HEADER HYDROLASE 10-NOV-19 6TDT TITLE THROMBIN IN COMPLEX WITH A D-DIPHE-PRO-P-PYRIDINE DERIVATIVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: H; 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: L; 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 BLOOD CLOTTING INHIBITOR, THROMBIN INHIBITOR, PREORGANIZATION, KEYWDS 3 GLYCOSYLATION, BLOOD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.NGO,A.HEINE,G.KLEBE REVDAT 3 24-JAN-24 6TDT 1 HETSYN REVDAT 2 29-JUL-20 6TDT 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 13-MAY-20 6TDT 0 JRNL AUTH K.NGO,C.COLLINS-KAUTZ,S.GERSTENECKER,B.WAGNER,A.HEINE, JRNL AUTH 2 G.KLEBE JRNL TITL PROTEIN-INDUCED CHANGE IN LIGAND PROTONATION DURING TRYPSIN JRNL TITL 2 AND THROMBIN BINDING: HINT ON DIFFERENCES IN SELECTIVITY JRNL TITL 3 DETERMINANTS OF BOTH PROTEINS? JRNL REF J.MED.CHEM. V. 63 3274 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32011145 JRNL DOI 10.1021/ACS.JMEDCHEM.9B02061 REMARK 2 REMARK 2 RESOLUTION. 1.53 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 52250 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2611 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 43.3600 - 4.0800 0.99 2695 142 0.1567 0.1594 REMARK 3 2 4.0800 - 3.2400 0.96 2588 137 0.1450 0.1490 REMARK 3 3 3.2400 - 2.8300 0.99 2626 138 0.1629 0.1815 REMARK 3 4 2.8300 - 2.5700 0.99 2638 139 0.1591 0.1892 REMARK 3 5 2.5700 - 2.3900 0.99 2624 138 0.1484 0.1773 REMARK 3 6 2.3900 - 2.2500 0.99 2647 139 0.1485 0.1568 REMARK 3 7 2.2500 - 2.1300 0.99 2636 139 0.1429 0.1732 REMARK 3 8 2.1300 - 2.0400 0.99 2619 138 0.1490 0.1674 REMARK 3 9 2.0400 - 1.9600 0.99 2599 137 0.1493 0.1766 REMARK 3 10 1.9600 - 1.8900 0.94 2477 129 0.1692 0.2110 REMARK 3 11 1.8900 - 1.8300 0.98 2582 136 0.1624 0.1779 REMARK 3 12 1.8300 - 1.7800 0.99 2599 136 0.1662 0.1945 REMARK 3 13 1.7800 - 1.7400 0.99 2641 138 0.1660 0.1937 REMARK 3 14 1.7400 - 1.6900 0.99 2633 139 0.1793 0.2075 REMARK 3 15 1.6900 - 1.6500 0.99 2604 137 0.1795 0.2147 REMARK 3 16 1.6500 - 1.6200 1.00 2620 138 0.1880 0.1884 REMARK 3 17 1.6200 - 1.5900 1.00 2644 139 0.2010 0.2310 REMARK 3 18 1.5900 - 1.5600 0.99 2613 138 0.2279 0.2496 REMARK 3 19 1.5600 - 1.5300 0.98 2554 134 0.2530 0.2888 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) : 0.153 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.434 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.16 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 2512 REMARK 3 ANGLE : 1.031 3404 REMARK 3 CHIRALITY : 0.066 353 REMARK 3 PLANARITY : 0.008 461 REMARK 3 DIHEDRAL : 16.314 1528 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 14 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 16 THROUGH 29 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.3368 0.5932 17.1977 REMARK 3 T TENSOR REMARK 3 T11: 0.1347 T22: 0.1556 REMARK 3 T33: 0.1741 T12: 0.0040 REMARK 3 T13: -0.0152 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 0.1201 L22: 0.0436 REMARK 3 L33: 0.0307 L12: -0.0491 REMARK 3 L13: -0.0070 L23: -0.0275 REMARK 3 S TENSOR REMARK 3 S11: 0.1526 S12: -0.0109 S13: -0.1556 REMARK 3 S21: 0.0067 S22: -0.1979 S23: 0.1046 REMARK 3 S31: 0.0231 S32: -0.1471 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 30 THROUGH 50 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.1286 -0.6938 9.0339 REMARK 3 T TENSOR REMARK 3 T11: 0.1959 T22: 0.2006 REMARK 3 T33: 0.1327 T12: 0.0687 REMARK 3 T13: 0.0032 T23: -0.0216 REMARK 3 L TENSOR REMARK 3 L11: 0.3943 L22: 0.0805 REMARK 3 L33: 0.1618 L12: -0.1803 REMARK 3 L13: 0.0565 L23: -0.0120 REMARK 3 S TENSOR REMARK 3 S11: 0.1648 S12: 0.3412 S13: -0.0751 REMARK 3 S21: -0.2675 S22: -0.1531 S23: -0.0283 REMARK 3 S31: 0.0801 S32: 0.1062 S33: 0.0015 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 51 THROUGH 125 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.5132 -0.0106 12.2999 REMARK 3 T TENSOR REMARK 3 T11: 0.1408 T22: 0.1778 REMARK 3 T33: 0.1110 T12: 0.0507 REMARK 3 T13: 0.0112 T23: 0.0111 REMARK 3 L TENSOR REMARK 3 L11: 0.9403 L22: 0.8178 REMARK 3 L33: 0.5583 L12: -0.5112 REMARK 3 L13: 0.2654 L23: -0.0852 REMARK 3 S TENSOR REMARK 3 S11: 0.1311 S12: 0.2285 S13: 0.0537 REMARK 3 S21: -0.1435 S22: -0.1508 S23: -0.1117 REMARK 3 S31: 0.0644 S32: 0.1382 S33: 0.0028 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 126 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.7098 4.6990 32.1480 REMARK 3 T TENSOR REMARK 3 T11: 0.1644 T22: 0.1574 REMARK 3 T33: 0.1500 T12: 0.0152 REMARK 3 T13: -0.0232 T23: -0.0251 REMARK 3 L TENSOR REMARK 3 L11: 0.2255 L22: 0.0680 REMARK 3 L33: 0.0776 L12: -0.1157 REMARK 3 L13: 0.0073 L23: 0.0287 REMARK 3 S TENSOR REMARK 3 S11: -0.0436 S12: -0.0845 S13: -0.0273 REMARK 3 S21: 0.1641 S22: 0.1194 S23: -0.0400 REMARK 3 S31: 0.0368 S32: 0.1323 S33: 0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 141 THROUGH 164 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.0200 -7.4629 20.1814 REMARK 3 T TENSOR REMARK 3 T11: 0.1798 T22: 0.1393 REMARK 3 T33: 0.1842 T12: 0.0039 REMARK 3 T13: -0.0345 T23: -0.0184 REMARK 3 L TENSOR REMARK 3 L11: 0.2950 L22: 0.2428 REMARK 3 L33: 0.1289 L12: -0.0186 REMARK 3 L13: -0.1092 L23: -0.1404 REMARK 3 S TENSOR REMARK 3 S11: 0.0597 S12: -0.0259 S13: -0.2290 REMARK 3 S21: -0.0101 S22: 0.0566 S23: 0.1210 REMARK 3 S31: 0.2444 S32: -0.0556 S33: 0.0002 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 165 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.6966 -10.6438 35.7461 REMARK 3 T TENSOR REMARK 3 T11: 0.1862 T22: 0.1505 REMARK 3 T33: 0.1555 T12: 0.0300 REMARK 3 T13: -0.0126 T23: 0.0180 REMARK 3 L TENSOR REMARK 3 L11: 0.0230 L22: 0.0725 REMARK 3 L33: 0.0453 L12: 0.0444 REMARK 3 L13: -0.0382 L23: -0.0607 REMARK 3 S TENSOR REMARK 3 S11: -0.0591 S12: -0.1080 S13: -0.0263 REMARK 3 S21: 0.2390 S22: 0.0554 S23: -0.0652 REMARK 3 S31: 0.0219 S32: 0.0098 S33: 0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 180 THROUGH 197 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.8946 -8.7784 27.9062 REMARK 3 T TENSOR REMARK 3 T11: 0.1540 T22: 0.1049 REMARK 3 T33: 0.1826 T12: 0.0012 REMARK 3 T13: 0.0097 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 0.2473 L22: 0.2219 REMARK 