HEADER TRANSFERASE/ANTIBIOTIC 28-FEB-16 5IH0 TITLE MACROLIDE 2'-PHOSPHOTRANSFERASE TYPE II Y92M MUTANT - COMPLEX WITH GDP TITLE 2 AND ERYTHROMYCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROLIDE 2'-PHOSPHOTRANSFERASE II; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MACROLIDE 2'-PHOSPHOTRANSFERASE II PROTEIN MPHB,MACROLIDE 2- COMPND 5 PHOSPHOTRANSFERASE,MPH(B); COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: BM2506; SOURCE 5 GENE: MPHB, PO103_99; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS MACROLIDE PHOSPHOTRANSFERASE, KINASE, TRANSFERASE, TRANSFERASE- KEYWDS 2 ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.M.BERGHUIS,D.H.FONG REVDAT 6 27-SEP-23 5IH0 1 REMARK REVDAT 5 08-JAN-20 5IH0 1 REMARK REVDAT 4 13-SEP-17 5IH0 1 REMARK REVDAT 3 17-MAY-17 5IH0 1 JRNL REVDAT 2 03-MAY-17 5IH0 1 JRNL REVDAT 1 26-APR-17 5IH0 0 JRNL AUTH D.H.FONG,D.L.BURK,J.BLANCHET,A.Y.YAN,A.M.BERGHUIS JRNL TITL STRUCTURAL BASIS FOR KINASE-MEDIATED MACROLIDE ANTIBIOTIC JRNL TITL 2 RESISTANCE. JRNL REF STRUCTURE V. 25 750 2017 JRNL REFN ISSN 1878-4186 JRNL PMID 28416110 JRNL DOI 10.1016/J.STR.2017.03.007 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 38086 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1902 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 41.4083 - 3.9757 1.00 2777 147 0.1696 0.1784 REMARK 3 2 3.9757 - 3.1559 1.00 2654 139 0.1550 0.1813 REMARK 3 3 3.1559 - 2.7571 1.00 2599 137 0.1742 0.2022 REMARK 3 4 2.7571 - 2.5051 1.00 2590 137 0.1743 0.2083 REMARK 3 5 2.5051 - 2.3255 1.00 2594 136 0.1761 0.2039 REMARK 3 6 2.3255 - 2.1884 1.00 2568 135 0.1842 0.2132 REMARK 3 7 2.1884 - 2.0788 1.00 2574 135 0.1831 0.2097 REMARK 3 8 2.0788 - 1.9883 1.00 2554 135 0.1923 0.2411 REMARK 3 9 1.9883 - 1.9118 1.00 2543 132 0.2054 0.2429 REMARK 3 10 1.9118 - 1.8458 1.00 2572 136 0.2173 0.2576 REMARK 3 11 1.8458 - 1.7881 1.00 2532 133 0.2128 0.2514 REMARK 3 12 1.7881 - 1.7370 1.00 2524 133 0.2204 0.2678 REMARK 3 13 1.7370 - 1.6913 1.00 2557 133 0.2238 0.2756 REMARK 3 14 1.6913 - 1.6500 1.00 2546 134 0.2451 0.2608 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.66 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 : 0.004 2593 REMARK 3 ANGLE : 0.874 3541 REMARK 3 CHIRALITY : 0.046 390 REMARK 3 PLANARITY : 0.003 447 REMARK 3 DIHEDRAL : 15.582 931 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 1:20) REMARK 3 ORIGIN FOR THE GROUP (A): 9.6022 -11.0437 52.0602 REMARK 3 T TENSOR REMARK 3 T11: 0.5263 T22: 0.3137 REMARK 3 T33: 0.2199 T12: -0.0099 REMARK 3 T13: -0.1535 T23: 0.0300 REMARK 3 L TENSOR REMARK 3 L11: 5.1749 L22: 2.1668 REMARK 3 L33: 5.2736 L12: 0.0986 REMARK 3 L13: -1.4876 L23: 1.6727 REMARK 3 S TENSOR REMARK 3 S11: 0.0186 S12: -0.7072 S13: -0.4196 REMARK 3 S21: 0.6249 S22: -0.1678 S23: -0.1839 REMARK 3 S31: 0.6699 S32: -0.1216 S33: 0.1195 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 21:44) REMARK 3 ORIGIN FOR THE GROUP (A): 2.0906 -8.1545 46.2085 REMARK 3 T TENSOR REMARK 3 T11: 0.3850 T22: 0.4597 REMARK 3 T33: 0.2221 T12: 0.0422 REMARK 3 T13: -0.0534 T23: -0.1457 REMARK 3 L TENSOR REMARK 3 L11: 1.7693 L22: 4.5388 REMARK 3 L33: 1.5643 L12: -0.5628 REMARK 3 L13: -1.4155 L23: 1.8196 REMARK 3 S TENSOR REMARK 3 S11: -0.2119 S12: -0.2081 S13: 0.1053 REMARK 3 S21: 0.3303 S22: -0.4613 S23: 0.5829 REMARK 3 S31: -0.0403 S32: -0.6850 S33: 0.6291 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 45:51) REMARK 3 ORIGIN FOR THE GROUP (A): 6.3463 -7.5808 42.5089 REMARK 3 T TENSOR REMARK 3 T11: 0.2406 T22: 0.2314 REMARK 3 T33: 0.1074 T12: 0.0514 REMARK 3 T13: -0.0589 T23: -0.0660 REMARK 3 L TENSOR REMARK 3 L11: 1.4379 L22: 5.1157 REMARK 3 L33: 3.6432 L12: 0.7326 REMARK 3 L13: 1.1493 L23: 1.6019 REMARK 3 S TENSOR REMARK 3 S11: -0.2054 S12: 0.1279 S13: 0.0777 REMARK 3 S21: -0.0306 S22: 0.0033 S23: 0.0925 REMARK 3 S31: -0.1094 S32: -0.2469 S33: 0.1253 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 52:81) REMARK 3 ORIGIN FOR THE GROUP (A): 10.4330 -6.9225 29.6410 REMARK 3 T TENSOR REMARK 3 T11: 0.0898 T22: 0.1377 REMARK 3 T33: 0.1759 T12: 0.0043 REMARK 3 T13: -0.0021 T23: -0.0106 REMARK 3 L TENSOR REMARK 3 L11: 0.4774 L22: 2.2488 REMARK 3 L33: 1.6281 L12: -0.9062 REMARK 3 L13: 0.8389 L23: -1.8147 REMARK 3 S TENSOR REMARK 3 S11: -0.0485 S12: 0.0222 S13: 0.0800 REMARK 3 S21: 0.0584 S22: -0.0386 S23: -0.3079 REMARK 3 S31: 0.0616 S32: 0.0822 S33: 0.0728 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 82:91) REMARK 3 ORIGIN FOR THE GROUP (A): 13.4960 -10.2509 39.0470 REMARK 3 T TENSOR REMARK 3 T11: 0.1477 T22: 0.1136 REMARK 3 T33: 0.2305 T12: 0.0105 REMARK 3 T13: -0.0764 T23: 0.0163 REMARK 3 L TENSOR REMARK 3 L11: 4.7626 L22: 1.1093 REMARK 3 L33: 6.0782 L12: 0.3287 REMARK 3 L13: -1.7859 L23: 0.5336 REMARK 3 S TENSOR REMARK 3 S11: -0.0784 S12: -0.3647 S13: 0.0098 REMARK 3 S21: 0.2943 S22: 0.0199 S23: -0.6795 REMARK 3 S31: 0.2278 S32: 0.2805 S33: 0.0631 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 92:100) REMARK 3 ORIGIN FOR THE GROUP (A): 0.7184 1.2853 38.3009 REMARK 3 T TENSOR REMARK 3 T11: 0.2178 T22: 0.2571 REMARK 3 T33: 0.1559 T12: 0.0648 REMARK 3 T13: -0.0773 T23: -0.0878 REMARK 3 L TENSOR REMARK 3 L11: 2.5013 L22: 1.4400 REMARK 3 L33: 1.1935 L12: -1.8859 REMARK 3 L13: 1.6458 L23: -1.2858 REMARK 3 S TENSOR REMARK 3 S11: -0.0895 S12: -0.5027 