HEADER VIRAL PROTEIN/INHIBITOR 17-JAN-19 6NPI TITLE CRYSTAL STRUCTURE OF EPSTEIN-BARR VIRUS NUCLEAR ANTIGEN-1, EBNA1, TITLE 2 BOUND TO FRAGMENTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPSTEIN-BARR NUCLEAR ANTIGEN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: EBV NUCLEAR ANTIGEN 1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EPSTEIN-BARR VIRUS (STRAIN B95-8); SOURCE 3 ORGANISM_COMMON: HHV-4; SOURCE 4 ORGANISM_TAXID: 10377; SOURCE 5 STRAIN: B95-8; SOURCE 6 GENE: EBNA1, BKRF1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EBNA1, DNA BINDING PROTEIN, EPSTEIN-BARR VIRUS, VIRAL PROTEIN, VIRAL KEYWDS 2 PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.E.MESSICK REVDAT 2 11-OCT-23 6NPI 1 REMARK REVDAT 1 20-MAR-19 6NPI 0 JRNL AUTH T.E.MESSICK,G.R.SMITH,S.S.SOLDAN,M.E.MCDONNELL,J.S.DEAKYNE, JRNL AUTH 2 K.A.MALECKA,L.TOLVINSKI,A.P.J.VAN DEN HEUVEL,B.W.GU, JRNL AUTH 3 J.A.CASSEL,D.H.TRAN,B.R.WASSERMANN,Y.ZHANG,V.VELVADAPU, JRNL AUTH 4 E.R.ZARTLER,P.BUSSON,A.B.REITZ,P.M.LIEBERMAN JRNL TITL STRUCTURE-BASED DESIGN OF SMALL-MOLECULE INHIBITORS OF EBNA1 JRNL TITL 2 DNA BINDING BLOCKS EPSTEIN-BARR VIRUS LATENT INFECTION AND JRNL TITL 3 TUMOR GROWTH. JRNL REF SCI TRANSL MED V. 11 2019 JRNL REFN ESSN 1946-6242 JRNL PMID 30842315 JRNL DOI 10.1126/SCITRANSLMED.AAU5612 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 42238 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 2015 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 30.3482 - 3.6152 0.80 2630 131 0.1594 0.1708 REMARK 3 2 3.6152 - 2.8702 0.89 2799 139 0.1462 0.1662 REMARK 3 3 2.8702 - 2.5075 0.91 2847 146 0.1427 0.1534 REMARK 3 4 2.5075 - 2.2784 0.92 2871 146 0.1325 0.1591 REMARK 3 5 2.2784 - 2.1151 0.93 2884 146 0.1275 0.1368 REMARK 3 6 2.1151 - 1.9904 0.94 2877 145 0.1280 0.1532 REMARK 3 7 1.9904 - 1.8908 0.94 2915 149 0.1312 0.1584 REMARK 3 8 1.8908 - 1.8085 0.95 2919 135 0.1346 0.1752 REMARK 3 9 1.8085 - 1.7389 0.95 2902 148 0.1392 0.1713 REMARK 3 10 1.7389 - 1.6789 0.95 2933 148 0.1371 0.1777 REMARK 3 11 1.6789 - 1.6264 0.95 2923 142 0.1381 0.1706 REMARK 3 12 1.6264 - 1.5799 0.96 2880 155 0.1343 0.1738 REMARK 3 13 1.5799 - 1.5383 0.96 2964 139 0.1453 0.1621 REMARK 3 14 1.5383 - 1.5008 0.94 2879 146 0.1525 0.1791 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 2316 REMARK 3 ANGLE : 1.044 3164 REMARK 3 CHIRALITY : 0.056 346 REMARK 3 PLANARITY : 0.008 422 REMARK 3 DIHEDRAL : 6.221 1858 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 20 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 468:474) REMARK 3 ORIGIN FOR THE GROUP (A): -17.4927 5.3533 21.6504 REMARK 3 T TENSOR REMARK 3 T11: 0.3149 T22: 0.2761 REMARK 3 T33: 0.2732 T12: 0.0578 REMARK 3 T13: 0.0320 T23: -0.0354 REMARK 