3 L33: 0.1889 L12: -0.2220 REMARK 3 L13: 0.0861 L23: -0.1477 REMARK 3 S TENSOR REMARK 3 S11: 0.0050 S12: -0.0345 S13: -0.2204 REMARK 3 S21: 0.0010 S22: 0.0209 S23: 0.0559 REMARK 3 S31: 0.1699 S32: 0.0691 S33: 0.0082 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 198 THROUGH 231 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.5285 -0.9708 27.3266 REMARK 3 T TENSOR REMARK 3 T11: 0.1233 T22: 0.1106 REMARK 3 T33: 0.1392 T12: 0.0193 REMARK 3 T13: 0.0055 T23: 0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.6261 L22: 0.1273 REMARK 3 L33: 0.4278 L12: -0.1105 REMARK 3 L13: -0.0410 L23: -0.1986 REMARK 3 S TENSOR REMARK 3 S11: -0.0238 S12: -0.0736 S13: -0.0855 REMARK 3 S21: 0.0418 S22: 0.0267 S23: 0.0388 REMARK 3 S31: 0.0256 S32: 0.0252 S33: 0.0025 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'H' AND (RESID 232 THROUGH 246 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.8388 8.6184 22.4068 REMARK 3 T TENSOR REMARK 3 T11: 0.1291 T22: 0.1695 REMARK 3 T33: 0.2760 T12: -0.0277 REMARK 3 T13: 0.0040 T23: 0.0201 REMARK 3 L TENSOR REMARK 3 L11: 0.0897 L22: 0.1154 REMARK 3 L33: 0.0172 L12: -0.0243 REMARK 3 L13: 0.0105 L23: -0.0008 REMARK 3 S TENSOR REMARK 3 S11: 0.0557 S12: -0.1312 S13: 0.2222 REMARK 3 S21: 0.0917 S22: -0.0986 S23: -0.2630 REMARK 3 S31: -0.1320 S32: 0.2464 S33: 0.0010 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 1C THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2538 14.8290 18.1129 REMARK 3 T TENSOR REMARK 3 T11: 0.1622 T22: 0.1333 REMARK 3 T33: 0.1538 T12: 0.0322 REMARK 3 T13: 0.0122 T23: 0.0093 REMARK 3 L TENSOR REMARK 3 L11: 0.0346 L22: 0.0443 REMARK 3 L33: 0.0274 L12: -0.0393 REMARK 3 L13: -0.0142 L23: 0.0113 REMARK 3 S TENSOR REMARK 3 S11: 0.0696 S12: 0.0604 S13: 0.0031 REMARK 3 S21: -0.0917 S22: -0.1115 S23: -0.0745 REMARK 3 S31: -0.2024 S32: -0.0239 S33: 0.0001 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 8 THROUGH 14B) REMARK 3 ORIGIN FOR THE GROUP (A): -3.2563 12.9772 20.2196 REMARK 3 T TENSOR REMARK 3 T11: 0.1472 T22: 0.1568 REMARK 3 T33: 0.1745 T12: 0.0594 REMARK 3 T13: 0.0010 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 0.1271 L22: 0.1285 REMARK 3 L33: 0.0875 L12: 0.1092 REMARK 3 L13: 0.0202 L23: -0.0338 REMARK 3 S TENSOR REMARK 3 S11: 0.0604 S12: -0.1160 S13: 0.0791 REMARK 3 S21: 0.0251 S22: -0.0980 S23: -0.0757 REMARK 3 S31: -0.1736 S32: -0.1007 S33: -0.0025 REMARK 3 TLS GROUP : 12 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 14C THROUGH 14I) REMARK 3 ORIGIN FOR THE GROUP (A): -2.2312 5.8669 30.9429 REMARK 3 T TENSOR REMARK 3 T11: 0.1484 T22: 0.1774 REMARK 3 T33: 0.1763 T12: 0.0352 REMARK 3 T13: 0.0202 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 0.0240 L22: 0.0157 REMARK 3 L33: 0.0403 L12: 0.0057 REMARK 3 L13: 0.0243 L23: -0.0123 REMARK 3 S TENSOR REMARK 3 S11: 0.0966 S12: -0.1166 S13: -0.0782 REMARK 3 S21: -0.0357 S22: 0.0350 S23: 0.0344 REMARK 3 S31: 0.0113 S32: -0.2574 S33: 0.0000 REMARK 3 TLS GROUP : 13 REMARK 3 SELECTION: CHAIN 'L' AND (RESID 14J THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.9671 9.5394 