S13: 0.2506 REMARK 3 S21: 0.2911 S22: 0.0582 S23: -0.2371 REMARK 3 S31: -0.1827 S32: -0.1284 S33: 0.0254 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 101:139) REMARK 3 ORIGIN FOR THE GROUP (A): -8.8354 2.0889 27.1211 REMARK 3 T TENSOR REMARK 3 T11: 0.1111 T22: 0.1233 REMARK 3 T33: 0.1259 T12: 0.0240 REMARK 3 T13: 0.0142 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.9040 L22: 1.5592 REMARK 3 L33: 1.7858 L12: -0.2129 REMARK 3 L13: 0.0004 L23: 0.0992 REMARK 3 S TENSOR REMARK 3 S11: -0.1905 S12: -0.2672 S13: -0.1072 REMARK 3 S21: 0.2063 S22: 0.0535 S23: 0.1483 REMARK 3 S31: 0.0071 S32: -0.2417 S33: 0.0768 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 140:145) REMARK 3 ORIGIN FOR THE GROUP (A): 17.7341 -3.9115 16.7238 REMARK 3 T TENSOR REMARK 3 T11: 0.0924 T22: 0.2506 REMARK 3 T33: 0.2368 T12: 0.0001 REMARK 3 T13: 0.0465 T23: 0.0541 REMARK 3 L TENSOR REMARK 3 L11: 8.3866 L22: 3.9319 REMARK 3 L33: 2.8070 L12: -2.2815 REMARK 3 L13: 1.2170 L23: 2.6201 REMARK 3 S TENSOR REMARK 3 S11: 0.0623 S12: 0.1730 S13: 0.2173 REMARK 3 S21: 0.0011 S22: 0.1479 S23: 0.8888 REMARK 3 S31: -0.0144 S32: -0.6125 S33: -0.2040 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 146:165) REMARK 3 ORIGIN FOR THE GROUP (A): 2.1175 -14.0345 9.7520 REMARK 3 T TENSOR REMARK 3 T11: 0.2558 T22: 0.1971 REMARK 3 T33: 0.2498 T12: -0.0357 REMARK 3 T13: 0.1271 T23: -0.1055 REMARK 3 L TENSOR REMARK 3 L11: 0.3795 L22: 0.9286 REMARK 3 L33: 0.9550 L12: 0.3218 REMARK 3 L13: -0.0817 L23: 0.4027 REMARK 3 S TENSOR REMARK 3 S11: -0.1326 S12: 0.1725 S13: -0.2877 REMARK 3 S21: -0.1033 S22: -0.0732 S23: 0.0537 REMARK 3 S31: 0.2880 S32: -0.1855 S33: -0.0153 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 166:177) REMARK 3 ORIGIN FOR THE GROUP (A): -12.6558 -23.3071 10.6199 REMARK 3 T TENSOR REMARK 3 T11: 0.5594 T22: 0.3831 REMARK 3 T33: 0.6982 T12: -0.1874 REMARK 3 T13: 0.1115 T23: -0.2322 REMARK 3 L TENSOR REMARK 3 L11: 0.1735 L22: 1.1656 REMARK 3 L33: 0.4258 L12: -0.2174 REMARK 3 L13: 0.2675 L23: -0.4410 REMARK 3 S TENSOR REMARK 3 S11: -0.2254 S12: 0.0960 S13: 0.0133 REMARK 3 S21: -0.4750 S22: 0.0841 S23: 0.0478 REMARK 3 S31: -0.0706 S32: 0.0122 S33: 0.1052 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 178:193) REMARK 3 ORIGIN FOR THE GROUP (A): -7.3934 -9.3601 4.0973 REMARK 3 T TENSOR REMARK 3 T11: 0.3106 T22: 0.4831 REMARK 3 T33: 0.1862 T12: -0.1089 REMARK 3 T13: 0.0294 T23: -0.1401 REMARK 3 L TENSOR REMARK 3 L11: 0.5728 L22: 0.6384 REMARK 3 L33: 0.2925 L12: 0.2891 REMARK 3 L13: 0.2060 L23: 0.3429 REMARK 3 S TENSOR REMARK 3 S11: -0.1567 S12: 0.2333 S13: -0.1307 REMARK 3 S21: -0.3379 S22: -0.0969 S23: 0.2228 