HEADER HYDROLASE 15-OCT-19 6T55 TITLE THROMBIN IN COMPLEX WITH METHYLBENZYLAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: COAGULATION FACTOR II; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROTHROMBIN; COMPND 8 CHAIN: H; COMPND 9 SYNONYM: COAGULATION FACTOR II; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HIRUDIN VARIANT-2; COMPND 13 CHAIN: I; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HIRUDO MEDICINALIS; SOURCE 12 ORGANISM_COMMON: MEDICINAL LEECH; SOURCE 13 ORGANISM_TAXID: 6421 KEYWDS COAGULATION, BLOOD CLOTTING, CONVERTION OF FIBRINOGEN TO FIBRIN, KEYWDS 2 SERINE PROTEASE, PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.NGO,N.ABAZI,A.HEINE,G.KLEBE REVDAT 2 24-JAN-24 6T55 1 REMARK REVDAT 1 18-NOV-20 6T55 0 JRNL AUTH K.NGO,N.ABAZI,A.HEINE,G.KLEBE JRNL TITL THROMBIN IN COMPLEX WITH METHYLBENZYLAMINE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 68508 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3425 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 49.6600 - 4.0200 0.96 2755 145 0.1569 0.1567 REMARK 3 2 4.0200 - 3.1900 0.99 2750 145 0.1407 0.1802 REMARK 3 3 3.1900 - 2.7900 0.96 2684 141 0.1542 0.1617 REMARK 3 4 2.7900 - 2.5300 0.98 2754 145 0.1449 0.1689 REMARK 3 5 2.5300 - 2.3500 0.98 2733 143 0.1359 0.1436 REMARK 3 6 2.3500 - 2.2100 0.98 2722 144 0.1349 0.1516 REMARK 3 7 2.2100 - 2.1000 0.96 2665 140 0.1290 0.1483 REMARK 3 8 2.1000 - 2.0100 0.98 2699 142 0.1359 0.1637 REMARK 3 9 2.0100 - 1.9300 0.98 2722 143 0.1322 0.1656 REMARK 3 10 1.9300 - 1.8700 0.99 2745 145 0.1412 0.1683 REMARK 3 11 1.8700 - 1.8100 0.98 2720 143 0.1461 0.1780 REMARK 3 12 1.8100 - 1.7600 0.98 2719 143 0.1444 0.1567 REMARK 3 13 1.7600 - 1.7100 0.99 2741 144 0.1533 0.1537 REMARK 3 14 1.7100 - 1.6700 0.96 2621 138 0.1615 0.2339 REMARK 3 15 1.6700 - 1.6300 0.98 2725 144 0.1655 0.1775 REMARK 3 16 1.6300 - 1.6000 0.98 2734 144 0.1737 0.1859 REMARK 3 17 1.6000 - 1.5600 0.98 2663 140 0.1827 0.2041 REMARK 3 18 1.5600 - 1.5300 0.98 2754 145 0.1852 0.1916 REMARK 3 19 1.5300 - 1.5100 0.98 2714 143 0.2089 0.2036 REMARK 3 20 1.5100 - 1.4800 0.98 2726 143 0.2332 0.2441 REMARK 3 21 1.4800 - 1.4600 0.98 2724 144 0.2437 0.2671 REMARK 3 22 1.4600 - 1.4300 0.98 2693 141 0.2656 0.2890 REMARK 3 23 1.4300 - 1.4100 0.96 2682 141 0.2783 0.2693 REMARK 3 24 1.4100 - 1.3900 0.97 2638 139 0.3030 0.3099 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) : 0.132 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.789 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.25 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 2508 REMARK 3 ANGLE : 1.023 3407 REMARK 3 CHIRALITY : 0.084 354 REMARK 3 PLANARITY : 0.007 451 REMARK 3 DIHEDRAL : 22.096 960 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1C THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 62.6716 14.9324 89.4680 REMARK 3 T TENSOR REMARK 3 T11: 0.2105 T22: 0.1574 REMARK 3 T33: 0.1939 T12: 0.0276 REMARK 3 T13: -0.0056 T23: 0.0113 REMARK 3 L TENSOR REMARK 3 L11: 0.0710 L22: 0.1053 REMARK 3 L33: 0.0147 L12: -0.0914 REMARK 3 L13: 0.0235 L23: 0.0096 REMARK 3 S TENSOR REMARK 3 S11: -0.0544 S12: 0.0299 S13: 0.2064 REMARK 3 S21: -0.1047 S22: -0.0896 S23: -0.0464 REMARK 