3 L TENSOR REMARK 3 L11: 2.4492 L22: 0.4708 REMARK 3 L33: 3.8185 L12: 1.0702 REMARK 3 L13: -3.0329 L23: -1.3040 REMARK 3 S TENSOR REMARK 3 S11: -0.2213 S12: 0.0962 S13: 0.4548 REMARK 3 S21: 0.1148 S22: -0.0500 S23: -0.1143 REMARK 3 S31: 0.1979 S32: 0.2343 S33: 0.1320 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 475:492) REMARK 3 ORIGIN FOR THE GROUP (A): -5.2036 -1.0707 15.5817 REMARK 3 T TENSOR REMARK 3 T11: 0.1255 T22: 0.1052 REMARK 3 T33: 0.1220 T12: 0.0026 REMARK 3 T13: 0.0157 T23: -0.0283 REMARK 3 L TENSOR REMARK 3 L11: 4.8958 L22: 1.4416 REMARK 3 L33: 1.4943 L12: 0.5528 REMARK 3 L13: -0.5400 L23: 0.4381 REMARK 3 S TENSOR REMARK 3 S11: 0.0776 S12: 0.1316 S13: 0.2928 REMARK 3 S21: 0.0257 S22: -0.0764 S23: 0.0943 REMARK 3 S31: -0.1123 S32: -0.1593 S33: -0.0173 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 493:501) REMARK 3 ORIGIN FOR THE GROUP (A): 7.4595 -1.3762 -0.4596 REMARK 3 T TENSOR REMARK 3 T11: 0.1984 T22: 0.1658 REMARK 3 T33: 0.1793 T12: -0.0622 REMARK 3 T13: 0.0412 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 2.3880 L22: 0.6357 REMARK 3 L33: 6.9503 L12: -0.6759 REMARK 3 L13: 0.8343 L23: 1.1749 REMARK 3 S TENSOR REMARK 3 S11: -0.0163 S12: 0.3332 S13: 0.2717 REMARK 3 S21: -0.4484 S22: 0.2962 S23: -0.1384 REMARK 3 S31: -0.7254 S32: 0.5655 S33: -0.1487 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 502:516) REMARK 3 ORIGIN FOR THE GROUP (A): -3.7599 -14.9310 6.9364 REMARK 3 T TENSOR REMARK 3 T11: 0.0618 T22: 0.0713 REMARK 3 T33: 0.0685 T12: -0.0003 REMARK 3 T13: -0.0049 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.9999 L22: 1.2859 REMARK 3 L33: 1.3447 L12: -0.0619 REMARK 3 L13: 0.2543 L23: 0.2950 REMARK 3 S TENSOR REMARK 3 S11: -0.0212 S12: 0.0367 S13: 0.0186 REMARK 3 S21: 0.0509 S22: 0.0065 S23: 0.0160 REMARK 3 S31: 0.1442 S32: -0.0282 S33: -0.0138 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 517:537) REMARK 3 ORIGIN FOR THE GROUP (A): -9.0952 -8.0148 6.8885 REMARK 3 T TENSOR REMARK 3 T11: 0.0973 T22: 0.0862 REMARK 3 T33: 0.1027 T12: 0.0208 REMARK 3 T13: 0.0074 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 0.5321 L22: 1.1007 REMARK 3 L33: 1.4368 L12: 0.2591 REMARK 3 L13: 0.2184 L23: 0.1002 REMARK 3 S TENSOR REMARK 3 S11: 0.0290 S12: -0.0271 S13: 0.1106 REMARK 3 S21: 0.0583 S22: -0.0630 S23: 0.0682 REMARK 3 S31: -0.1941 S32: -0.1086 S33: 0.0310 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 538:549) REMARK 3 ORIGIN FOR THE GROUP (A): -9.0795 -33.5908 8.7809 REMARK 3 T TENSOR REMARK 3 T11: 0.2107 T22: 0.1319 REMARK 3 T33: 0.2310 T12: -0.0417 REMARK 3 T13: -0.0354 T23: 0.0282 REMARK 3 L TENSOR REMARK 3 L11: 1.4647 L22: 1.4005 REMARK 3 L33: 1.4651 L12: 0.3766 REMARK 3 L13: -0.4579 L23: 0.3623 REMARK 