PDB Short entry for 3NXP HEADER HYDROLASE 14-JUL-10 3NXP TITLE CRYSTAL STRUCTURE OF HUMAN PRETHROMBIN-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRETHROMBIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 199-622; COMPND 5 SYNONYM: COAGULATION FACTOR II; COMPND 6 EC: 3.4.21.5; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F2; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BHK; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: HPC4 PNUT KEYWDS THROMBIN, PRETHROMBIN-1, ALLOSTERY, BLOOD COAGULATION, HYDROLASE, KEYWDS 2 KRINGLE, SERINE PROTEASE, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR Z.CHEN,L.A.BUSH-PELC,E.DI CERA REVDAT 4 06-SEP-23 3NXP 1 HETSYN REVDAT 3 29-JUL-20 3NXP 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE REVDAT 2 19-JAN-11 3NXP 1 JRNL REVDAT 1 10-NOV-10 3NXP 0 JRNL AUTH Z.CHEN,L.A.PELC,E.DI CERA JRNL TITL CRYSTAL STRUCTURE OF PRETHROMBIN-1. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 19278 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20974933 JRNL DOI 10.1073/PNAS.1010262107 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.E.PAPACONSTANTINOU,P.S.GANDHI,Z.CHEN,A.BAH,E.DI CERA REMARK 1 TITL NA(+) BINDING TO MEIZOTHROMBIN DESF1. REMARK 1 REF CELL.MOL.LIFE SCI. V. 65 3688 2008 REMARK 1 REFN ISSN 1420-682X REMARK 1 PMID 18854941 REMARK 1 DOI 10.1007/S00018-008-8502-7 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : -0.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 22995 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1244 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1643 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.2930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3112 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24000 REMARK 3 B22 (A**2) : -2.75000 REMARK 3 B33 (A**2) : 2.99000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.196 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3236 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4378 ; 1.331 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 385 ; 6.105 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;35.795 ;23.875 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 540 ;16.880 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.029 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 447 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2490 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1934 ; 0.465 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3106 ; 0.887 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1302 ; 1.594 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1272 ; 2.498 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 3 REMARK 3 ORIGIN FOR THE GROUP (A): 8.4910 -14.5390 31.8830 REMARK 3 T TENSOR REMARK 3 T11: 0.3150 T22: 0.2109 REMARK 3 T33: 0.0556 T12: 0.0132 REMARK 3 T13: -0.0466 T23: -0.0203 REMARK 3 L TENSOR REMARK 3 L11: 9.2247 L22: 1.4318 REMARK 3 L33: 3.1007 L12: -0.5155 REMARK 3 L13: -0.1738 L23: 0.5902 REMARK 3 S TENSOR REMARK 3 S11: 0.0151 S12: -0.6932 S13: 0.0551 REMARK 3 S21: 0.6529 S22: 0.1243 S23: -0.1335 REMARK 3 S31: 0.1578 S32: 0.0948 S33: -0.1394 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 37 REMARK 3 ORIGIN FOR THE GROUP (A): -10.1390 -18.8440 17.6210 REMARK 