HEADER VIRAL PROTEIN/INHIBITOR 17-JAN-19 6NPM 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 6NPM 1 REMARK REVDAT 1 20-MAR-19 6NPM 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. 1.60 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 37305 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.170 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.370 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 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 30.9610 - 3.8619 0.95 2584 146 0.1534 0.1631 REMARK 3 2 3.8619 - 3.0662 0.98 2547 144 0.1416 0.1701 REMARK 3 3 3.0662 - 2.6789 0.99 2554 141 0.1419 0.1706 REMARK 3 4 2.6789 - 2.4340 1.00 2542 149 0.1373 0.1508 REMARK 3 5 2.4340 - 2.2596 1.00 2536 145 0.1334 0.1763 REMARK 3 6 2.2596 - 2.1265 1.00 2510 144 0.1381 0.1682 REMARK 3 7 2.1265 - 2.0200 1.00 2551 139 0.1362 0.1700 REMARK 3 8 2.0200 - 1.9321 1.00 2499 142 0.1425 0.1683 REMARK 3 9 1.9321 - 1.8577 0.99 2523 139 0.1547 0.1861 REMARK 3 10 1.8577 - 1.7936 1.00 2498 150 0.1469 0.1834 REMARK 3 11 1.7936 - 1.7375 1.00 2512 135 0.1437 0.1667 REMARK 3 12 1.7375 - 1.6879 1.00 2518 145 0.1436 0.1833 REMARK 3 13 1.6879 - 1.6434 1.00 2496 142 0.1439 0.1816 REMARK 3 14 1.6434 - 1.6033 0.97 2432 142 0.1476 0.1772 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.44 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.99 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 2238 REMARK 3 ANGLE : 1.020 3051 REMARK 3 CHIRALITY : 0.058 341 REMARK 3 PLANARITY : 0.008 403 REMARK 3 DIHEDRAL : 3.370 1831 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): -17.3435 5.3738 21.7741 REMARK 3 T TENSOR REMARK 3 T11: 0.2717 T22: 0.2523 REMARK 3 T33: 0.2307 T12: 0.0322 REMARK 3 T13: 0.0038 T23: -0.0400 REMARK 3 L TENSOR REMARK 3 L11: 3.0416 L22: 0.3245 REMARK 3 L33: 3.3646 L12: 0.9559 REMARK 3 L13: -3.1989 L23: -1.0097 REMARK 3 S TENSOR REMARK 3 S11: -0.1476 S12: -0.3553 S13: 0.3706 REMARK 3 S21: 0.3768 S22: 0.0359 S23: 0.0602 REMARK 3 S31: 0.2035 S32: 0.5743 S33: 0.2649 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 475:492) REMARK 3 ORIGIN FOR THE GROUP (A): -5.1492 -1.1375 15.5260 REMARK 3 T TENSOR REMARK 3 T11: 0.1465 T22: 0.1151 REMARK 3 T33: 0.1331 T12: 0.0039 REMARK 3 T13: -0.0001 T23: -0.0341 REMARK 3 L TENSOR REMARK 3 L11: 4.6941 L22: 0.8066 REMARK 3 L33: 1.3229 L12: 0.3512 REMARK 3 L13: -0.5576 L23: 0.0716 REMARK 3 S TENSOR REMARK 3 S11: 0.0660 S12: -0.0050 S13: 0.0665 REMARK 3 S21: -0.0107 S22: -0.1402 S23: 0.0359 REMARK 3 S31: -0.1117 S32: -0.0370 S33: -0.0164 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 493:501) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0852 -1.4644 -1.0217 REMARK 3 T TENSOR REMARK 3 T11: 0.2287 T22: 0.1629 REMARK 3 T33: 0.1787 T12: -0.0433 REMARK 3 T13: 0.0145 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 2.0374 L22: 1.5913 REMARK 3 L33: 8.2244 L12: 0.1157 REMARK 3 L13: 0.7834 L23: 2.0381 REMARK 3 S TENSOR REMARK 3 S11: 0.0493 S12: 0.2569 S13: 0.2172 REMARK 3 S21: -0.3746 S22: 0.2057 S23: -0.0279 REMARK 3 S31: -0.6959 S32: 0.4415 S33: -0.3389 