HEADER HYDROLASE 26-MAY-11 3S7H TITLE STRUCTURE OF THROMBIN MUTANT Y225P IN THE E* FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: THROMBIN LIGHT CHAIN; COMPND 5 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 6 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT CHAIN, THROMBIN HEAVY COMPND 7 CHAIN; COMPND 8 EC: 3.4.21.5; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: PROTHROMBIN; COMPND 13 CHAIN: B; COMPND 14 FRAGMENT: THROMBIN HEAVY CHAIN; COMPND 15 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 16 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT CHAIN, THROMBIN HEAVY COMPND 17 CHAIN; COMPND 18 EC: 3.4.21.5; COMPND 19 ENGINEERED: 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_COMMON: CHINESE HAMSTER; SOURCE 7 EXPRESSION_SYSTEM_ORGAN: KIDNEY; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: HPC4-MODIFIED PNUT; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: F2; SOURCE 14 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 15 EXPRESSION_SYSTEM_ORGAN: KIDNEY; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: HPC4-MODIFIED PNUT KEYWDS SERINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR W.NIU,Z.CHEN,P.GANDHI,A.VOGT,N.POZZI,L.A.PELE,F.ZAPATA,E.DI CERA REVDAT 4 13-SEP-23 3S7H 1 HETSYN REVDAT 3 29-JUL-20 3S7H 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE REVDAT 2 24-AUG-11 3S7H 1 JRNL VERSN REVDAT 1 06-JUL-11 3S7H 0 JRNL AUTH W.NIU,Z.CHEN,P.S.GANDHI,A.D.VOGT,N.POZZI,L.A.PELC,F.ZAPATA, JRNL AUTH 2 E.DI CERA JRNL TITL CRYSTALLOGRAPHIC AND KINETIC EVIDENCE OF ALLOSTERY IN A JRNL TITL 2 TRYPSIN-LIKE PROTEASE. JRNL REF BIOCHEMISTRY V. 50 6301 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21707111 JRNL DOI 10.1021/BI200878C REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.S.GANDHI,Z.CHEN,F.S.MATHEWS,E.DI CERA REMARK 1 TITL STRUCTURAL IDENTIFICATION OF THE PATHWAY OF LONG-RANGE REMARK 1 TITL 2 COMMUNICATION IN AN ALLOSTERIC ENZYME. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 105 1832 2008 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 18250335 REMARK 1 DOI 10.1073/PNAS.0710894105 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : -0.700 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 28549 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1518 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1921 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2224 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 191 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.03000 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): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.382 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2365 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3203 ; 1.142 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 287 ; 5.600 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;34.353 ;23.148 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 422 ;14.974 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;13.970 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 332 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1800 ; 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): 1413 ; 0.386 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2288 ; 0.760 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 952 ; 1.321 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 915 ; 2.257 ; 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 8 REMARK 3 ORIGIN FOR THE GROUP (A): -14.6830 25.3200 10.6170 REMARK 3 T TENSOR REMARK 3 T11: 0.2174 T22: 0.0551 REMARK 3 T33: 0.1303 T12: 0.0185 REMARK 3 T13: 0.0324 T23: -0.0082 REMARK 3 L TENSOR REMARK 3 L11: 6.2448 L22: 9.2106 REMARK 3 L33: 5.8026 L12: -1.8976 REMARK 3 L13: -1.4300 L23: -1.2847 REMARK 3 S TENSOR REMARK 3 S11: -0.0498 S12: -0.1480 S13: 0.4614 REMARK 3 S21: 0.4539 S22: 0.0970 S23: -0.2612 REMARK 3 S31: -0.5627 S32: 0.0318 S33: -0.0472 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 9 A 12 REMARK 3 ORIGIN FOR THE GROUP (A): -20.563 28.730 13.264 REMARK 3 T TENSOR REMARK 3 T11: 0.3376 T22: 0.1887 REMARK 3 T33: 0.4426 T12: 0.0736 REMARK 3 T13: -0.0852 T23: -0.0484 REMARK 3 L TENSOR REMARK 3 L11: 31.8938 L22: 13.7687 REMARK 3 L33: 22.8173 L12: -1.2111 REMARK 3 L13: 10.3861 L23: 3.2929 REMARK 3 S TENSOR REMARK 3 S11: 1.8506 S12: 0.5901 S13: -2.3792 REMARK 3 S21: 0.4661 S22: -0.8029 S23: 0.9869 REMARK 3 S31: 1.6506 S32: -1.0704 S33: -1.0478 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 13 A 14 REMARK 3 ORIGIN FOR THE GROUP (A): -23.815 12.848 12.561 REMARK 3 T TENSOR REMARK 3 T11: 0.1408 T22: 0.2102 REMARK 3 T33: 0.1939 T12: -0.0221 REMARK 3 T13: 0.0777 T23: 0.0478 REMARK 3 L TENSOR REMARK 3 L11: 5.8318 L22: 21.3795 REMARK 3 L33: 4.7491 L12: -1.7893 REMARK 3 L13: -1.3966 L23: -3.2414 REMARK 3 S TENSOR REMARK 3 S11: -0.2848 S12: -0.4090 S13: -0.5126 REMARK 3 S21: 0.7711 S22: 0.1387 S23: -0.1457 REMARK 3 S31: 0.2717 S32: -0.1908 S33: 0.1462 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 : B 16 B 59 REMARK 3 ORIGIN FOR THE GROUP (A): -8.7930 16.5020 -6.9220 REMARK 3 T TENSOR REMARK 3 T11: 0.1105 T22: 0.1110 REMARK 3 T33: 0.1219 T12: -0.0283 REMARK 3 T13: -0.0027 T23: 0.0197 REMARK 3 L TENSOR REMARK 3 L11: 2.6806 L22: 3.4815 REMARK 3 L33: 2.3182 L12: -0.4894 REMARK 3 L13: -0.6500 L23: 0.2063 REMARK 3 S TENSOR REMARK 3 S11: -0.0028 S12: 0.2948 S13: -0.0481 REMARK 3 S21: -0.3701 S22: 0.0331 S23: -0.0195 REMARK 3 S31: -0.1342 S32: -0.1115 S33: -0.0303 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 : B 60 B 84 REMARK 3 ORIGIN FOR THE GROUP (A): -8.238 21.112 -11.714 REMARK 3 T TENSOR REMARK 3 T11: 0.2280 T22: 0.1699 REMARK 3 T33: 0.1643 T12: -0.0110 REMARK 3 T13: 0.0187 T23: 0.0645 REMARK 3 L TENSOR REMARK 3 L11: 1.2238 L22: 5.7005 REMARK 3 L33: 1.2815 L12: -1.4844 REMARK 3 L13: -0.4295 L23: 1.2319 REMARK 3 S TENSOR REMARK 3 S11: 0.0287 S12: 0.2120 S13: 0.2110 REMARK 3 S21: -0.3999 S22: 0.1370 S23: -0.0986 REMARK 3 S31: -0.2798 S32: -0.0792 S33: -0.1657 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 : B 85 B 123 REMARK 3 ORIGIN FOR THE GROUP (A): -0.8910 15.0910 -2.5850 REMARK 3 T TENSOR REMARK 3 T11: 0.0484 T22: 0.1231 REMARK 3 T33: 0.1437 T12: -0.0408 REMARK 3 T13: -0.0211 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 2.0055 L22: 3.9582 REMARK 3 L33: 2.8929 L12: -0.7906 REMARK 3 L13: -0.5299 L23: 0.5472 REMARK 3 S TENSOR REMARK 3 S11: 0.0430 S12: 0.0515 S13: 0.0597 REMARK 3 S21: -0.1086 S22: 0.1038 S23: -0.3907 REMARK 3 S31: 0.0052 S32: 0.2758 S33: -0.1468 