3 S TENSOR REMARK 3 S11: 0.1233 S12: -0.1946 S13: -0.5395 REMARK 3 S21: 0.1108 S22: 0.0433 S23: 0.5527 REMARK 3 S31: 0.5015 S32: -0.2575 S33: -0.0311 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 550:560) REMARK 3 ORIGIN FOR THE GROUP (A): -11.2725 -31.6384 6.0471 REMARK 3 T TENSOR REMARK 3 T11: 0.1571 T22: 0.1276 REMARK 3 T33: 0.1849 T12: -0.0375 REMARK 3 T13: 0.0166 T23: -0.0256 REMARK 3 L TENSOR REMARK 3 L11: 1.1513 L22: 3.7398 REMARK 3 L33: 2.6069 L12: -0.7401 REMARK 3 L13: -0.7307 L23: 2.2341 REMARK 3 S TENSOR REMARK 3 S11: 0.0140 S12: 0.1201 S13: -0.2312 REMARK 3 S21: 0.3064 S22: -0.3432 S23: 0.6161 REMARK 3 S31: 0.3728 S32: -0.3308 S33: 0.2688 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 561:576) REMARK 3 ORIGIN FOR THE GROUP (A): 1.6272 -10.9000 4.5112 REMARK 3 T TENSOR REMARK 3 T11: 0.0771 T22: 0.0965 REMARK 3 T33: 0.1003 T12: 0.0025 REMARK 3 T13: 0.0144 T23: -0.0064 REMARK 3 L TENSOR REMARK 3 L11: 0.6989 L22: 0.2315 REMARK 3 L33: 0.2111 L12: 0.4342 REMARK 3 L13: -0.0680 L23: -0.0679 REMARK 3 S TENSOR REMARK 3 S11: 0.0231 S12: 0.0749 S13: 0.0785 REMARK 3 S21: -0.0030 S22: 0.0462 S23: -0.0035 REMARK 3 S31: 0.0090 S32: 0.0842 S33: -0.0569 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 577:599) REMARK 3 ORIGIN FOR THE GROUP (A): -1.0496 -13.4545 17.4171 REMARK 3 T TENSOR REMARK 3 T11: 0.1236 T22: 0.1194 REMARK 3 T33: 0.0979 T12: 0.0005 REMARK 3 T13: 0.0055 T23: -0.0174 REMARK 3 L TENSOR REMARK 3 L11: 1.1844 L22: 1.3188 REMARK 3 L33: 1.5725 L12: 0.3440 REMARK 3 L13: -0.3141 L23: 0.0719 REMARK 3 S TENSOR REMARK 3 S11: 0.0366 S12: -0.1882 S13: 0.0471 REMARK 3 S21: 0.2111 S22: -0.0338 S23: 0.0238 REMARK 3 S31: 0.1202 S32: 0.1032 S33: -0.0227 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 600:607) REMARK 3 ORIGIN FOR THE GROUP (A): 0.8609 -14.7309 -7.4146 REMARK 3 T TENSOR REMARK 3 T11: 0.1006 T22: 0.1370 REMARK 3 T33: 0.1083 T12: 0.0081 REMARK 3 T13: 0.0104 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 3.0766 L22: 1.2857 REMARK 3 L33: 1.1394 L12: -0.7931 REMARK 3 L13: -0.0244 L23: 0.4968 REMARK 3 S TENSOR REMARK 3 S11: -0.0202 S12: 0.3662 S13: 0.0433 REMARK 3 S21: -0.2159 S22: -0.0276 S23: -0.0514 REMARK 3 S31: 0.0350 S32: 0.1382 S33: 0.0013 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN B AND RESID 474:483) REMARK 3 ORIGIN FOR THE GROUP (A): -11.1151 -39.3605 -11.9339 REMARK 3 T TENSOR REMARK 3 T11: 0.2430 T22: 0.1763 REMARK 3 T33: 0.2460 T12: 0.0035 REMARK 3 T13: -0.0563 T23: -0.0889 REMARK 3 L TENSOR REMARK 3 L11: 6.2821 L22: 1.7130 REMARK 3 L33: 3.8569 L12: -0.3507 REMARK 3 L13: -0.8408 L23: 0.8111 REMARK 3 S TENSOR REMARK 3 S11: 0.1553 S12: 0.2395 S13: -0.8104 REMARK 3 S21: -0.0928 S22: -0.1006 S23: 0.2770 REMARK 3 S31: 