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 502:516) REMARK 3 ORIGIN FOR THE GROUP (A): -3.9665 -15.1810 6.9927 REMARK 3 T TENSOR REMARK 3 T11: 0.1010 T22: 0.0735 REMARK 3 T33: 0.0975 T12: 0.0020 REMARK 3 T13: -0.0132 T23: -0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.9563 L22: 0.8720 REMARK 3 L33: 1.0964 L12: 0.0352 REMARK 3 L13: 0.1581 L23: 0.1080 REMARK 3 S TENSOR REMARK 3 S11: -0.0385 S12: 0.0043 S13: -0.0211 REMARK 3 S21: -0.0217 S22: 0.0039 S23: -0.0138 REMARK 3 S31: 0.1327 S32: 0.0258 S33: 0.0117 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 517:537) REMARK 3 ORIGIN FOR THE GROUP (A): -8.7419 -8.3156 6.6871 REMARK 3 T TENSOR REMARK 3 T11: 0.1181 T22: 0.0840 REMARK 3 T33: 0.1083 T12: 0.0075 REMARK 3 T13: 0.0019 T23: -0.0096 REMARK 3 L TENSOR REMARK 3 L11: 0.6526 L22: 0.8751 REMARK 3 L33: 1.5539 L12: -0.0525 REMARK 3 L13: -0.0616 L23: 0.0914 REMARK 3 S TENSOR REMARK 3 S11: 0.0467 S12: -0.0372 S13: 0.0549 REMARK 3 S21: 0.0422 S22: -0.0593 S23: 0.0274 REMARK 3 S31: -0.1529 S32: -0.0803 S33: -0.0249 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 538:549) REMARK 3 ORIGIN FOR THE GROUP (A): -9.1634 -33.6369 8.9153 REMARK 3 T TENSOR REMARK 3 T11: 0.1672 T22: 0.1181 REMARK 3 T33: 0.1845 T12: -0.0236 REMARK 3 T13: -0.0075 T23: 0.0180 REMARK 3 L TENSOR REMARK 3 L11: 0.8766 L22: 2.5384 REMARK 3 L33: 1.5153 L12: 0.2908 REMARK 3 L13: -0.3800 L23: -0.4529 REMARK 3 S TENSOR REMARK 3 S11: 0.0078 S12: -0.0517 S13: -0.2163 REMARK 3 S21: 0.2563 S22: 0.1158 S23: 0.4334 REMARK 3 S31: 0.2008 S32: -0.2141 S33: -0.0376 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 550:560) REMARK 3 ORIGIN FOR THE GROUP (A): -11.3528 -31.6346 6.2028 REMARK 3 T TENSOR REMARK 3 T11: 0.1315 T22: 0.1133 REMARK 3 T33: 0.1757 T12: -0.0252 REMARK 3 T13: 0.0169 T23: 0.0092 REMARK 3 L TENSOR REMARK 3 L11: 0.9008 L22: 3.7301 REMARK 3 L33: 2.7951 L12: -1.0359 REMARK 3 L13: -0.5677 L23: 2.5678 REMARK 3 S TENSOR REMARK 3 S11: 0.0311 S12: -0.0308 S13: -0.1212 REMARK 3 S21: 0.1692 S22: -0.2961 S23: 0.4845 REMARK 3 S31: 0.2645 S32: -0.2139 S33: 0.3540 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 561:576) REMARK 3 ORIGIN FOR THE GROUP (A): 2.0084 -10.7085 4.5808 REMARK 3 T TENSOR REMARK 3 T11: 0.0998 T22: 0.0859 REMARK 3 T33: 0.1084 T12: -0.0007 REMARK 3 T13: 0.0051 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 0.7028 L22: 0.4312 REMARK 3 L33: 0.6069 L12: 0.3777 REMARK 3 L13: -0.0487 L23: -0.3120 REMARK 3 S TENSOR REMARK 3 S11: 0.0061 S12: -0.0082 S13: 0.0459 REMARK 3 S21: 0.0137 S22: -0.0201 S23: 0.0141 REMARK 3 S31: -0.0093 S32: 0.0871 S33: -0.0016 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 577:599) REMARK 3 ORIGIN FOR THE GROUP (A): -1.3038 -13.6345 17.0876 REMARK 3 T TENSOR REMARK 3 T11: 0.1234 T22: 0.1199 REMARK 3 T33: 0.1084 T12: 0.0003 REMARK 3 T13: -0.0068 T23: -0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.9420 L22: 1.0213 REMARK 3 L33: 1.6277 L12: -0.0549 REMARK 3 L13: -0.6695 L23: 0.0046 REMARK 3 S TENSOR REMARK 3 S11: 0.0086 S12: -0.1439 S13: 0.0790 REMARK 3 S21: 0.1341 S22: 0.0187 S23: 