HEADER TRANSFERASE 06-FEB-19 6NW6 TITLE CRYSTAL STRUCTURE OF TRMD, A TRNA-(N1G37) METHYLTRANSFERASE, FROM TITLE 2 MYCOBACTERIUM ABSCESSUS IN COMPLEX WITH S-ADENOSYL METHIONINE 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 GENE: TRMD, MAB_3226C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 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 24-JAN-24 6NW6 1 REMARK REVDAT 3 26-AUG-20 6NW6 1 JRNL REVDAT 2 05-AUG-20 6NW6 1 JRNL REVDAT 1 19-FEB-20 6NW6 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. 1.67 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 61334 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 2999 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 56.9406 - 4.5986 1.00 2992 143 0.1711 0.2038 REMARK 3 2 4.5986 - 3.6503 1.00 2833 168 0.1492 0.1849 REMARK 3 3 3.6503 - 3.1889 1.00 2807 156 0.1794 0.1875 REMARK 3 4 3.1889 - 2.8973 1.00 2779 165 0.1904 0.2171 REMARK 3 5 2.8973 - 2.6897 1.00 2781 146 0.1958 0.2334 REMARK 3 6 2.6897 - 2.5311 1.00 2804 143 0.1884 0.1938 REMARK 3 7 2.5311 - 2.4043 1.00 2763 138 0.1827 0.1841 REMARK 3 8 2.4043 - 2.2997 1.00 2769 156 0.1846 0.2046 REMARK 3 9 2.2997 - 2.2111 1.00 2750 155 0.1873 0.2212 REMARK 3 10 2.2111 - 2.1348 1.00 2738 143 0.1840 0.1961 REMARK 3 11 2.1348 - 2.0681 1.00 2791 132 0.1833 0.2136 REMARK 3 12 2.0681 - 2.0090 1.00 2769 147 0.1866 0.2157 REMARK 3 13 2.0090 - 1.9561 1.00 2724 158 0.1773 0.2177 REMARK 3 14 1.9561 - 1.9083 1.00 2762 135 0.1895 0.1957 REMARK 3 15 1.9083 - 1.8650 1.00 2725 138 0.1915 0.2164 REMARK 3 16 1.8650 - 1.8253 1.00 2766 128 0.2027 0.2160 REMARK 3 17 1.8253 - 1.7888 1.00 2756 116 0.2075 0.2637 REMARK 3 18 1.7888 - 1.7550 1.00 2775 128 0.2158 0.2565 REMARK 3 19 1.7550 - 1.7237 1.00 2733 145 0.2286 0.2551 REMARK 3 20 1.7237 - 1.6944 1.00 2765 137 0.2443 0.2825 REMARK 3 21 1.6944 - 1.6671 1.00 2753 122 0.2571 0.2893 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.07 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 3447 REMARK 3 ANGLE : 1.142 4730 REMARK 3 CHIRALITY : 0.051 538 REMARK 3 PLANARITY : 0.006 607 REMARK 3 DIHEDRAL : 14.714 1273 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 14 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 19 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.7258 -13.3112 23.0850 REMARK 3 T TENSOR REMARK 3 T11: 0.3075 T22: 0.3430 REMARK 3 T33: 0.2266 T12: -0.0110 REMARK 3 T13: 0.0188 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 1.7353 L22: 2.8613 REMARK 3 L33: 2.8381 L12: 0.0838 REMARK 3 L13: 0.8411 L23: 0.2068 REMARK 3 S TENSOR REMARK 3 S11: -0.0314 S12: -0.7191 S13: 0.0618 REMARK 3 S21: 0.9156 S22: -0.0930 S23: 0.1690 REMARK 3 S31: -0.1209 S32: -0.1614 S33: 0.0788 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 20 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): -39.0352 -14.5839 19.8189 REMARK 3 T TENSOR REMARK 3 T11: 0.2656 T22: 0.2706 REMARK 3 T33: 0.2411 T12: 0.0153 REMARK 3 T13: 0.0524 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 2.6807 L22: 2.8182 REMARK 3 L33: 2.3572 L12: 0.3875 REMARK 3 L13: 0.6875 L23: 1.2167 REMARK 3 S TENSOR REMARK 3 S11: -0.0639 S12: -0.2543 S13: 0.2897 REMARK 3 S21: 0.1555 S22: 0.0494 S23: 0.2939 REMARK 3 S31: -0.1088 S32: -0.2403 S33: -0.0252 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.6682 -17.4571 6.4811 REMARK 3 T TENSOR REMARK 3 T11: 0.1812 T22: 0.2111 REMARK 3 T33: 0.2087 T12: -0.0059 REMARK 3 T13: 0.0035 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.9271 L22: 1.7022 REMARK 3 L33: 1.8296 L12: 0.3480 REMARK 3 L13: 0.4969 L23: 0.7024 REMARK 3 S TENSOR REMARK 3 S11: 0.0133 S12: 0.0159 S13: -0.0841 REMARK 3 S21: 0.1243 S22: 0.0208 S23: 0.0129 REMARK 3 S31: 0.1102 S32: -0.0324 S33: -0.0314 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 84 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.3337 -10.2076 12.1078 REMARK 3 T TENSOR REMARK 3 T11: 0.1878 T22: 0.1730 REMARK 3 T33: 0.2030 T12: 0.0024 REMARK 3 T13: 0.0064 T23: -0.0054 REMARK 3 L TENSOR REMARK 3 L11: 2.2575 L22: 0.0093 REMARK 3 L33: 1.4486 L12: -0.0707 REMARK 3 L13: 0.7996 L23: 0.0338 REMARK 3 S TENSOR REMARK 3 S11: -0.0377 S12: 0.0316 S13: 0.0672 REMARK 3 S21: 0.0093 S22: 0.0332 S23: -0.0114 REMARK 3 S31: -0.0588 S32: 0.0423 S33: 0.0055 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 156 THROUGH 180 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.4823 -0.4900 25.4894 REMARK 3 T TENSOR REMARK 3 T11: 0.3760 T22: 0.2772 REMARK 3 T33: 0.3509 T12: -0.0200 REMARK 3 T13: 0.0452 T23: -0.1576 REMARK 3 L TENSOR REMARK 3 L11: 3.0659 L22: 1.1929 REMARK 3 L33: 0.6111 L12: -1.4439 REMARK 3 L13: 1.2822 L23: -0.4167 REMARK 3 S TENSOR REMARK 3 S11: 0.0201 S12: -0.3056 S13: 0.6059 REMARK 3 S21: 0.3296 S22: -0.2999 S23: 0.2387 REMARK 3 S31: -0.1283 S32: -0.1475 S33: 0.2025 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 181 THROUGH 203 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4235 -4.5259 40.8975 REMARK 3 T TENSOR REMARK 3 T11: 0.3016 T22: 0.2524 REMARK 3 T33: 0.2287 T12: 0.0374 REMARK 3 T13: -0.0566 T23: -0.0144 REMARK 3 L TENSOR REMARK 3 L11: 1.2669 L22: 2.0180 REMARK 3 L33: 0.6899 L12: 0.4156 REMARK 3 L13: -0.0084 L23: -0.3312 REMARK 3 S TENSOR REMARK 3 S11: 0.0910 S12: -0.0403 S13: -0.2057 REMARK 3 S21: 0.5337 S22: 0.0504 S23: -0.3052 REMARK 3 S31: 0.0803 S32: 0.2290 S33: -0.1404 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 204 THROUGH 227 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.9486 -2.0731 24.2861 REMARK 3 T TENSOR REMARK 3 T11: 0.2624 T22: 0.3185 REMARK 3 T33: 0.2500 T12: -0.0489 REMARK 3 T13: 0.0314 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 1.1012 L22: 3.4499 REMARK 3 L33: 2.2463 L12: 0.4892 REMARK 3 L13: 0.8197 L23: 2.5064 REMARK 3 S TENSOR REMARK 3 S11: -0.0508 S12: 0.1288 S13: -0.1492 REMARK 3 S21: -0.1509 S22: 0.2587 S23: -0.3598 REMARK 3 S31: -0.0954 S32: 0.4774 S33: -0.1992 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 0 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.1483 -21.7393 32.7258 REMARK 3 T TENSOR REMARK 3 T11: 0.3243 T22: 0.3437 REMARK 3 T33: 0.2979 T12: -0.0848 REMARK 3 T13: 0.0071 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 3.1490 L22: 3.6918 REMARK 3 L33: 2.0331 L12: -1.0545 REMARK 3 L13: 0.4212 L23: 0.3093 REMARK 3 S TENSOR REMARK 3 S11: 0.0934 S12: -0.0887 S13: -0.1953 REMARK 3 S21: -0.0034 S22: -0.1231 S23: 0.6738 REMARK 3 S31: 0.1895 S32: -0.4723 S33: 0.0825 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 18 THROUGH 40 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.0711 -26.4359 34.5362 REMARK 3 T TENSOR REMARK 3 T11: 0.3421 T22: 0.4021 REMARK 3 T33: 0.3780 T12: -0.1320 REMARK 3 T13: 0.0081 T23: -0.0392 REMARK 3 L TENSOR REMARK 3 L11: 2.6585 L22: 3.8009 REMARK 3 L33: 2.9786 L12: -0.7983 REMARK 3 L13: -0.3278 L23: 