0.6956 S32: -0.3223 S33: -0.1032 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN B AND RESID 484:491) REMARK 3 ORIGIN FOR THE GROUP (A): 2.2689 -38.3628 -12.3170 REMARK 3 T TENSOR REMARK 3 T11: 0.1952 T22: 0.2816 REMARK 3 T33: 0.2107 T12: 0.0690 REMARK 3 T13: -0.0307 T23: -0.0900 REMARK 3 L TENSOR REMARK 3 L11: 2.3098 L22: 4.8519 REMARK 3 L33: 3.7793 L12: -1.6330 REMARK 3 L13: 2.1970 L23: 0.1746 REMARK 3 S TENSOR REMARK 3 S11: -0.0232 S12: 0.1767 S13: -0.0484 REMARK 3 S21: 0.0889 S22: 0.0252 S23: -0.4550 REMARK 3 S31: 0.1706 S32: 0.4399 S33: 0.0515 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN B AND RESID 492:497) REMARK 3 ORIGIN FOR THE GROUP (A): 9.2892 -38.3900 -3.1007 REMARK 3 T TENSOR REMARK 3 T11: 0.2799 T22: 0.1976 REMARK 3 T33: 0.2273 T12: 0.1079 REMARK 3 T13: -0.0082 T23: -0.0570 REMARK 3 L TENSOR REMARK 3 L11: 4.3399 L22: 1.2127 REMARK 3 L33: 2.8304 L12: 0.9071 REMARK 3 L13: -1.5201 L23: 1.1587 REMARK 3 S TENSOR REMARK 3 S11: -0.1089 S12: 0.1770 S13: -0.8723 REMARK 3 S21: -0.2983 S22: 0.1265 S23: -0.2684 REMARK 3 S31: 1.0593 S32: 0.5512 S33: -0.0547 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN B AND RESID 498:514) REMARK 3 ORIGIN FOR THE GROUP (A): 0.2600 -26.8149 0.0504 REMARK 3 T TENSOR REMARK 3 T11: 0.0900 T22: 0.1062 REMARK 3 T33: 0.0900 T12: 0.0122 REMARK 3 T13: -0.0011 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.3994 L22: 1.0010 REMARK 3 L33: 0.5415 L12: 0.0170 REMARK 3 L13: -0.2875 L23: -0.1986 REMARK 3 S TENSOR REMARK 3 S11: -0.0297 S12: 0.0346 S13: -0.0228 REMARK 3 S21: 0.0264 S22: -0.0216 S23: -0.0349 REMARK 3 S31: 0.0029 S32: 0.0486 S33: 0.0814 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN B AND RESID 515:537) REMARK 3 ORIGIN FOR THE GROUP (A): -8.1119 -31.4748 -3.9650 REMARK 3 T TENSOR REMARK 3 T11: 0.1171 T22: 0.0942 REMARK 3 T33: 0.1209 T12: 0.0163 REMARK 3 T13: -0.0196 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 0.7632 L22: 0.8884 REMARK 3 L33: 0.9377 L12: 0.1102 REMARK 3 L13: 0.0526 L23: 0.4305 REMARK 3 S TENSOR REMARK 3 S11: 0.0635 S12: 0.1133 S13: -0.1597 REMARK 3 S21: 0.0030 S22: -0.0252 S23: 0.0931 REMARK 3 S31: 0.1481 S32: -0.0198 S33: -0.0035 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: (CHAIN B AND RESID 538:548) REMARK 3 ORIGIN FOR THE GROUP (A): -8.0127 -6.3554 -7.3020 REMARK 3 T TENSOR REMARK 3 T11: 0.1269 T22: 0.1164 REMARK 3 T33: 0.1083 T12: 0.0165 REMARK 3 T13: 0.0114 T23: 0.0349 REMARK 3 L TENSOR REMARK 3 L11: 1.8866 L22: 3.6588 REMARK 3 L33: 3.1593 L12: 0.6104 REMARK 3 L13: -0.4686 L23: -1.6223 REMARK 3 S TENSOR REMARK 3 S11: 0.1206 S12: 0.3131 S13: 0.2611 REMARK 3 S21: -0.2485 S22: 0.1260 S23: 0.2186 REMARK 3 S31: -0.1527 S32: -0.0040 S33: -0.1285 