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 : B 124 B 129 REMARK 3 ORIGIN FOR THE GROUP (A): -6.9020 8.8040 16.5040 REMARK 3 T TENSOR REMARK 3 T11: 0.2778 T22: 0.2064 REMARK 3 T33: 0.2204 T12: 0.0734 REMARK 3 T13: 0.0212 T23: 0.0360 REMARK 3 L TENSOR REMARK 3 L11: 12.0741 L22: 0.4170 REMARK 3 L33: 6.5716 L12: 4.1885 REMARK 3 L13: 0.2432 L23: -0.0844 REMARK 3 S TENSOR REMARK 3 S11: 0.1410 S12: -0.5410 S13: 0.7489 REMARK 3 S21: 0.2553 S22: -0.0688 S23: 0.3366 REMARK 3 S31: -0.3214 S32: -0.2885 S33: -0.0722 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 : B 130 B 167 REMARK 3 ORIGIN FOR THE GROUP (A): -18.4850 7.9780 1.7910 REMARK 3 T TENSOR REMARK 3 T11: 0.1201 T22: 0.1470 REMARK 3 T33: 0.1440 T12: -0.0638 REMARK 3 T13: -0.0051 T23: -0.0059 REMARK 3 L TENSOR REMARK 3 L11: 3.6733 L22: 6.9425 REMARK 3 L33: 3.2226 L12: -1.0824 REMARK 3 L13: 0.4917 L23: -1.5170 REMARK 3 S TENSOR REMARK 3 S11: -0.0265 S12: 0.1851 S13: -0.0092 REMARK 3 S21: -0.5732 S22: 0.0707 S23: 0.2988 REMARK 3 S31: 0.3709 S32: -0.2387 S33: -0.0442 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 : B 168 B 185 REMARK 3 ORIGIN FOR THE GROUP (A): -12.0650 -4.5860 1.1850 REMARK 3 T TENSOR REMARK 3 T11: 0.3039 T22: 0.1979 REMARK 3 T33: 0.2787 T12: -0.0675 REMARK 3 T13: -0.0163 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 3.6310 L22: 8.4158 REMARK 3 L33: 3.4551 L12: 0.8910 REMARK 3 L13: 0.3798 L23: 2.6229 REMARK 3 S TENSOR REMARK 3 S11: 0.0129 S12: 0.3228 S13: -0.6737 REMARK 3 S21: 0.0316 S22: -0.0362 S23: 0.4123 REMARK 3 S31: 0.6724 S32: -0.1584 S33: 0.0233 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 : B 186 B 192 REMARK 3 ORIGIN FOR THE GROUP (A): -23.4210 3.5160 -2.7920 REMARK 3 T TENSOR REMARK 3 T11: 0.3769 T22: 0.8007 REMARK 3 T33: 0.6163 T12: -0.3376 REMARK 3 T13: -0.0136 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 7.4865 L22: 12.2703 REMARK 3 L33: 25.9739 L12: 0.8522 REMARK 3 L13: -1.5577 L23: -9.1712 REMARK 3 S TENSOR REMARK 3 S11: -0.1056 S12: 0.4379 S13: -1.2371 REMARK 3 S21: -0.1165 S22: 1.1788 S23: 1.2574 REMARK 3 S31: 2.1339 S32: -3.5682 S33: -1.0732 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 : B 193 B 217 REMARK 3 ORIGIN FOR THE GROUP (A): -12.0620 12.0590 5.4500 REMARK 3 T TENSOR REMARK 3 T11: 0.0589 T22: 0.0420 REMARK 3 T33: 0.0888 T12: -0.0182 REMARK 3 T13: 0.0082 T23: 0.0176 REMARK 3 L TENSOR REMARK 3 L11: 2.4395 L22: 2.9983 REMARK 3 L33: 6.7222 L12: -0.6175 REMARK 3 L13: -0.9102 L23: 2.2639 REMARK 3 S TENSOR REMARK 3 S11: -0.0439 S12: -0.0497 S13: -0.0262 REMARK 3 S21: 0.1049 S22: 0.0675 S23: 0.0469 REMARK 3 S31: 0.0472 S32: 0.0739 S33: -0.0237 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 : B 219 B 223 REMARK 3 ORIGIN FOR THE GROUP (A): -19.2410 -0.2760 -8.8960 REMARK 3 T TENSOR REMARK 3 T11: 0.8594 T22: 0.4545 REMARK 3 T33: 0.7179 T12: -0.1676 REMARK 3 T13: -0.3106 T23: -0.1661 REMARK 3 L TENSOR REMARK 3 L11: 3.8833 L22: 80.7695 REMARK 3 L33: -4.6872 L12: 17.7285 REMARK 3 L13: -11.8277 L23: -23.9388 REMARK 3 S TENSOR REMARK 3 S11: -0.1850 S12: -0.2390 S13: -0.0677 REMARK 3 S21: -3.9642 S22: -0.3217 S23: 3.3585 REMARK 3 S31: 1.1831 S32: -0.7983 S33: 0.5067 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 : B 224 B 244 REMARK 3 ORIGIN FOR THE GROUP (A): -0.7340 