3 T TENSOR REMARK 3 T11: 0.0976 T22: 0.1484 REMARK 3 T33: 0.1070 T12: 0.0193 REMARK 3 T13: 0.0009 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 2.1535 L22: 2.7152 REMARK 3 L33: 1.6922 L12: 0.4599 REMARK 3 L13: -0.2776 L23: -0.0610 REMARK 3 S TENSOR REMARK 3 S11: 0.0231 S12: -0.0574 S13: -0.1386 REMARK 3 S21: -0.0900 S22: -0.0026 S23: 0.3725 REMARK 3 S31: 0.2238 S32: -0.2320 S33: -0.0205 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 38 A 126 REMARK 3 ORIGIN FOR THE GROUP (A): 5.0830 -7.9630 15.5510 REMARK 3 T TENSOR REMARK 3 T11: 0.0948 T22: 0.0872 REMARK 3 T33: 0.0764 T12: -0.0198 REMARK 3 T13: -0.0072 T23: -0.0173 REMARK 3 L TENSOR REMARK 3 L11: 1.8744 L22: 1.2134 REMARK 3 L33: 1.3360 L12: -0.3383 REMARK 3 L13: -0.6188 L23: 0.1569 REMARK 3 S TENSOR REMARK 3 S11: 0.0862 S12: 0.0064 S13: 0.1803 REMARK 3 S21: -0.0275 S22: 0.0021 S23: 0.0036 REMARK 3 S31: -0.1538 S32: -0.0039 S33: -0.0883 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 127 A 145 REMARK 3 ORIGIN FOR THE GROUP (A): -2.3520 -24.3780 14.1750 REMARK 3 T TENSOR REMARK 3 T11: 0.0789 T22: 0.0926 REMARK 3 T33: 0.0614 T12: -0.0083 REMARK 3 T13: 0.0010 T23: -0.0031 REMARK 3 L TENSOR REMARK 3 L11: 1.1355 L22: 3.4951 REMARK 3 L33: 0.4369 L12: -0.5435 REMARK 3 L13: 0.1562 L23: -0.4549 REMARK 3 S TENSOR REMARK 3 S11: 0.0063 S12: 0.0776 S13: -0.1664 REMARK 3 S21: -0.2338 S22: -0.0216 S23: 0.2337 REMARK 3 S31: 0.1390 S32: -0.0601 S33: 0.0153 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 146 A 175 REMARK 3 ORIGIN FOR THE GROUP (A): -0.7840 -21.4560 3.2660 REMARK 3 T TENSOR REMARK 3 T11: 0.1371 T22: 0.1716 REMARK 3 T33: 0.1221 T12: -0.0134 REMARK 3 T13: -0.0729 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 3.0826 L22: 3.0260 REMARK 3 L33: 2.6607 L12: -0.3316 REMARK 3 L13: -1.4499 L23: 0.5184 REMARK 3 S TENSOR REMARK 3 S11: 0.0594 S12: 0.3037 S13: -0.0253 REMARK 3 S21: -0.2956 S22: -0.0306 S23: -0.2633 REMARK 3 S31: -0.1858 S32: 0.1139 S33: -0.0288 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 176 A 192 REMARK 3 ORIGIN FOR THE GROUP (A): -2.5050 -26.6360 2.0930 REMARK 3 T TENSOR REMARK 3 T11: 0.1351 T22: 0.1263 REMARK 3 T33: 0.1329 T12: 0.0063 REMARK 3 T13: -0.0108 T23: -0.0436 REMARK 3 L TENSOR REMARK 3 L11: 5.8357 L22: 0.5211 REMARK 3 L33: 2.6647 L12: -0.5188 REMARK 3 L13: 2.8530 L23: -0.9231 REMARK 3 S TENSOR REMARK 3 S11: 0.0890 S12: 0.3586 S13: -0.2282 REMARK 3 S21: -0.0659 S22: 0.0333 S23: -0.0958 REMARK 3 S31: 0.1353 S32: 0.1207 S33: -0.1222 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 193 A 247 REMARK 3 ORIGIN FOR THE GROUP (A): 5.6050 -20.2180 15.0590 REMARK 3 T TENSOR REMARK 3 T11: 0.0877 T22: 0.0746 REMARK 3 T33: 0.0823 T12: 0.0075 REMARK 3 T13: 0.0051 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 2.2302 L22: 1.1861 REMARK 3 L33: 0.7427 L12: 0.1261 REMARK 3 L13: 0.2876 L23: -0.0698 REMARK 3 S TENSOR REMARK 3 S11: 0.0091 S12: -0.0200 S13: -0.0191 REMARK 3 S21: 0.0334 S22: 0.0249 S23: -0.0312 REMARK 3 S31: -0.0276 S32: 0.1624 S33: -0.0340 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 7 F 15 REMARK 3 ORIGIN FOR THE GROUP (A): 24.1560 -34.0700 15.1650 REMARK 3 T TENSOR REMARK 3 T11: 0.3000 T22: 0.1621 REMARK 3 T33: 0.3616 T12: 0.1096 REMARK 3 T13: 0.0816 T23: 0.0717 REMARK 3 L TENSOR REMARK 3 L11: 12.3933 L22: 