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: (CHAIN B AND RESID 549:558) REMARK 3 ORIGIN FOR THE GROUP (A): -11.5256 -5.8554 -3.7695 REMARK 3 T TENSOR REMARK 3 T11: 0.0984 T22: 0.1195 REMARK 3 T33: 0.1288 T12: 0.0318 REMARK 3 T13: 0.0029 T23: 0.0234 REMARK 3 L TENSOR REMARK 3 L11: 2.6142 L22: 2.1438 REMARK 3 L33: 2.3820 L12: 0.3048 REMARK 3 L13: 0.3015 L23: 1.2347 REMARK 3 S TENSOR REMARK 3 S11: 0.1736 S12: 0.1145 S13: 0.1384 REMARK 3 S21: -0.0029 S22: -0.1144 S23: 0.1818 REMARK 3 S31: -0.1623 S32: -0.2336 S33: 0.0164 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: (CHAIN B AND RESID 559:582) REMARK 3 ORIGIN FOR THE GROUP (A): 1.3118 -27.5342 -5.4867 REMARK 3 T TENSOR REMARK 3 T11: 0.0928 T22: 0.1100 REMARK 3 T33: 0.0933 T12: 0.0155 REMARK 3 T13: -0.0043 T23: -0.0124 REMARK 3 L TENSOR REMARK 3 L11: 0.9534 L22: 0.8540 REMARK 3 L33: 0.5864 L12: -0.4299 REMARK 3 L13: 0.3035 L23: -0.2995 REMARK 3 S TENSOR REMARK 3 S11: 0.0127 S12: 0.1580 S13: -0.0753 REMARK 3 S21: -0.0527 S22: -0.0227 S23: -0.0143 REMARK 3 S31: 0.0284 S32: 0.0887 S33: -0.0116 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: (CHAIN B AND RESID 583:598) REMARK 3 ORIGIN FOR THE GROUP (A): -3.7767 -24.5705 -15.4089 REMARK 3 T TENSOR REMARK 3 T11: 0.1808 T22: 0.2556 REMARK 3 T33: 0.0992 T12: 0.0358 REMARK 3 T13: -0.0185 T23: -0.0201 REMARK 3 L TENSOR REMARK 3 L11: 2.0546 L22: 0.8281 REMARK 3 L33: 2.0917 L12: -0.1404 REMARK 3 L13: 1.3876 L23: 0.0678 REMARK 3 S TENSOR REMARK 3 S11: 0.0587 S12: 0.5317 S13: -0.1195 REMARK 3 S21: -0.2811 S22: 0.0035 S23: -0.0103 REMARK 3 S31: -0.0262 S32: 0.1275 S33: -0.0185 REMARK 3 TLS GROUP : 20 REMARK 3 SELECTION: (CHAIN B AND RESID 599:607) REMARK 3 ORIGIN FOR THE GROUP (A): 2.7078 -23.7993 8.9923 REMARK 3 T TENSOR REMARK 3 T11: 0.1266 T22: 0.0894 REMARK 3 T33: 0.1070 T12: 0.0198 REMARK 3 T13: -0.0212 T23: -0.0113 REMARK 3 L TENSOR REMARK 3 L11: 2.9234 L22: 2.1567 REMARK 3 L33: 1.4556 L12: 1.4570 REMARK 3 L13: -0.1246 L23: -0.0335 REMARK 3 S TENSOR REMARK 3 S11: 0.0842 S12: -0.1990 S13: 0.1293 REMARK 3 S21: 0.0959 S22: -0.0479 S23: -0.0071 REMARK 3 S31: 0.1444 S32: 0.1317 S33: 0.0259 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 6NPI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000239168. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42238 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 1VHI REMARK 200 REMARK 200 REMARK: RECTANGULAR RODS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM MES, PH 6.5, AND 0-100 MM NACL, REMARK 280 10 MM DTT, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 29.85200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.74900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.72600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.74900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.85200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.72600 