REMARK 3 S31: 0.0818 S32: -0.4314 S33: 0.1786 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN A AND RESID 194:240) REMARK 3 ORIGIN FOR THE GROUP (A): -3.4503 -2.0051 24.4043 REMARK 3 T TENSOR REMARK 3 T11: 0.0595 T22: 0.0693 REMARK 3 T33: 0.0549 T12: 0.0173 REMARK 3 T13: 0.0005 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 1.9891 L22: 1.3585 REMARK 3 L33: 1.5228 L12: 0.0152 REMARK 3 L13: -0.5212 L23: -0.2742 REMARK 3 S TENSOR REMARK 3 S11: -0.1132 S12: -0.1049 S13: 0.0983 REMARK 3 S21: 0.0649 S22: 0.0918 S23: -0.0587 REMARK 3 S31: -0.0252 S32: -0.0542 S33: 0.0030 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN A AND RESID 241:256) REMARK 3 ORIGIN FOR THE GROUP (A): -9.2430 6.9773 14.9463 REMARK 3 T TENSOR REMARK 3 T11: 0.0883 T22: 0.1130 REMARK 3 T33: 0.0929 T12: 0.0182 REMARK 3 T13: -0.0073 T23: 0.0492 REMARK 3 L TENSOR REMARK 3 L11: 4.2022 L22: 3.5808 REMARK 3 L33: 3.0045 L12: -0.5327 REMARK 3 L13: -2.0082 L23: -0.1479 REMARK 3 S TENSOR REMARK 3 S11: -0.0775 S12: 0.4673 S13: 0.3135 REMARK 3 S21: -0.2936 S22: 0.1766 S23: 0.3007 REMARK 3 S31: -0.1193 S32: -0.2711 S33: -0.0681 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN A AND RESID 257:280) REMARK 3 ORIGIN FOR THE GROUP (A): -8.5548 -6.8974 12.6877 REMARK 3 T TENSOR REMARK 3 T11: 0.1494 T22: 0.1515 REMARK 3 T33: 0.0920 T12: -0.0384 REMARK 3 T13: 0.0320 T23: -0.0358 REMARK 3 L TENSOR REMARK 3 L11: 2.6211 L22: 4.2500 REMARK 3 L33: 1.3681 L12: 0.9824 REMARK 3 L13: -0.8652 L23: -0.7001 REMARK 3 S TENSOR REMARK 3 S11: -0.1958 S12: 0.3595 S13: -0.2109 REMARK 3 S21: -0.2774 S22: -0.0199 S23: 0.1525 REMARK 3 S31: 0.2936 S32: -0.1383 S33: 0.1544 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN A AND RESID 281:299) REMARK 3 ORIGIN FOR THE GROUP (A): -12.5422 -23.1424 23.4756 REMARK 3 T TENSOR REMARK 3 T11: 0.6411 T22: 0.3039 REMARK 3 T33: 0.8102 T12: -0.0600 REMARK 3 T13: 0.4402 T23: -0.0800 REMARK 3 L TENSOR REMARK 3 L11: 0.7736 L22: 0.8142 REMARK 3 L33: 0.7527 L12: -0.3918 REMARK 3 L13: -0.1019 L23: -0.0179 REMARK 3 S TENSOR REMARK 3 S11: -0.2052 S12: -0.0167 S13: -0.2284 REMARK 3 S21: 0.1490 S22: -0.0865 S23: 0.1606 REMARK 3 S31: 0.3495 S32: -0.1111 S33: 0.2178 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 5IH0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218814. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DCM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38102 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 41.395 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.57200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.790 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5IWU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CALCIUM ACETATE, 0.1M TRIS, 25 REMARK 280 -40% PEG 4000, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 295K 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 19.96000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.35500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.04500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.35500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.96000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.04500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 300 REMARK 465 GLY A 301 REMARK 465 SER A 302 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 MET A 1 CG SD CE REMARK 470 SER A 2 OG REMARK 470 ASN A 106 CG OD1 ND2 REMARK 470 ILE A 107 CG1 CG2 CD1 REMARK 470 LYS A 169 CG CD CE NZ REMARK 470 GLU A 174 CG CD OE1 OE2 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 HD22 ASN A 185 O HOH A 521 1.50 REMARK 500 HE2 HIS A 205 MG MG A 401 1.59 REMARK 500 O HOH A 788 O HOH A 903 1.64 REMARK 500 O HOH A 543 O HOH A 620 1.83 REMARK 500 O HOH A 904 O HOH A 937 1.87 REMARK 500 O HOH A 577 O HOH A 833 1.87 REMARK 500 O HOH A 821 O HOH A 825 1.89 REMARK 500 OD2 ASP A 96 O HOH A 501 1.91 REMARK 500 O HOH A 948 O HOH A 950 1.92 REMARK 500 OE2 GLU A 287 O HOH A 502 1.97 REMARK 500 O HOH A 501 O HOH A 812 1.98 REMARK 500 O HOH A 948 O HOH A 951 2.00 REMARK 500 NH2 ARG A 49 O HOH A 503 2.00 REMARK 500 O HOH A 873 O HOH A 888 2.00 REMARK 500 O HOH A 755 O HOH A 771 2.03 REMARK 500 O HOH A 533 O HOH A 739 2.06 REMARK 500 O ASN A 175 O HOH A 504 2.06 REMARK 500 OE1 GLU A 298 O HOH A 505 2.07 REMARK 500 O1B GDP A 403 O HOH A 506 2.07 REMARK 500 O HOH A 880 O HOH A 895 2.09 REMARK 500 O GLY A 285 O HOH A 507 2.11 REMARK 500 OE1 GLU A 153 O HOH A 508 2.11 REMARK 500 O HOH A 536 O HOH A 841 2.11 REMARK 500 OE1 GLU A 287 O HOH A 509 2.12 REMARK 500 O HOH A 549 O HOH A 572 2.12 REMARK 500 O HOH A 811 O HOH A 938 2.12 REMARK 500 O HOH A 510 O HOH A 708 2.12 REMARK 500 OE1 GLU A 290 O HOH A 510 2.12 REMARK 500 O HOH A 551 O HOH A 819 2.13 REMARK 500 O HOH A 509 O HOH A 510 2.13 REMARK 500 O HOH A 554 O HOH A 795 2.16 REMARK 500 O HOH A 706 O HOH A 829 2.16 REMARK 500 O HOH A 799 O HOH A 829 2.17 REMARK 500 OE1 GLN A 291 O HOH A 511 2.17 REMARK 500 O HOH A 706 O HOH A 786 2.18 REMARK 500 O HOH A 749 O HOH A 892 2.19 REMARK 500 O HOH A 721 O HOH A 904 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 944 O HOH A 945 3555 2.09 REMARK 500 O HOH A 531 O HOH A 897 3545 2.09 REMARK 500 O HOH A 868 O HOH A 941 2555 2.13 REMARK 500 O HOH A 527 O HOH A 771 3555 2.14 REMARK 500 O HOH A 502 O HOH A 767 