0.4620 REMARK 3 S TENSOR REMARK 3 S11: 0.0629 S12: -0.0513 S13: -0.6669 REMARK 3 S21: 0.3644 S22: -0.2663 S23: 0.8718 REMARK 3 S31: 0.5849 S32: -0.8836 S33: -0.0229 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 41 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.5331 -5.6428 43.8689 REMARK 3 T TENSOR REMARK 3 T11: 0.3591 T22: 0.3210 REMARK 3 T33: 0.2741 T12: 0.0285 REMARK 3 T13: 0.0327 T23: -0.0358 REMARK 3 L TENSOR REMARK 3 L11: 4.5211 L22: 5.4985 REMARK 3 L33: 2.1230 L12: 0.7622 REMARK 3 L13: 0.8483 L23: 0.5272 REMARK 3 S TENSOR REMARK 3 S11: -0.1017 S12: -0.4537 S13: 0.0448 REMARK 3 S21: 0.8281 S22: 0.0816 S23: 0.6953 REMARK 3 S31: 0.0933 S32: -0.4387 S33: 0.0637 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 63 THROUGH 155 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.3344 -19.3697 28.8551 REMARK 3 T TENSOR REMARK 3 T11: 0.2090 T22: 0.1686 REMARK 3 T33: 0.1892 T12: 0.0088 REMARK 3 T13: -0.0039 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.2256 L22: 1.4073 REMARK 3 L33: 1.9856 L12: 0.0316 REMARK 3 L13: 0.6278 L23: 0.5226 REMARK 3 S TENSOR REMARK 3 S11: 0.0075 S12: -0.0758 S13: -0.1486 REMARK 3 S21: 0.2613 S22: 0.0371 S23: -0.0566 REMARK 3 S31: 0.2080 S32: -0.0024 S33: -0.0314 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 156 THROUGH 181 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.4646 -27.4471 9.1982 REMARK 3 T TENSOR REMARK 3 T11: 0.3759 T22: 0.3664 REMARK 3 T33: 0.5455 T12: 0.0180 REMARK 3 T13: 0.0000 T23: 0.0410 REMARK 3 L TENSOR REMARK 3 L11: 0.5068 L22: 0.2402 REMARK 3 L33: 0.1393 L12: -0.3576 REMARK 3 L13: 0.2648 L23: -0.1788 REMARK 3 S TENSOR REMARK 3 S11: 0.0518 S12: 0.3317 S13: -0.3340 REMARK 3 S21: 0.0127 S22: -0.0962 S23: -0.4036 REMARK 3 S31: 0.3922 S32: 0.1192 S33: -0.4599 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 182 THROUGH 203 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.1066 -22.9039 -6.1477 REMARK 3 T TENSOR REMARK 3 T11: 0.2286 T22: 0.3203 REMARK 3 T33: 0.2551 T12: -0.0107 REMARK 3 T13: -0.0007 T23: -0.0667 REMARK 3 L TENSOR REMARK 3 L11: 2.7019 L22: 1.4597 REMARK 3 L33: 1.2249 L12: -0.1812 REMARK 3 L13: 0.0275 L23: 0.2234 REMARK 3 S TENSOR REMARK 3 S11: 0.0388 S12: 0.3909 S13: -0.4144 REMARK 3 S21: -0.2893 S22: -0.0254 S23: 0.1569 REMARK 3 S31: -0.1203 S32: -0.0014 S33: 0.0241 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 204 THROUGH 231 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.9011 -16.9809 -3.4878 REMARK 3 T TENSOR REMARK 3 T11: 0.2709 T22: 0.4380 REMARK 3 T33: 0.3685 T12: -0.0090 REMARK 3 T13: 0.0783 T23: -0.0787 REMARK 3 L TENSOR REMARK 3 L11: 2.4532 L22: 1.5428 REMARK 3 L33: 0.2665 L12: 0.6747 REMARK 3 L13: 0.7107 L23: 0.5688 REMARK 3 S TENSOR REMARK 3 S11: -0.1611 S12: 0.3552 S13: -0.5204 REMARK 3 S21: -0.3436 S22: 0.1815 S23: -0.4068 REMARK 3 S31: -0.1359 S32: -0.2549 S33: -0.0781 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 6NW6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1000239544. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-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 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 0.5.12 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61408 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 75.030 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) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.92700 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: 6NVR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08M SODIUM CACODYLATE PH 6.5 -7.0, 1 REMARK 280 -2 M AMMONIUM SULPHATE, VAPOR DIFFUSION, HANGING 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 37.51700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.65650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.62000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.65650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.51700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.62000 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: 7090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 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 LEU B 20 REMARK 465 PRO B 21 REMARK 465 GLY B 22 REMARK 465 LYS B 23 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 18 CG CD OE1 NE2 REMARK 470 LYS A 23 CG CD CE NZ REMARK 470 SER A 177 OG REMARK 470 ARG B 17 NE CZ NH1 NH2 REMARK 470 ILE B 25 CG1 CG2 CD1 REMARK 470 ASP B 26 CG OD1 OD2 REMARK 470 ARG B 39 CZ NH1 NH2 REMARK 470 VAL B 44 CG1 CG2 REMARK 470 LYS B 46 CE NZ REMARK 470 GLU B 77 CD OE1 OE2 REMARK 470 LEU B 160 CG CD1 CD2 REMARK 470 HIS B 204 ND1 CD2 CE1 NE2 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 -129.65 60.70 REMARK 500 VAL A 159 -87.17 -96.62 REMARK 500 TYR B 111 -130.92 54.27 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 SAM A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6NVR RELATED DB: PDB DBREF 6NW6 A 1 242 UNP B1MDI3 B1MDI3_MYCA9 1 242 DBREF 6NW6 B 1 242 UNP B1MDI3 B1MDI3_MYCA9 1 242 SEQADV 6NW6 GLY A -1 UNP B1MDI3 EXPRESSION TAG SEQADV 6NW6 SER A 0 UNP B1MDI3 EXPRESSION TAG SEQADV 6NW6 GLY B -1 UNP B1MDI3 EXPRESSION TAG SEQADV 6NW6 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 SAM A 301 27 HET SAM B 301 27 HET SO4 B 302 5 HETNAM SAM S-ADENOSYLMETHIONINE HETNAM SO4 SULFATE ION FORMUL 3 SAM 2(C15 H22 N6 O5 S) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *287(H2 O) HELIX 1 AA1 PHE A 9 TYR A 12 5 4 HELIX 2 AA2 LEU A 13 SER A 19 1 7 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 GLN B 18 5 10 HELIX 13 AB4 ARG B 38 THR B 41 5 4 HELIX 14 AB5 LYS B 62 CYS B 74 1 13 HELIX 15 AB6 THR B 91 SER B 99 1 9 HELIX 16 AB7 GLN B 116 ALA B 123 1 8 HELIX 17 AB8 GLY B 141 ARG B 154 1 14 HELIX 18 AB9 PRO B 196 SER B 201 5 6 HELIX 19 AC1 ASP B 203 ARG B 223 1 21 HELIX 20 AC2 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 GLU A 130 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 ILE B 3 O ASP B 31 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 SER B 132 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 2.86 CISPEP 2 ARG B 186 PRO B 187 0 2.14 SITE 1 AC1 15 PRO A 83 THR A 84 PRO A 85 GLY A 109 SITE 2 AC1 15 TYR A 111 GLU A 112 GLY A 113 VAL A 131 SITE 3 AC1 15 SER A 132 ILE A 133 GLY A 134 TYR A 136 SITE 4 AC1 15 LEU A 138 GLY A 140 GLY A 141 SITE 1 AC2 17 PRO B 83 THR B 84 PRO B 85 GLY B 109 SITE 2 AC2 17 TYR B 111 GLU B 112 GLY B 113 SER B 132 SITE 3 AC2 17 ILE B 133 GLY B 134 TYR B 136 LEU B 138 SITE 4 AC2 17 ASN B 139 GLY B 140 GLY B 141 HOH B 404 SITE 5 AC2 17 HOH B 431 SITE 1 AC3 3 ARG B 127 ARG B 129 HOH B 408 CRYST1 75.034 79.240 87.313 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 0.013327 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012620 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011453 0.00000