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: 3880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 SER A 467 REMARK 465 SER B 467 REMARK 465 HIS B 468 REMARK 465 MET B 469 REMARK 465 GLY B 470 REMARK 465 GLN B 471 REMARK 465 GLY B 472 REMARK 465 GLY B 473 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 HZ3 LYS B 477 O08 60Q B 701 1.51 REMARK 500 O HOH A 891 O HOH A 893 1.77 REMARK 500 OD2 ASP B 577 O HOH B 801 1.90 REMARK 500 OE1 GLU B 495 O HOH B 802 1.91 REMARK 500 O HOH A 890 O HOH A 893 1.91 REMARK 500 O HOH A 804 O HOH A 827 1.92 REMARK 500 O HOH A 890 O HOH A 891 2.02 REMARK 500 O HOH A 830 O HOH A 845 2.04 REMARK 500 O HOH A 874 O HOH A 897 2.05 REMARK 500 NZ LYS B 477 O08 60Q B 701 2.06 REMARK 500 O HOH A 702 O HOH A 840 2.06 REMARK 500 O HOH A 710 O HOH A 842 2.11 REMARK 500 O HOH A 862 O HOH A 892 2.12 REMARK 500 O HOH A 737 O HOH A 868 2.13 REMARK 500 O HOH B 895 O HOH B 967 2.14 REMARK 500 O HOH B 809 O HOH B 865 2.16 REMARK 500 O HOH B 886 O HOH B 959 2.16 REMARK 500 O HOH B 861 O HOH B 919 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 885 O HOH A 893 3545 2.11 REMARK 500 OE2 GLU A 495 OH TYR B 518 4545 2.12 REMARK 500 O HOH A 815 O HOH A 861 4545 2.18 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 60Q B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KW1 B 702 DBREF 6NPI A 471 607 UNP P03211 EBNA1_EBVB9 471 607 DBREF 6NPI B 471 607 UNP P03211 EBNA1_EBVB9 471 607 SEQADV 6NPI SER A 467 UNP P03211 EXPRESSION TAG SEQADV 6NPI HIS A 468 UNP P03211 EXPRESSION TAG SEQADV 6NPI MET A 469 UNP P03211 EXPRESSION TAG SEQADV 6NPI GLY A 470 UNP P03211 EXPRESSION TAG SEQADV 6NPI SER B 467 UNP P03211 EXPRESSION TAG SEQADV 6NPI HIS B 468 UNP P03211 EXPRESSION TAG SEQADV 6NPI MET B 469 UNP P03211 EXPRESSION TAG SEQADV 6NPI GLY B 470 UNP P03211 EXPRESSION TAG SEQRES 1 A 141 SER HIS MET GLY GLN GLY GLY SER ASN PRO LYS PHE GLU SEQRES 2 A 141 ASN ILE ALA GLU GLY LEU ARG ALA LEU LEU ALA ARG SER SEQRES 3 A 141 HIS VAL GLU ARG THR THR ASP GLU GLY THR TRP VAL ALA SEQRES 4 A 141 GLY VAL PHE VAL TYR GLY GLY SER LYS THR SER LEU TYR SEQRES 5 A 141 ASN LEU ARG ARG GLY THR ALA LEU ALA ILE PRO GLN CYS SEQRES 6 A 141 ARG LEU THR PRO LEU SER ARG LEU PRO PHE GLY MET ALA SEQRES 7 A 141 PRO GLY PRO GLY PRO GLN PRO GLY PRO LEU ARG GLU SER SEQRES 8 A 141 ILE VAL CYS TYR PHE MET VAL PHE LEU GLN THR HIS ILE SEQRES 9 A 141 PHE ALA GLU VAL LEU LYS ASP ALA ILE LYS ASP LEU VAL SEQRES 10 A 141 MET THR LYS PRO ALA PRO THR CYS ASN ILE ARG VAL THR SEQRES 11 A 141 VAL CYS SER PHE ASP ASP GLY VAL ASP LEU PRO SEQRES 1 B 141 SER HIS MET