3545 2.15 REMARK 500 O HOH A 874 O HOH A 931 3545 2.17 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 ASN A 118 62.47 -157.08 REMARK 500 ASN A 118 60.30 -154.73 REMARK 500 ALA A 144 70.79 -156.27 REMARK 500 ASP A 200 46.38 -146.41 REMARK 500 ASP A 219 81.90 60.60 REMARK 500 THR A 226 -161.60 -164.73 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 A 949 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 950 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A 951 DISTANCE = 7.37 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 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 219 OD2 REMARK 620 2 GDP A 403 O2B 98.7 REMARK 620 3 GDP A 403 O1A 82.1 84.4 REMARK 620 4 HOH A 645 O 174.1 86.9 100.3 REMARK 620 5 HOH A 705 O 85.4 83.4 161.0 93.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ERY A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IGU RELATED DB: PDB REMARK 900 RELATED ID: 5IGV RELATED DB: PDB REMARK 900 RELATED ID: 5IGW RELATED DB: PDB REMARK 900 RELATED ID: 5IGY RELATED DB: PDB REMARK 900 RELATED ID: 5IGZ RELATED DB: PDB REMARK 900 RELATED ID: 5IH1 RELATED DB: PDB DBREF 5IH0 A 1 302 UNP O32553 O32553_ECOLX 1 302 SEQADV 5IH0 MET A 92 UNP O32553 TYR 92 ENGINEERED MUTATION SEQRES 1 A 302 MET SER LYS ASP ILE LYS GLN VAL ILE GLU ILE ALA LYS SEQRES 2 A 302 LYS HIS ASN LEU PHE LEU LYS GLU GLU THR ILE GLN PHE SEQRES 3 A 302 ASN GLU SER GLY LEU ASP PHE GLN ALA VAL PHE ALA GLN SEQRES 4 A 302 ASP ASN ASN GLY ILE ASP TRP VAL LEU ARG LEU PRO ARG SEQRES 5 A 302 ARG GLU ASP VAL MET PRO ARG THR LYS VAL GLU LYS GLN SEQRES 6 A 302 ALA LEU ASP LEU VAL ASN LYS TYR ALA ILE SER PHE GLN SEQRES 7 A 302 ALA PRO ASN TRP ILE ILE TYR THR GLU GLU LEU ILE ALA SEQRES 8 A 302 MET LYS LYS LEU ASP GLY VAL PRO ALA GLY THR ILE ASP SEQRES 9 A 302 HIS ASN ILE GLY ASN TYR ILE TRP GLU ILE ASP ILE ASN SEQRES 10 A 302 ASN VAL PRO GLU LEU PHE HIS LYS SER LEU GLY ARG VAL SEQRES 11 A 302 LEU ALA GLU LEU HIS SER ILE PRO SER ASN LYS ALA ALA SEQRES 12 A 302 ALA LEU ASP LEU VAL VAL HIS THR PRO GLU GLU ALA ARG SEQRES 13 A 302 MET SER MET LYS GLN ARG MET ASP ALA VAL ARG ALA LYS SEQRES 14 A 302 PHE GLY VAL GLY GLU ASN LEU TRP ASN ARG TRP GLN ALA SEQRES 15 A 302 TRP LEU ASN ASP ASP ASP MET TRP PRO LYS LYS THR GLY SEQRES 16 A 302 LEU ILE HIS GLY ASP VAL HIS ALA GLY HIS THR MET ILE SEQRES 17 A 302 ASP LYS ASP ALA ASN VAL THR GLY LEU ILE ASP TRP THR SEQRES 18 A 302 GLU ALA LYS VAL THR ASP VAL SER HIS ASP PHE ILE PHE SEQRES 19 A 302 ASN TYR ARG ALA PHE GLY GLU GLU GLY LEU GLU ALA LEU SEQRES 20 A 302 ILE LEU ALA TYR LYS GLU ILE GLY GLY TYR TYR TRP PRO SEQRES 21 A 302 LYS MET LYS GLU HIS ILE ILE GLU LEU ASN ALA ALA