3 S31: -0.3134 S32: -0.1141 S33: 0.0005 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 8 THROUGH 14B) REMARK 3 ORIGIN FOR THE GROUP (A): 53.7560 11.9422 92.2528 REMARK 3 T TENSOR REMARK 3 T11: 0.1869 T22: 0.2054 REMARK 3 T33: 0.2244 T12: 0.0605 REMARK 3 T13: -0.0103 T23: -0.0147 REMARK 3 L TENSOR REMARK 3 L11: 0.0419 L22: 0.0552 REMARK 3 L33: 0.1087 L12: -0.0400 REMARK 3 L13: 0.0373 L23: 0.0064 REMARK 3 S TENSOR REMARK 3 S11: 0.1115 S12: -0.0423 S13: 0.0568 REMARK 3 S21: -0.1376 S22: -0.1304 S23: 0.1505 REMARK 3 S31: -0.1421 S32: -0.1481 S33: -0.0003 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 14C THROUGH 14L) REMARK 3 ORIGIN FOR THE GROUP (A): 56.7175 6.1829 104.1161 REMARK 3 T TENSOR REMARK 3 T11: 0.1996 T22: 0.2196 REMARK 3 T33: 0.2018 T12: 0.0286 REMARK 3 T13: 0.0309 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 0.0395 L22: 0.0460 REMARK 3 L33: 0.0506 L12: 0.0184 REMARK 3 L13: 0.0209 L23: -0.0480 REMARK 3 S TENSOR REMARK 3 S11: 0.0123 S12: -0.1258 S13: -0.0631 REMARK 3 S21: 0.1060 S22: 0.0693 S23: 0.1133 REMARK 3 S31: 0.0608 S32: -0.2629 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 16 THROUGH 50 ) REMARK 3 ORIGIN FOR THE GROUP (A): 67.4005 -0.6686 83.0982 REMARK 3 T TENSOR REMARK 3 T11: 0.2358 T22: 0.1870 REMARK 3 T33: 0.1721 T12: 0.0587 REMARK 3 T13: -0.0235 T23: -0.0287 REMARK 3 L TENSOR REMARK 3 L11: 1.1191 L22: 0.4925 REMARK 3 L33: 0.4630 L12: -0.3390 REMARK 3 L13: 0.4276 L23: -0.3485 REMARK 3 S TENSOR REMARK 3 S11: 0.2556 S12: 0.2608 S13: -0.1483 REMARK 3 S21: -0.2572 S22: -0.1879 S23: 0.0715 REMARK 3 S31: 0.1846 S32: 0.0293 S33: 0.0372 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 51 THROUGH 60I) REMARK 3 ORIGIN FOR THE GROUP (A): 81.0601 -6.6753 85.4226 REMARK 3 T TENSOR REMARK 3 T11: 0.2058 T22: 0.2547 REMARK 3 T33: 0.1807 T12: 0.1105 REMARK 3 T13: -0.0014 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 0.3239 L22: 0.6662 REMARK 3 L33: 0.4704 L12: -0.0376 REMARK 3 L13: 0.2318 L23: -0.0111 REMARK 3 S TENSOR REMARK 3 S11: 0.3546 S12: 0.3279 S13: 0.1557 REMARK 3 S21: -0.3106 S22: -0.1968 S23: -0.2156 REMARK 3 S31: 0.1522 S32: 0.2288 S33: 0.2146 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 61 THROUGH 80 ) REMARK 3 ORIGIN FOR THE GROUP (A): 66.4239 0.6393 74.7438 REMARK 3 T TENSOR REMARK 3 T11: 0.3401 T22: 0.3166 REMARK 3 T33: 0.1503 T12: 0.1351 REMARK 3 T13: -0.0336 T23: -0.0360 REMARK 3 L TENSOR REMARK 3 L11: 0.0838 L22: 0.6896 REMARK 3 L33: 0.0704 L12: -0.0536 REMARK 3 L13: -0.0013 L23: -0.1406 REMARK 3 S TENSOR REMARK 3 S11: 0.3037 S12: 0.3705 S13: -0.1063 REMARK 3 S21: -0.5189 S22: -0.1997 S23: 0.1733 REMARK 3 S31: 0.3884 S32: 0.1434 S33: -0.0554 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 81 THROUGH 125 ) REMARK 3 ORIGIN FOR THE GROUP (A): 78.6199 2.8300 86.9805 REMARK 3 T TENSOR REMARK 3 T11: 0.1590 T22: 0.2232 REMARK 3 T33: 0.1848 T12: 0.0494 REMARK 3 T13: 0.0350 T23: 0.0361 REMARK 3 L TENSOR REMARK 3 L11: 0.9191 L22: 0.5710 REMARK 3 L33: 0.4477 L12: -0.1433 REMARK 3 L13: 0.2561 L23: 0.4287 REMARK 3 S TENSOR REMARK 3 S11: 0.0889 S12: 0.2114 S13: 0.1681 REMARK 3 S21: -0.0746 S22: -0.1120 S23: -0.2324 REMARK 3 S31: -0.0417 S32: 0.1820 S33: -0.0065 