU A 180 CD OE1 OE2 REMARK 470 GLU B 11 CG CD OE1 OE2 REMARK 470 LYS B 23 CG CD CE NZ REMARK 470 ILE B 25 CG1 CG2 CD1 REMARK 470 LEU B 29 CG CD1 CD2 REMARK 470 ASP B 31 CG OD1 OD2 REMARK 470 ARG B 39 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 44 CG1 CG2 REMARK 470 HIS B 45 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 46 CG CD CE NZ REMARK 470 GLU B 77 CD OE1 OE2 REMARK 470 VAL B 159 CG1 CG2 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 SER B 132 CA CB OG 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 CG PRO A 21 O VAL A 159 1.96 REMARK 500 O LEU B 179 OG SER B 215 2.01 REMARK 500 OG1 THR A 7 OE2 GLU A 142 2.08 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 LEU A 37 -14.31 -46.38 REMARK 500 LYS A 46 73.38 60.55 REMARK 500 TYR A 111 -138.49 49.55 REMARK 500 GLU A 112 32.34 -85.36 REMARK 500 ARG A 154 4.13 -69.72 REMARK 500 VAL A 159 -69.15 -102.37 REMARK 500 PRO A 182 150.18 -45.66 REMARK 500 LEU B 13 67.28 -69.37 REMARK 500 ALA B 27 51.76 -97.94 REMARK 500 TYR B 111 -140.51 57.96 REMARK 500 ALA B 123 -5.01 -57.38 REMARK 500 PRO B 157 113.60 -36.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JBB B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6NVR RELATED DB: PDB DBREF 6QOE A 1 242 UNP B1MDI3 B1MDI3_MYCA9 1 242 DBREF 6QOE B 1 242 UNP B1MDI3 B1MDI3_MYCA9 1 242 SEQADV 6QOE GLY A -1 UNP B1MDI3 EXPRESSION TAG SEQADV 6QOE SER A 0 UNP B1MDI3 EXPRESSION TAG SEQADV 6QOE GLY B -1 UNP B1MDI3 EXPRESSION TAG SEQADV 6QOE 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 JBB B 301 16 HETNAM JBB 3-(THIOPHEN-2-YLSULFANYLMETHYL)BENZOIC ACID FORMUL 3 JBB C12 H10 O2 S2 FORMUL 4 HOH *(H2 O) HELIX 1 AA1 PRO A 10 TYR A 12 5 3 HELIX 2 AA2 LEU A 13 GLN A 18 1 6 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 ASP A 115 ALA A 123 1 9 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 ARG B 38 THR B 41 5 4 HELIX 12 AB3 LYS B 62 CYS B 74 1 13 HELIX 13 AB4 THR B 91 SER B 99 1 9 HELIX 14 AB5 ASP B 115 ALA B 123 1 9 HELIX 15 AB6 GLY B 141 ARG B 154 1 14 HELIX 16 AB7 PRO B 196 GLY B 202 1 7 HELIX 17 AB8 ASP B 203 ARG B 223 1 21 HELIX 18 AB9 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 LEU B 104 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 127 N LEU B 80 SHEET 6 AA4 6 TYR B 88 PRO B 89 1 N TYR B 88 O SER B 132 SHEET 1 AA5 3 ASP B 49 ASP B 50 0 SHEET 2 AA5 3 VAL B 60 MET B 61 -1 O VAL B 60 N ASP B 50 SHEET 3 AA5 3 GLY B 113 ILE B 114 1 O GLY B 113 N MET B 61 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 6.70 CISPEP 2 ARG B 186 PRO B 187 0 4.83 SITE 1 AC1 13 PRO B 85 ARG B 110 TYR B 111 GLU B 112 SITE 2 AC1 13 GLY B 113 ILE B 114 SER B 132 ILE B 133 SITE 3 AC1 13 GLY B 134 TYR B 136 LEU B 138 GLY B 140 SITE 4 AC1 13 GLY B 141 CRYST1 74.596 79.739 86.758 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 0.013406 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012541 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011526 0.00000