TYR SEQRES 22 A 302 PRO VAL SER ILE ALA GLU PHE ALA LEU VAL SER GLY ILE SEQRES 23 A 302 GLU GLU TYR GLU GLN MET ALA LYS GLU ALA LEU GLU VAL SEQRES 24 A 302 GLN GLY SER HET MG A 401 1 HET ACT A 402 7 HET GDP A 403 40 HET ERY A 404 118 HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM ERY ERYTHROMYCIN A FORMUL 2 MG MG 2+ FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 GDP C10 H15 N5 O11 P2 FORMUL 5 ERY C37 H67 N O13 FORMUL 6 HOH *451(H2 O) HELIX 1 AA1 MET A 1 HIS A 15 1 15 HELIX 2 AA2 LYS A 20 ILE A 24 5 5 HELIX 3 AA3 ASP A 55 ALA A 74 1 20 HELIX 4 AA4 PRO A 120 SER A 136 1 17 HELIX 5 AA5 ILE A 137 ALA A 142 5 6 HELIX 6 AA6 THR A 151 PHE A 170 1 20 HELIX 7 AA7 GLY A 173 ASN A 185 1 13 HELIX 8 AA8 ASP A 186 TRP A 190 5 5 HELIX 9 AA9 ASP A 227 ASP A 231 5 5 HELIX 10 AB1 PHE A 232 ILE A 254 1 23 HELIX 11 AB2 LYS A 261 ALA A 272 1 12 HELIX 12 AB3 ALA A 272 GLY A 285 1 14 HELIX 13 AB4 ILE A 286 GLU A 298 1 13 SHEET 1 AA1 5 GLN A 25 PHE A 26 0 SHEET 2 AA1 5 PHE A 33 GLN A 39 -1 O PHE A 37 N GLN A 25 SHEET 3 AA1 5 ASP A 45 PRO A 51 -1 O LEU A 48 N VAL A 36 SHEET 4 AA1 5 ILE A 90 LYS A 93 -1 O MET A 92 N VAL A 47 SHEET 5 AA1 5 ILE A 84 TYR A 85 -1 N ILE A 84 O ALA A 91 SHEET 1 AA2 3 VAL A 98 PRO A 99 0 SHEET 2 AA2 3 THR A 206 ILE A 208 -1 O ILE A 208 N VAL A 98 SHEET 3 AA2 3 VAL A 214 LEU A 217 -1 O THR A 215 N MET A 207 SHEET 1 AA3 2 GLY A 101 ASP A 104 0 SHEET 2 AA3 2 ASN A 109 TRP A 112 -1 O ASN A 109 N ASP A 104 SHEET 1 AA4 2 GLY A 195 ILE A 197 0 SHEET 2 AA4 2 LYS A 224 THR A 226 -1 O LYS A 224 N ILE A 197 LINK OD2 ASP A 219 MG MG A 401 1555 1555 2.23 LINK MG MG A 401 O2B GDP A 403 1555 1555 2.18 LINK MG MG A 401 O1A GDP A 403 1555 1555 2.09 LINK MG MG A 401 O HOH A 645 1555 1555 1.97 LINK MG MG A 401 O HOH A 705 1555 1555 2.16 SITE 1 AC1 5 HIS A 205 ASP A 219 GDP A 403 HOH A 645 SITE 2 AC1 5 HOH A 705 SITE 1 AC2 5 PHE A 33 ARG A 49 ARG A 59 HOH A 534 SITE 2 AC2 5 HOH A 562 SITE 1 AC3 18 PHE A 33 PHE A 37 ARG A 49 LYS A 94 SITE 2 AC3 18 LEU A 95 HIS A 205 ASP A 219 MG A 401 SITE 3 AC3 18 HOH A 506 HOH A 524 HOH A 556 HOH A 560 SITE 4 AC3 18 HOH A 604 HOH A 615 HOH A 645 HOH A 705 SITE 5 AC3 18 HOH A 714 HOH A 725 SITE 1 AC4 20 HIS A 105 GLY A 108 ASN A 109 TYR A 110 SITE 2 AC4 20 ASP A 200 VAL A 201 HIS A 202 GLU A 222 SITE 3 AC4 20 HIS A 230 ILE A 233 ARG A 237 TYR A 273 SITE 4 AC4 20 SER A 276 ILE A 277 MET A 292 HOH A 573 SITE 5 AC4 20 HOH A 581 HOH A 609 HOH A 633 HOH A 661 CRYST1 39.920 80.090 96.710 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.025050 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012486 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010340 0.00000