0.0100 REMARK 3 S31: 0.1155 S32: 0.1174 S33: -0.0026 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 600:607) REMARK 3 ORIGIN FOR THE GROUP (A): 0.8794 -14.8926 -7.4225 REMARK 3 T TENSOR REMARK 3 T11: 0.1351 T22: 0.1587 REMARK 3 T33: 0.1306 T12: -0.0057 REMARK 3 T13: 0.0137 T23: 0.0026 REMARK 3 L TENSOR REMARK 3 L11: 3.6151 L22: 1.3283 REMARK 3 L33: 1.0488 L12: -1.0440 REMARK 3 L13: -0.7769 L23: 0.9315 REMARK 3 S TENSOR REMARK 3 S11: 0.0314 S12: 0.4919 S13: 0.0261 REMARK 3 S21: -0.1553 S22: -0.1286 S23: -0.0498 REMARK 3 S31: 0.0851 S32: 0.0654 S33: 0.0002 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN B AND RESID 474:483) REMARK 3 ORIGIN FOR THE GROUP (A): -11.1015 -40.0008 -11.6982 REMARK 3 T TENSOR REMARK 3 T11: 0.1939 T22: 0.1567 REMARK 3 T33: 0.2631 T12: -0.0277 REMARK 3 T13: -0.0240 T23: -0.0493 REMARK 3 L TENSOR REMARK 3 L11: 6.9069 L22: 2.2211 REMARK 3 L33: 3.6667 L12: -0.0679 REMARK 3 L13: -0.8054 L23: 1.0484 REMARK 3 S TENSOR REMARK 3 S11: -0.0577 S12: -0.0051 S13: -0.6849 REMARK 3 S21: -0.1418 S22: -0.2097 S23: 0.6123 REMARK 3 S31: 0.4513 S32: -0.4358 S33: 0.1433 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: (CHAIN B AND RESID 484:491) REMARK 3 ORIGIN FOR THE GROUP (A): 3.1242 -38.9763 -12.7769 REMARK 3 T TENSOR REMARK 3 T11: 0.1918 T22: 0.2419 REMARK 3 T33: 0.1875 T12: 0.0433 REMARK 3 T13: -0.0248 T23: -0.0551 REMARK 3 L TENSOR REMARK 3 L11: 1.8107 L22: 4.2461 REMARK 3 L33: 1.3040 L12: -0.1511 REMARK 3 L13: 1.3188 L23: -1.2173 REMARK 3 S TENSOR REMARK 3 S11: 0.2293 S12: 0.1979 S13: -0.2850 REMARK 3 S21: 0.0903 S22: -0.0567 S23: -0.3489 REMARK 3 S31: 0.2139 S32: 0.7167 S33: -0.2317 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: (CHAIN B AND RESID 492:497) REMARK 3 ORIGIN FOR THE GROUP (A): 8.9413 -38.7150 -2.8696 REMARK 3 T TENSOR REMARK 3 T11: 0.2649 T22: 0.1979 REMARK 3 T33: 0.2155 T12: 0.0727 REMARK 3 T13: -0.0270 T23: -0.0389 REMARK 3 L TENSOR REMARK 3 L11: 3.9094 L22: 1.7728 REMARK 3 L33: 5.6490 L12: 0.8069 REMARK 3 L13: -0.6648 L23: 1.4304 REMARK 3 S TENSOR REMARK 3 S11: 0.0651 S12: 0.1572 S13: -0.6504 REMARK 3 S21: -0.1775 S22: 0.1901 S23: -0.2617 REMARK 3 S31: 0.9895 S32: 0.4769 S33: -0.2960 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: (CHAIN B AND RESID 498:514) REMARK 3 ORIGIN FOR THE GROUP (A): 0.2690 -26.9681 -0.1491 REMARK 3 T TENSOR REMARK 3 T11: 0.1068 T22: 0.0951 REMARK 3 T33: 0.1128 T12: 0.0032 REMARK 3 T13: 0.0029 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.1142 L22: 0.7511 REMARK 3 L33: 0.7185 L12: -0.0230 REMARK 3 L13: -0.1121 L23: -0.0737 REMARK 3 S TENSOR REMARK 3 S11: -0.0429 S12: -0.0390 S13: 0.0157 REMARK 3 S21: 0.0589 S22: -0.0078 S23: -0.0137 REMARK 3 S31: -0.0656 S32: 0.0204 S33: 0.0451 REMARK 3 TLS GROUP : 15 REMARK 3 SELECTION: (CHAIN B AND RESID 515:537) REMARK 3 ORIGIN FOR THE GROUP (A): -8.1576 -31.6314 -3.9611 REMARK 3 T TENSOR REMARK 3 T11: 0.1179 T22: 0.0890 REMARK 3 T33: 0.1358 T12: -0.0005 REMARK 3 T13: -0.0013 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.4227 L22: 0.7638 REMARK 3 L33: 1.0236 L12: 0.0151 REMARK 3 L13: 