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 126 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 67.1682 5.0706 103.6741 REMARK 3 T TENSOR REMARK 3 T11: 0.2054 T22: 0.1854 REMARK 3 T33: 0.1867 T12: 0.0202 REMARK 3 T13: -0.0223 T23: -0.0214 REMARK 3 L TENSOR REMARK 3 L11: 0.2916 L22: 0.2356 REMARK 3 L33: 0.1403 L12: -0.2742 REMARK 3 L13: -0.0608 L23: 0.0259 REMARK 3 S TENSOR REMARK 3 S11: -0.0437 S12: -0.0824 S13: -0.0106 REMARK 3 S21: 0.2138 S22: 0.1489 S23: -0.0874 REMARK 3 S31: 0.0178 S32: 0.1127 S33: 0.0007 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 141 THROUGH 164 ) REMARK 3 ORIGIN FOR THE GROUP (A): 61.3010 -7.3524 90.9051 REMARK 3 T TENSOR REMARK 3 T11: 0.2446 T22: 0.1690 REMARK 3 T33: 0.2366 T12: 0.0083 REMARK 3 T13: -0.0736 T23: -0.0156 REMARK 3 L TENSOR REMARK 3 L11: 0.3750 L22: 0.2280 REMARK 3 L33: 0.1392 L12: -0.1181 REMARK 3 L13: -0.0617 L23: -0.0429 REMARK 3 S TENSOR REMARK 3 S11: 0.1987 S12: -0.0241 S13: -0.2876 REMARK 3 S21: -0.0240 S22: 0.0375 S23: 0.2499 REMARK 3 S31: 0.4684 S32: -0.1364 S33: 0.0135 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 165 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): 76.1344 -10.0095 107.2152 REMARK 3 T TENSOR REMARK 3 T11: 0.2508 T22: 0.1839 REMARK 3 T33: 0.1892 T12: 0.0273 REMARK 3 T13: -0.0097 T23: 0.0224 REMARK 3 L TENSOR REMARK 3 L11: 0.0328 L22: 0.0742 REMARK 3 L33: 0.1010 L12: -0.0018 REMARK 3 L13: -0.0862 L23: -0.0741 REMARK 3 S TENSOR REMARK 3 S11: -0.1076 S12: -0.1123 S13: 0.0123 REMARK 3 S21: 0.2776 S22: 0.0729 S23: -0.0883 REMARK 3 S31: 0.0135 S32: 0.1485 S33: 0.0000 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 180 THROUGH 231 ) REMARK 3 ORIGIN FOR THE GROUP (A): 66.7258 -3.6905 98.8267 REMARK 3 T TENSOR REMARK 3 T11: 0.1683 T22: 0.1404 REMARK 3 T33: 0.1685 T12: 0.0085 REMARK 3 T13: -0.0025 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.9402 L22: 0.3794 REMARK 3 L33: 0.8872 L12: -0.4443 REMARK 3 L13: 0.2099 L23: -0.1166 REMARK 3 S TENSOR REMARK 3 S11: 0.0499 S12: -0.0801 S13: -0.1420 REMARK 3 S21: 0.0081 S22: 0.0140 S23: 0.0816 REMARK 3 S31: 0.1485 S32: -0.0072 S33: 0.0002 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 232 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): 83.9450 8.6212 94.1928 REMARK 3 T TENSOR REMARK 3 T11: 0.1713 T22: 0.2012 REMARK 3 T33: 0.3435 T12: -0.0277 REMARK 3 T13: 0.0461 T23: 0.0231 REMARK 3 L TENSOR REMARK 3 L11: 0.2478 L22: 0.2059 REMARK 3 L33: 0.0322 L12: 0.1006 REMARK 3 L13: 0.0399 L23: 0.0709 REMARK 3 S TENSOR REMARK 3 S11: 0.0690 S12: -0.0360 S13: 0.4770 REMARK 3 S21: 0.0820 S22: -0.0702 S23: -0.3613 REMARK 3 S31: -0.3621 S32: 0.3679 S33: -0.0194 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 518 THROUGH 528 ) REMARK 3 ORIGIN FOR THE GROUP (A): 69.4864 -0.8347 67.9623 REMARK 3 T TENSOR REMARK 3 T11: 0.5199 T22: 0.5647 REMARK 3 T33: 0.1756 T12: 0.1448 REMARK 3 T13: 0.0248 T23: -0.1183 REMARK 3 L TENSOR REMARK 3 L11: 0.2531 L22: 0.3996 REMARK 3 L33: 0.0195 L12: -0.3048 REMARK 3 L13: 0.0131 L23: 0.0079 REMARK 3 S TENSOR REMARK 3 S11: 0.2892 S12: 0.6038 S13: -0.0188 REMARK 3 S21: -0.5019 S22: -0.0897 S23: -0.0458 REMARK 3 S31: 0.0983 S32: 0.0213 S33: 0.1885 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 6T55 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1292104829. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-17 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68518 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 49.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 2.860 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 14.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.73 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50100 REMARK 200 FOR SHELL : 1.910 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4UE7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM NAH2PO4, 350 MM NACL, 27% (W/V) REMARK 280 PEG8000, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.13550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.66800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.13550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.66800 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, I 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CZ ARG H 75 LIES ON A SPECIAL POSITION. 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 THR L -4 REMARK 465 PHE L -3 REMARK 465 GLY L -2 REMARK 465 SER L -1 REMARK 465 GLY L 0 REMARK 465 GLY L 15 REMARK 465 ARG L 16 REMARK 465 TRP H 147A REMARK 465 THR H 147B REMARK 465 ALA H 147C REMARK 465 ASN H 147D REMARK 465 VAL H 147E REMARK 465 GLY H 147F REMARK 465 LYS H 147G REMARK 465 GLY H 246 REMARK 465 GLU H 247 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 GLU L 1C CG CD OE1 OE2 REMARK 470 ILE L 14K CD1 REMARK 470 ASP L 14L CG OD1 OD2 REMARK 470 SER H 36A OG REMARK 470 ARG H 50 CG CD NE CZ NH1 NH2 REMARK 470 ASN H 62 ND2 REMARK 470 LYS H 87 CE NZ REMARK 470 LYS H 110 CE NZ REMARK 470 LEU H 130 CD1 REMARK 470 THR H 147 OG1 CG2 REMARK 470 ASP H 186A CG OD1 OD2 REMARK 470 LYS H 186D CE NZ REMARK 470 ASN H 205 ND2 REMARK 470 LYS H 236 CD CE NZ REMARK 470 GLN H 239 CG CD OE1 NE2 REMARK 470 LYS H 240 CG CD CE NZ REMARK 470 GLN H 244 CG CD OE1 NE2 REMARK 470 ASP I 518 CG OD1 OD2 REMARK 470 GLU I 521 CG CD OE1 OE2 REMARK 470 GLU I 524 CG CD OE1 OE2 REMARK 470 LEU I 527 CD2 REMARK 470 GLN I 528 CD OE1 NE2 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 HZ2 LYS L 9 O HOH L 101 1.58 REMARK 500 OD2 ASP L 1A NZ LYS L 9 2.19 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 PHE L 7 -88.76 -128.89 REMARK 500 TYR H 60A 84.20 -153.07 REMARK 500 ASN H 60G 78.19 -156.47 REMARK 500 HIS H 71 -61.68 -130.42 REMARK 500 ILE H 79 -62.45 -127.80 REMARK 500 GLU H 97A -71.34 -112.83 REMARK 500 GLU H 97A -71.34 -108.22 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 H 605 DISTANCE = 5.84 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 NA H 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS H 169 O REMARK 620 2 THR H 172 O 81.8 REMARK 620 3 PHE H 204A O 18.7 90.9 REMARK 620 4 HOH H 455 O 70.7 79.3 56.3 REMARK 620 5 HOH H 489 O 175.1 95.2 158.9 105.0 REMARK 620 6 HOH H 561 O 82.2 163.8 74.6 97.8 100.