39.0606 REMARK 3 T TENSOR REMARK 3 T11: 0.3067 T22: 0.1893 REMARK 3 T33: 0.2612 T12: 0.0742 REMARK 3 T13: 0.0167 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 0.0376 L22: 0.0018 REMARK 3 L33: 0.1071 L12: -0.0014 REMARK 3 L13: 0.0629 L23: 0.0017 REMARK 3 S TENSOR REMARK 3 S11: -0.2556 S12: -0.1148 S13: 0.2449 REMARK 3 S21: 0.4283 S22: 0.0749 S23: -0.0772 REMARK 3 S31: -0.0520 S32: 0.0588 S33: -0.0041 REMARK 3 TLS GROUP : 14 REMARK 3 SELECTION: CHAIN 'I' AND (RESID 555 THROUGH 565 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.8620 -1.3659 -3.0938 REMARK 3 T TENSOR REMARK 3 T11: 0.3885 T22: 0.4918 REMARK 3 T33: 0.1580 T12: 0.1030 REMARK 3 T13: 0.0182 T23: -0.0814 REMARK 3 L TENSOR REMARK 3 L11: 0.1880 L22: 0.2624 REMARK 3 L33: 0.0021 L12: -0.2195 REMARK 3 L13: 0.0136 L23: -0.0132 REMARK 3 S TENSOR REMARK 3 S11: 0.1596 S12: 0.5221 S13: -0.0401 REMARK 3 S21: -0.3134 S22: -0.0930 S23: -0.0140 REMARK 3 S31: -0.1670 S32: -0.0074 S33: 0.0900 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 6TDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105319. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-19 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 : 52277 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.529 REMARK 200 RESOLUTION RANGE LOW (A) : 43.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.47300 REMARK 200 FOR SHELL : 2.100 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: 1H8D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM SODIUM DIHYDROGEN PHOSPHATE, 350 REMARK 280 MM NACL, 27% (W/V) PEG 8000, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 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 34.93600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.86300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.93600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.86300 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: 4150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, 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 HOH H 411 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 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 GLU H 247 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 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 SER H 36A OG REMARK 470 GLN H 38 CD OE1 NE2 REMARK 470 LEU H 41 CD1 REMARK 470 LYS H 87 CE NZ REMARK 470 LYS H 110 CD CE NZ REMARK 470 THR H 147 OG1 CG2 REMARK 470 GLN H 151 OE1 NE2 REMARK 470 ASP H 186A CG OD1 OD2 REMARK 470 LYS H 186D CE NZ REMARK 470 LYS H 236 CD CE NZ REMARK 470 GLN H 239 CG CD OE1 NE2 REMARK 470 LYS H 240 CE NZ REMARK 470 GLU L 1C CG CD OE1 OE2 REMARK 470 LYS L 14A CD CE NZ REMARK 470 GLU I 558 CG CD OE1 OE2 REMARK 470 GLU I 561 CG CD OE1 OE2 REMARK 470 GLN I 565 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR H 60A 84.88 -156.77 REMARK 500 ASN H 60G 83.61 -156.50 REMARK 500 HIS H 71 -61.43 -132.04 REMARK 500 ILE H 79 -61.98 -127.35 REMARK 500 GLU H 97A -70.55 -119.50 REMARK 500 GLU H 97A -70.55 -113.94 REMARK 500 SER H 214 -61.56 -120.65 REMARK 500 PHE L 7 -87.09 -130.96 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 608 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 79.9 REMARK 620 3 PHE H 204A O 21.8 87.8 REMARK 620 4 HOH H 468 O 77.2 75.6 59.4 REMARK 620 5 HOH H 489 O 173.4 93.8 161.5 103.2 REMARK 620 6 HOH H 576 O 84.7 162.3 80.8 109.5 101.