0.1034 L23: 0.2949 REMARK 3 S TENSOR REMARK 3 S11: 0.0242 S12: 0.0157 S13: -0.0847 REMARK 3 S21: 0.0217 S22: -0.0143 S23: 0.0517 REMARK 3 S31: 0.1105 S32: -0.0797 S33: 0.0138 REMARK 3 TLS GROUP : 16 REMARK 3 SELECTION: (CHAIN B AND RESID 538:548) REMARK 3 ORIGIN FOR THE GROUP (A): -8.5394 -6.8354 -7.2180 REMARK 3 T TENSOR REMARK 3 T11: 0.1368 T22: 0.1171 REMARK 3 T33: 0.1222 T12: 0.0208 REMARK 3 T13: 0.0119 T23: 0.0387 REMARK 3 L TENSOR REMARK 3 L11: 1.8623 L22: 4.4760 REMARK 3 L33: 3.0018 L12: 1.2147 REMARK 3 L13: -0.5989 L23: -2.2771 REMARK 3 S TENSOR REMARK 3 S11: 0.0300 S12: 0.2746 S13: 0.2042 REMARK 3 S21: 0.1985 S22: 0.2608 S23: 0.2077 REMARK 3 S31: -0.2262 S32: -0.1398 S33: -0.2240 REMARK 3 TLS GROUP : 17 REMARK 3 SELECTION: (CHAIN B AND RESID 549:558) REMARK 3 ORIGIN FOR THE GROUP (A): -11.4809 -5.9912 -3.8438 REMARK 3 T TENSOR REMARK 3 T11: 0.1051 T22: 0.1258 REMARK 3 T33: 0.1405 T12: 0.0376 REMARK 3 T13: 0.0006 T23: 0.0188 REMARK 3 L TENSOR REMARK 3 L11: 2.8300 L22: 2.7325 REMARK 3 L33: 2.3789 L12: 1.3203 REMARK 3 L13: 0.3399 L23: 1.0920 REMARK 3 S TENSOR REMARK 3 S11: 0.1703 S12: 0.1457 S13: 0.1367 REMARK 3 S21: 0.0282 S22: -0.1191 S23: 0.0729 REMARK 3 S31: -0.1135 S32: -0.2049 S33: 0.0336 REMARK 3 TLS GROUP : 18 REMARK 3 SELECTION: (CHAIN B AND RESID 559:582) REMARK 3 ORIGIN FOR THE GROUP (A): 1.3679 -27.7653 -5.4352 REMARK 3 T TENSOR REMARK 3 T11: 0.1019 T22: 0.0868 REMARK 3 T33: 0.1133 T12: 0.0059 REMARK 3 T13: -0.0007 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.4798 L22: 0.6784 REMARK 3 L33: 0.8220 L12: -0.2298 REMARK 3 L13: 0.3408 L23: -0.4381 REMARK 3 S TENSOR REMARK 3 S11: 0.0002 S12: 0.1029 S13: -0.0644 REMARK 3 S21: -0.0234 S22: -0.0242 S23: 0.0130 REMARK 3 S31: 0.0003 S32: 0.0758 S33: 0.0239 REMARK 3 TLS GROUP : 19 REMARK 3 SELECTION: (CHAIN B AND RESID 583:598) REMARK 3 ORIGIN FOR THE GROUP (A): -3.7312 -24.9301 -15.4169 REMARK 3 T TENSOR REMARK 3 T11: 0.1465 T22: 0.1695 REMARK 3 T33: 0.1149 T12: 0.0220 REMARK 3 T13: -0.0023 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 2.3968 L22: 1.5337 REMARK 3 L33: 2.0852 L12: 0.1552 REMARK 3 L13: 1.2485 L23: 0.1091 REMARK 3 S TENSOR REMARK 3 S11: -0.0289 S12: 0.2799 S13: -0.1136 REMARK 3 S21: -0.2239 S22: 0.0267 S23: -0.0053 REMARK 3 S31: -0.2162 S32: 0.0807 S33: 0.0251 REMARK 3 TLS GROUP : 20 REMARK 3 SELECTION: (CHAIN B AND RESID 599:607) REMARK 3 ORIGIN FOR THE GROUP (A): 2.6605 -23.9821 9.0078 REMARK 3 T TENSOR REMARK 3 T11: 0.1367 T22: 0.1154 REMARK 3 T33: 0.1158 T12: 0.0240 REMARK 3 T13: -0.0078 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 4.4758 L22: 2.3664 REMARK 3 L33: 1.2715 L12: 2.0710 REMARK 3 L13: 0.0302 L23: 0.3535 REMARK 3 S TENSOR REMARK 3 S11: 0.0128 S12: -0.3028 S13: 0.1238 REMARK 3 S21: 0.0333 S22: -0.0806 S23: -0.0260 REMARK 3 S31: 0.0319 S32: 0.0710 S33: 0.0752 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 6NPM 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_1000239176. 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 PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37306 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.955 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 (%): 46.