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 301 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 94.3 REMARK 620 3 HOH H 472 O 159.9 70.6 REMARK 620 4 HOH H 484 O 87.0 90.3 80.1 REMARK 620 5 HOH H 485 O 106.1 157.8 87.5 82.3 REMARK 620 6 HOH H 581 O 100.0 84.7 91.9 171.6 99.9 REMARK 620 N 1 2 3 4 5 DBREF 6T55 L -4 16 UNP P00734 THRB_HUMAN 328 363 DBREF 6T55 H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 6T55 I 518 528 UNP P09945 HIRV2_HIRME 62 72 SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 I 11 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN MODRES 6T55 TYS I 526 TYR MODIFIED RESIDUE HET TYS I 526 25 HET NA H 301 1 HET NA H 302 1 HET 02N H 303 9 HET PO4 H 304 5 HET GOL H 305 6 HET NAG H 306 14 HETNAM TYS O-SULFO-L-TYROSINE HETNAM NA SODIUM ION HETNAM 02N 1-(4-METHYLPHENYL)METHANAMINE HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 TYS C9 H11 N O6 S FORMUL 4 NA 2(NA 1+) FORMUL 6 02N C8 H11 N FORMUL 7 PO4 O4 P 3- FORMUL 8 GOL C3 H8 O3 FORMUL 9 NAG C8 H15 N O6 FORMUL 10 HOH *246(H2 O) HELIX 1 AA1 PHE L 7 SER L 11 5 5 HELIX 2 AA2 THR L 14B TYR L 14J 1 9 HELIX 3 AA3 ALA H 55 CYS H 58 5 4 HELIX 4 AA4 PRO H 60B ASP H 60E 5 4 HELIX 5 AA5 THR H 60I ASN H 62 5 3 HELIX 6 AA6 ASP H 125 LEU H 130 1 9 HELIX 7 AA7 GLU H 164 SER H 171 1 8 HELIX 8 AA8 LYS H 185 GLY H 186C 5 5 HELIX 9 AA9 LEU H 234 PHE H 245 1 12 HELIX 10 AB1 PRO I 523 LEU I 527 5 5 SHEET 1 AA1 7 SER H 20 ASP H 21 0 SHEET 2 AA1 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 AA1 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158 SHEET 4 AA1 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 AA1 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 AA1 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215 SHEET 7 AA1 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 AA2 7 GLN H 30 ARG H 35 0 SHEET 2 AA2 7 GLU H 39 LEU H 46 -1 O GLU H 39 N ARG H 35 SHEET 3 AA2 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 AA2 7 ALA H 104 LEU H 108 -1 O MET H 106 N VAL H 52 SHEET 5 AA2 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 AA2 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 7 AA2 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 1 AA3 2 LEU H 60 TYR H 60A 0 SHEET 2 AA3 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.07 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.05 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.02 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.05 LINK ND2 ASN H 60G C1 NAG H 306 1555 1555 1.43 LINK C GLU I 525 N TYS I 526 1555 1555 1.33 LINK C TYS I 526 N LEU I 527 1555 1555 1.33 LINK O LYS H 169 NA NA H 302 1555 1555 2.37 LINK O THR H 172 NA NA H 302 1555 1555 2.32 LINK O PHE H 204A NA NA H 302 1555 4758 2.39 LINK O ARG H 221A NA NA H 301 1555 1555 2.30 LINK O LYS H 224 NA NA H 301 1555 1555 2.39 LINK NA NA H 301 O HOH H 472 1555 1555 2.48 LINK NA NA H 301 O HOH H 484 1555 1555 2.72 LINK NA NA H 301 O HOH H 485 1555 1555 2.38 LINK NA NA H 301 O HOH H 581 1555 1555 2.31 LINK NA NA H 302 O HOH H 455 1555 1555 2.60 LINK NA NA H 302 O HOH H 489 1555 4748 2.40 LINK NA NA H 302 O HOH H 561 1555 1555 2.43 CISPEP 1 SER H 36A PRO H 37 0 -4.72 CRYST1 70.271 71.336 72.395 90.00 100.18 90.00 C 1 2 1 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 0.014231 0.000000 0.002554 0.00000 SCALE2 0.000000 0.014018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014034 0.00000