GLY GLN GLY GLY SER ASN PRO LYS PHE GLU SEQRES 2 B 141 ASN ILE ALA GLU GLY LEU ARG ALA LEU LEU ALA ARG SER SEQRES 3 B 141 HIS VAL GLU ARG THR THR ASP GLU GLY THR TRP VAL ALA SEQRES 4 B 141 GLY VAL PHE VAL TYR GLY GLY SER LYS THR SER LEU TYR SEQRES 5 B 141 ASN LEU ARG ARG GLY THR ALA LEU ALA ILE PRO GLN CYS SEQRES 6 B 141 ARG LEU THR PRO LEU SER ARG LEU PRO PHE GLY MET ALA SEQRES 7 B 141 PRO GLY PRO GLY PRO GLN PRO GLY PRO LEU ARG GLU SER SEQRES 8 B 141 ILE VAL CYS TYR PHE MET VAL PHE LEU GLN THR HIS ILE SEQRES 9 B 141 PHE ALA GLU VAL LEU LYS ASP ALA ILE LYS ASP LEU VAL SEQRES 10 B 141 MET THR LYS PRO ALA PRO THR CYS ASN ILE ARG VAL THR SEQRES 11 B 141 VAL CYS SER PHE ASP ASP GLY VAL ASP LEU PRO HET 60Q B 701 22 HET KW1 B 702 48 HETNAM 60Q 2-PYRROL-1-YLBENZOIC ACID HETNAM KW1 ({2-[(4-BROMO-5-METHYL-1,2-OXAZOL-3-YL)AMINO]-2- HETNAM 2 KW1 OXOETHYL}SULFANYL)ACETIC ACID FORMUL 3 60Q C11 H9 N O2 FORMUL 4 KW1 C8 H9 BR N2 O4 S FORMUL 5 HOH *372(H2 O) HELIX 1 AA1 PRO A 476 ALA A 490 1 15 HELIX 2 AA2 SER A 513 ILE A 528 1 16 HELIX 3 AA3 PRO A 551 LEU A 554 5 4 HELIX 4 AA4 THR A 568 MET A 584 1 17 HELIX 5 AA5 PRO A 589 CYS A 591 5 3 HELIX 6 AA6 ASN B 475 ALA B 490 1 16 HELIX 7 AA7 SER B 513 ILE B 528 1 16 HELIX 8 AA8 THR B 568 MET B 584 1 17 HELIX 9 AA9 PRO B 589 CYS B 591 5 3 SHEET 1 AA1 8 ARG A 532 LEU A 533 0 SHEET 2 AA1 8 GLU A 556 LEU A 566 -1 O PHE A 565 N ARG A 532 SHEET 3 AA1 8 TRP A 503 GLY A 511 -1 N VAL A 507 O VAL A 564 SHEET 4 AA1 8 ILE A 593 VAL A 604 -1 O ARG A 594 N TYR A 510 SHEET 5 AA1 8 ILE B 593 VAL B 604 -1 O ASP B 601 N VAL A 597 SHEET 6 AA1 8 TRP B 503 GLY B 511 -1 N TYR B 510 O ARG B 594 SHEET 7 AA1 8 GLU B 556 LEU B 566 -1 O VAL B 564 N VAL B 507 SHEET 8 AA1 8 ARG B 532 LEU B 533 -1 N ARG B 532 O PHE B 565 SHEET 1 AA2 8 SER A 537 PRO A 540 0 SHEET 2 AA2 8 GLU A 556 LEU A 566 -1 O SER A 557 N LEU A 539 SHEET 3 AA2 8 TRP A 503 GLY A 511 -1 N VAL A 507 O VAL A 564 SHEET 4 AA2 8 ILE A 593 VAL A 604 -1 O ARG A 594 N TYR A 510 SHEET 5 AA2 8 ILE B 593 VAL B 604 -1 O ASP B 601 N VAL A 597 SHEET 6 AA2 8 TRP B 503 GLY B 511 -1 N TYR B 510 O ARG B 594 SHEET 7 AA2 8 GLU B 556 LEU B 566 -1 O VAL B 564 N VAL B 507 SHEET 8 AA2 8 SER B 537 PRO B 540 -1 N LEU B 539 O VAL B 559 CISPEP 1 ALA A 588 PRO A 589 0 6.15 CISPEP 2 ALA B 588 PRO B 589 0 5.81 SITE 1 AC1 5 LYS B 477 SER B 516 ASN B 519 THR B 590 SITE 2 AC1 5 HOH B 827 SITE 1 AC2 10 GLU A 495 GLU A 556 THR A 568 HIS A 569 SITE 2 AC2 10 ILE A 570 LYS B 514 ARG B 521 PRO B 535 SITE 3 AC2 10 LEU B 536 HOH B 853 CRYST1 59.704 67.452 69.498 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 0.016749 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014825 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014389 0.00000