5.8139 REMARK 3 L33: 17.7197 L12: 3.5813 REMARK 3 L13: 8.2019 L23: -1.3144 REMARK 3 S TENSOR REMARK 3 S11: -0.1901 S12: -0.3390 S13: -1.4063 REMARK 3 S21: -0.1082 S22: 0.2370 S23: -0.2250 REMARK 3 S31: 1.2320 S32: 0.2084 S33: -0.0469 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 16 F 33 REMARK 3 ORIGIN FOR THE GROUP (A): 32.4330 -21.0880 14.1730 REMARK 3 T TENSOR REMARK 3 T11: 0.0606 T22: 0.2624 REMARK 3 T33: 0.1570 T12: 0.0212 REMARK 3 T13: 0.0143 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 4.9697 L22: 3.0484 REMARK 3 L33: 3.3762 L12: -0.8813 REMARK 3 L13: 0.9709 L23: -0.5564 REMARK 3 S TENSOR REMARK 3 S11: 0.1049 S12: -0.2430 S13: -0.1135 REMARK 3 S21: 0.0041 S22: -0.0707 S23: -0.4612 REMARK 3 S31: 0.0517 S32: 0.5426 S33: -0.0342 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 34 F 46 REMARK 3 ORIGIN FOR THE GROUP (A): 30.6140 -16.0930 29.4550 REMARK 3 T TENSOR REMARK 3 T11: 2.1838 T22: 1.5511 REMARK 3 T33: 2.2639 T12: -0.1786 REMARK 3 T13: 0.0840 T23: 0.0884 REMARK 3 L TENSOR REMARK 3 L11: 0.0161 L22: 0.0312 REMARK 3 L33: 0.0652 L12: -0.0113 REMARK 3 L13: 0.0059 L23: 0.0336 REMARK 3 S TENSOR REMARK 3 S11: -0.0059 S12: 0.0748 S13: 0.1718 REMARK 3 S21: 0.1993 S22: -0.1476 S23: -0.0558 REMARK 3 S31: 0.3406 S32: -0.0970 S33: 0.1535 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 47 F 57 REMARK 3 ORIGIN FOR THE GROUP (A): 34.1520 -26.4890 22.1010 REMARK 3 T TENSOR REMARK 3 T11: 0.2117 T22: 0.7399 REMARK 3 T33: 0.3083 T12: 0.1725 REMARK 3 T13: -0.0547 T23: 0.2024 REMARK 3 L TENSOR REMARK 3 L11: 2.3065 L22: 14.0644 REMARK 3 L33: 1.8857 L12: -0.8995 REMARK 3 L13: 1.4988 L23: 2.9276 REMARK 3 S TENSOR REMARK 3 S11: 0.1527 S12: -0.5989 S13: -0.7760 REMARK 3 S21: 0.5958 S22: 0.3548 S23: 0.2910 REMARK 3 S31: 0.3027 S32: -0.2741 S33: -0.5075 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 58 F 87 REMARK 3 ORIGIN FOR THE GROUP (A): 24.7350 -21.7740 17.1790 REMARK 3 T TENSOR REMARK 3 T11: 0.0820 T22: 0.1841 REMARK 3 T33: 0.0802 T12: 0.0246 REMARK 3 T13: -0.0193 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 4.5700 L22: 3.3053 REMARK 3 L33: 3.3022 L12: 1.3618 REMARK 3 L13: -0.3782 L23: 0.2902 REMARK 3 S TENSOR REMARK 3 S11: 0.0023 S12: -0.1653 S13: 0.0108 REMARK 3 S21: -0.0176 S22: 0.0169 S23: 0.1269 REMARK 3 S31: 0.0589 S32: 0.3459 S33: -0.0192 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 88 F 95 REMARK 3 ORIGIN FOR THE GROUP (A): 8.1770 -37.4760 11.3100 REMARK 3 T TENSOR REMARK 3 T11: 0.6732 T22: 1.3016 REMARK 3 T33: 1.2250 T12: 0.0510 REMARK 3 T13: 0.3296 T23: -0.8484 REMARK 3 L TENSOR REMARK 3 L11: 81.5747 L22: 3.3127 REMARK 3 L33: 63.5671 L12: 16.1785 REMARK 3 L13: 44.8777 L23: 10.4961 REMARK 3 S TENSOR REMARK 3 S11: 0.2745 S12: 2.8187 S13: -4.7641 REMARK 3 S21: 0.0442 S22: 0.6888 S23: -0.9948 REMARK 3 S31: -0.4220 S32: -2.1573 S33: -0.9634 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3NXP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060409. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NE-CAT, 24-ID-E REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24257 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP FROM CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 3E6P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL, PH 8.5 AND 20% PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 33.94650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.23150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.50300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.23150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.94650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.50300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 156 REMARK 465 GLU A 157 REMARK 465 GLY A 158 REMARK 465 SER A 159 REMARK 465 SER A 160 REMARK 465 VAL A 161 REMARK 465 ASN A 162 REMARK 465 LEU A 163 REMARK 465 SER A 164 REMARK 465 PRO A 165 REMARK 465 PRO A 166 REMARK 465 LEU A 167 REMARK 465 GLU A 168 REMARK 465 GLU A 255 REMARK 465 THR A 256 REMARK 465 GLY A 257 REMARK 465 ASP A 258 REMARK 465 GLY A 259 REMARK 465 LEU A 260 REMARK 465 ASP A 261 REMARK 465 GLU A 262 REMARK 465 ASP A 263 REMARK 465 SER A 264 REMARK 465 ASP A 265 REMARK 465 ARG A 266 REMARK 465 ALA A 267 REMARK 465 ILE A 268 REMARK 465 GLU A 269 REMARK 465 GLY A 270 REMARK 465 ALA A 271 REMARK 465 THR A 272 REMARK 465 ALA A 273 REMARK 465 VAL A 549C REMARK 465 GLY A 549D REMARK 465 LYS A 549E REMARK 465 GLY A 549F 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 SER A 203 38.48 -152.93 REMARK 500 GLU A 216 -122.38 44.74 REMARK 500 GLU A 276 102.66 -58.53 REMARK 500 PHE A 299 -81.74 -128.37 REMARK 500 ILE A 317 17.82 -58.24 REMARK 500 ASP A 318 -142.43 53.45 REMARK 500 ARG A 450 -21.20 -150.67 REMARK 500 TYR A 460A 85.74 -151.90 REMARK 500 ILE A 479 -64.24 -121.96 REMARK 500 GLU A 497A 76.43 -109.90 REMARK 500 ASP A 502 70.69 -69.93 REMARK 500 SER A 614 -152.00 -127.05 REMARK 500 LYS A 624 -73.17 -96.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3E6P RELATED DB: PDB REMARK 900 NA(+) BINDING TO MEIZOTHROMBIN DESF1. DBREF 3NXP A 156 647 UNP P00734 THRB_HUMAN 199 622 SEQADV 3NXP ALA A 271 UNP P00734 ARG 314 ENGINEERED MUTATION SEQADV 3NXP ALA A 284 UNP P00734 ARG 327 ENGINEERED MUTATION SEQRES 1 A 424 SER GLU GLY SER SER VAL ASN LEU SER PRO PRO LEU GLU SEQRES 2 A 424 GLN CYS VAL PRO ASP ARG GLY GLN GLN TYR GLN GLY ARG SEQRES 3 A 424 LEU ALA VAL THR THR HIS GLY LEU PRO CYS LEU ALA TRP SEQRES 4 A 424 ALA SER ALA GLN ALA LYS ALA LEU SER LYS HIS GLN ASP SEQRES 5 A 424 PHE ASN SER ALA VAL GLN LEU VAL GLU ASN PHE CYS ARG SEQRES 6 A 424 ASN PRO ASP GLY ASP GLU GLU GLY VAL TRP CYS TYR VAL SEQRES 7 A 424 ALA GLY LYS PRO GLY ASP PHE GLY TYR CYS ASP LEU ASN SEQRES 8 A 424 TYR CYS GLU GLU ALA VAL GLU GLU GLU THR GLY ASP GLY SEQRES 9 A 424 LEU ASP GLU ASP SER ASP ARG ALA ILE GLU GLY ALA THR SEQRES 10 A 424 ALA THR SER GLU TYR GLN THR PHE PHE ASN PRO ALA THR SEQRES 11 A 424 PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO LEU SEQRES 12 A 424 PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG GLU SEQRES 13 A 424 LEU LEU GLU SER TYR ILE ASP GLY ARG ILE VAL GLU GLY SEQRES 14 A 424 SER ASP ALA GLU ILE GLY MET SER PRO TRP GLN VAL MET SEQRES 15 A 424 LEU PHE ARG LYS SER PRO GLN GLU LEU LEU CYS GLY ALA SEQRES 16 A 424 SER LEU ILE SER ASP ARG TRP VAL LEU THR ALA ALA HIS SEQRES 17 A 424 CYS LEU LEU TYR PRO PRO TRP ASP LYS ASN PHE THR GLU SEQRES 18 A 424 ASN ASP LEU LEU VAL ARG ILE GLY LYS HIS SER ARG THR SEQRES 19 A 424 ARG TYR GLU ARG ASN ILE GLU LYS ILE SER MET LEU GLU SEQRES 20 A 424 LYS ILE TYR ILE HIS PRO ARG TYR ASN