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM MES PH 6.5, 0-100 MM NACL, 10 MM REMARK 280 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 29.72900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.77300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.97550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.77300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.72900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.97550 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: 3840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12760 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 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 O HOH A 703 O HOH A 852 1.83 REMARK 500 OE1 GLN A 550 O HOH A 701 1.84 REMARK 500 O HOH B 985 O HOH B 1015 1.89 REMARK 500 O HOH B 863 O HOH B 969 1.91 REMARK 500 O HOH A 849 O HOH A 860 2.03 REMARK 500 O HOH A 702 O HOH B 814 2.03 REMARK 500 O HOH A 714 O HOH A 898 2.04 REMARK 500 O HOH A 791 O HOH A 912 2.06 REMARK 500 OD1 ASN B 480 O HOH B 801 2.07 REMARK 500 NH2 ARG B 538 O HOH B 802 2.10 REMARK 500 O HOH B 808 O HOH B 935 2.12 REMARK 500 O HOH B 882 O HOH B 971 2.12 REMARK 500 OD1 ASP A 601 O HOH A 702 2.18 REMARK 500 O HOH A 850 O HOH A 881 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 921 O HOH B 988 3554 2.06 REMARK 500 O HOH A 712 O HOH A 789 3555 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 CYS A 598 10.05 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 925 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH B1022 DISTANCE = 6.12 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KVD B 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6NPI RELATED DB: PDB DBREF 6NPM A 471 607 UNP P03211 EBNA1_EBVB9 471 607 DBREF 6NPM B 471 607 UNP P03211 EBNA1_EBVB9 471 607 SEQADV 6NPM SER A 467 UNP P03211 EXPRESSION TAG SEQADV 6NPM HIS A 468 UNP P03211 EXPRESSION TAG SEQADV 6NPM MET A 469 UNP P03211 EXPRESSION TAG SEQADV 6NPM GLY A 470 UNP P03211 EXPRESSION TAG SEQADV 6NPM SER B 467 UNP P03211 EXPRESSION TAG SEQADV 6NPM HIS B 468 UNP P03211 EXPRESSION TAG SEQADV 6NPM MET B 469 UNP P03211 EXPRESSION TAG SEQADV 6NPM 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 KVD B 701 25 HETNAM KVD 5-(PHENYLETHYNYL)PYRIDINE-3-CARBOXYLIC ACID FORMUL 3 KVD C14 H9 N O2 FORMUL 4 HOH *447(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 ALA A 505 O LEU A 566 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 ALA A 505 O LEU A 566 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 6.65 CISPEP 2 ALA B 588 PRO B 589 0 6.26 SITE 1 AC1 14 ASN B 480 ILE B 481 GLY B 484 SER B 516 SITE 2 AC1 14 ASN B 519 LEU B 520 LEU B 582 THR B 585 SITE 3 AC1 14 LYS B 586 THR B 590 HOH B 819 HOH B 831 SITE 4 AC1 14 HOH B 833 HOH B 915 CRYST1 59.458 67.951 69.546 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 0.016819 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014716 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014379 0.00000