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG H 221A O REMARK 620 2 LYS H 224 O 95.1 REMARK 620 3 HOH H 459 O 105.8 157.6 REMARK 620 4 HOH H 462 O 159.1 70.6 87.1 REMARK 620 5 HOH H 471 O 86.0 91.4 82.4 79.5 REMARK 620 6 HOH H 580 O 101.6 85.7 97.5 92.6 172.1 REMARK 620 N 1 2 3 4 5 DBREF 6TDT H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 6TDT L -4 15 UNP P00734 THRB_HUMAN 328 363 DBREF 6TDT I 555 565 UNP P09945 HIRV2_HIRME 62 72 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 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 I 11 ASP PHE GLU GLU ILE PRO GLU GLU TYS LEU GLN MODRES 6TDT TYS I 563 TYR MODIFIED RESIDUE HET TYS I 563 25 HET PO4 H 301 5 HET NA H 302 1 HET NA H 303 1 HET DMS H 304 4 HET LXW H 305 32 HET NAG H 306 14 HETNAM TYS O-SULFO-L-TYROSINE HETNAM PO4 PHOSPHATE ION HETNAM NA SODIUM ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM LXW (2~{S})-1-[(2~{R})-2-AZANYL-3,3-DIPHENYL-PROPANOYL]- HETNAM 2 LXW ~{N}-(PYRIDIN-4-YLMETHYL)PYRROLIDINE-2-CARBOXAMIDE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 PO4 O4 P 3- FORMUL 5 NA 2(NA 1+) FORMUL 7 DMS C2 H6 O S FORMUL 8 LXW C26 H28 N4 O2 FORMUL 9 NAG C8 H15 N O6 FORMUL 10 HOH *248(H2 O) HELIX 1 AA1 ALA H 55 CYS H 58 5 4 HELIX 2 AA2 PRO H 60B ASP H 60E 5 4 HELIX 3 AA3 THR H 60I ASN H 62 5 3 HELIX 4 AA4 ASP H 125 LEU H 130 1 9 HELIX 5 AA5 GLU H 164 SER H 171 1 8 HELIX 6 AA6 LYS H 185 GLY H 186C 5 5 HELIX 7 AA7 LEU H 234 GLY H 246 1 13 HELIX 8 AA8 PHE L 7 SER L 11 5 5 HELIX 9 AA9 THR L 14B TYR L 14J 1 9 HELIX 10 AB1 PRO I 560 GLN I 565 5 6 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 LEU H 41 N LEU H 33 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 H 42 CYS H 58 1555 1555 2.04 SSBOND 2 CYS H 122 CYS L 1 1555 1555 2.07 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.04 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04 LINK ND2 ASN H 60G C1 NAG H 306 1555 1555 1.43 LINK C GLU I 562 N TYS I 563 1555 1555 1.33 LINK C TYS I 563 N LEU I 564 1555 1555 1.33 LINK O LYS H 169 NA NA H 302 1555 1555 2.45 LINK O THR H 172 NA NA H 302 1555 1555 2.42 LINK O PHE H 204A NA NA H 302 1555 4556 2.48 LINK O ARG H 221A NA NA H 303 1555 1555 2.29 LINK O LYS H 224 NA NA H 303 1555 1555 2.35 LINK NA NA H 302 O HOH H 468 1555 1555 2.62 LINK NA NA H 302 O HOH H 489 1555 4546 2.41 LINK NA NA H 302 O HOH H 576 1555 1555 2.53 LINK NA NA H 303 O HOH H 459 1555 1555 2.42 LINK NA NA H 303 O HOH H 462 1555 1555 2.44 LINK NA NA H 303 O HOH H 471 1555 1555 2.86 LINK NA NA H 303 O HOH H 580 1555 1555 2.22 CISPEP 1 SER H 36A PRO H 37 0 -7.45 CRYST1 69.872 71.726 72.099 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 0.014312 0.000000 0.002569 0.00000 SCALE2 0.000000 0.013942 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014091 0.00000