TRP ARG GLU ASN SEQRES 21 A 424 LEU ASP ARG ASP ILE ALA LEU MET LYS LEU LYS LYS PRO SEQRES 22 A 424 VAL ALA PHE SER ASP TYR ILE HIS PRO VAL CYS LEU PRO SEQRES 23 A 424 ASP ARG GLU THR ALA ALA SER LEU LEU GLN ALA GLY TYR SEQRES 24 A 424 LYS GLY ARG VAL THR GLY TRP GLY ASN LEU LYS GLU THR SEQRES 25 A 424 TRP THR ALA ASN VAL GLY LYS GLY GLN PRO SER VAL LEU SEQRES 26 A 424 GLN VAL VAL ASN LEU PRO ILE VAL GLU ARG PRO VAL CYS SEQRES 27 A 424 LYS ASP SER THR ARG ILE ARG ILE THR ASP ASN MET PHE SEQRES 28 A 424 CYS ALA GLY TYR LYS PRO ASP GLU GLY LYS ARG GLY ASP SEQRES 29 A 424 ALA CYS GLU GLY ASP SER GLY GLY PRO PHE VAL MET LYS SEQRES 30 A 424 SER PRO PHE ASN ASN ARG TRP TYR GLN MET GLY ILE VAL SEQRES 31 A 424 SER TRP GLY GLU GLY CYS ASP ARG ASP GLY LYS TYR GLY SEQRES 32 A 424 PHE TYR THR HIS VAL PHE ARG LEU LYS LYS TRP ILE GLN SEQRES 33 A 424 LYS VAL ILE ASP GLN PHE GLY GLU MODRES 3NXP ASN A 460G ASN GLYCOSYLATION SITE HET NAG A 701 14 HET TRS A 702 8 HET TRS A 703 8 HET GOL A 704 6 HET GOL A 705 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM GOL GLYCEROL 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 HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG C8 H15 N O6 FORMUL 3 TRS 2(C4 H12 N O3 1+) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 HOH *197(H2 O) HELIX 1 1 PRO A 172 GLN A 176 5 5 HELIX 2 2 SER A 196 ALA A 201 1 6 HELIX 3 3 ASN A 282 GLY A 287 1 6 HELIX 4 4 PHE A 299 SER A 303 5 5 HELIX 5 5 THR A 308 GLU A 314 5 7 HELIX 6 6 ALA A 455 LEU A 459 1 5 HELIX 7 7 PRO A 460B ASP A 460E 5 4 HELIX 8 8 THR A 460I ASN A 462 5 3 HELIX 9 9 ASP A 525 GLY A 533 1 12 HELIX 10 10 GLY A 542 ASN A 549B 1 10 HELIX 11 11 GLU A 564 SER A 571 1 8 HELIX 12 12 LEU A 634 GLY A 646 1 13 SHEET 1 A 2 TRP A 230 TYR A 232 0 SHEET 2 A 2 PHE A 240 TYR A 242 -1 O GLY A 241 N CYS A 231 SHEET 1 B 7 SER A 420 ASP A 421 0 SHEET 2 B 7 GLN A 556 PRO A 561 -1 O VAL A 557 N SER A 420 SHEET 3 B 7 LYS A 535 GLY A 540 -1 N GLY A 540 O GLN A 556 SHEET 4 B 7 PRO A 598 LYS A 602 -1 O VAL A 600 N ARG A 537 SHEET 5 B 7 TRP A 607 VAL A 613 -1 O MET A 610 N PHE A 599 SHEET 6 B 7 GLY A 626 HIS A 630 -1 O THR A 629 N ILE A 612 SHEET 7 B 7 MET A 580 ALA A 583 -1 N PHE A 581 O TYR A 628 SHEET 1 C 7 LYS A 481 SER A 483 0 SHEET 2 C 7 LEU A 464 ILE A 468 -1 N ILE A 468 O LYS A 481 SHEET 3 C 7 GLN A 430 ARG A 435 -1 N PHE A 434 O LEU A 465 SHEET 4 C 7 GLU A 439 LEU A 446 -1 O GLU A 439 N ARG A 435 SHEET 5 C 7 TRP A 451 THR A 454 -1 O LEU A 453 N SER A 445 SHEET 6 C 7 ALA A 504 LEU A 508 -1 O ALA A 504 N THR A 454 SHEET 7 C 7 LEU A 485 ILE A 490 -1 N LYS A 487 O LYS A 507 SHEET 1 D 2 LEU A 460 TYR A 460A 0 SHEET 2 D 2 LYS A 460F ASN A 460G-1 O LYS A 460F N TYR A 460A SSBOND 1 CYS A 170 CYS A 248 1555 1555 2.06 SSBOND 2 CYS A 191 CYS A 231 1555 1555 2.04 SSBOND 3 CYS A 219 CYS A 243 1555 1555 1.99 SSBOND 4 CYS A 293 CYS A 522 1555 1555 2.05 SSBOND 5 CYS A 442 CYS A 458 1555 1555 2.04 SSBOND 6 CYS A 568 CYS A 582 1555 1555 2.08 SSBOND 7 CYS A 591 CYS A 620 1555 1555 2.04 LINK ND2 ASN A 460G C1 NAG A 701 1555 1555 1.45 CISPEP 1 SER A 436A PRO A 437 0 -9.11 CRYST1 67.893 81.006 88.463 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014729 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012345 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011304 0.00000