8.5920 4.5000 REMARK 3 T TENSOR REMARK 3 T11: 0.0958 T22: 0.1084 REMARK 3 T33: 0.1172 T12: 0.0129 REMARK 3 T13: -0.0128 T23: -0.0336 REMARK 3 L TENSOR REMARK 3 L11: 6.1447 L22: 4.3645 REMARK 3 L33: 4.2422 L12: 1.1747 REMARK 3 L13: 0.4849 L23: -0.9952 REMARK 3 S TENSOR REMARK 3 S11: 0.0114 S12: -0.1185 S13: 0.0194 REMARK 3 S21: 0.3121 S22: 0.0401 S23: -0.3750 REMARK 3 S31: -0.0009 S32: 0.4305 S33: -0.0515 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 3S7H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000065857. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRROR+NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30093 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.41800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 3BEI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS AND 8% PEG 8000 , PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 59.95700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 89.93550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.97850 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: 2710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 PHE A 1G REMARK 465 GLY A 1F REMARK 465 SER A 1E REMARK 465 GLY A 1D REMARK 465 GLU A 1C REMARK 465 ASP A 14L REMARK 465 GLY A 14M REMARK 465 ARG A 15 REMARK 465 THR B 147 REMARK 465 TRP B 148 REMARK 465 THR B 149 REMARK 465 ALA B 149A REMARK 465 ASN B 149B REMARK 465 VAL B 149C REMARK 465 GLY B 149D REMARK 465 LYS B 149E REMARK 465 PHE B 245 REMARK 465 GLY B 246 REMARK 465 GLU B 247 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 A 7 -85.51 -128.34 REMARK 500 CYS B 42 -165.11 178.92 REMARK 500 TYR B 60A 85.46 -150.74 REMARK 500 ASN B 60G 75.56 -158.43 REMARK 500 GLU B 97A -76.21 -104.24 REMARK 500 ASP B 186A -166.53 -71.81 REMARK 500 ARG B 187 45.09 -147.16 REMARK 500 SER B 214 -150.53 -91.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BEI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SLOW FORM OF THROMBIN IN A SELF_INHIBITED REMARK 900 CONFORMATION REMARK 900 RELATED ID: 3S7K RELATED DB: PDB DBREF 3S7H A 1G 15 UNP P00734 THRB_HUMAN 329 363 DBREF 3S7H B 16 247 UNP P00734 THRB_HUMAN 364 622 SEQADV 3S7H PRO B 225 UNP P00734 TYR 600 ENGINEERED MUTATION SEQRES 1 A 35 PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO LEU SEQRES 2 A 35 PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG GLU SEQRES 3 A 35 LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 B 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 B 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 B 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 B 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 B 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 B 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 B 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 B 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 B 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 B 259 GLY LYS PRO GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU MODRES 3S7H ASN B 60G ASN GLYCOSYLATION SITE HET NAG B 400 14 HET GOL B 401 6 HET GOL B 402 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAG C8 H15 N O6 FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 HOH *191(H2 O) HELIX 1 1 PHE A 7 SER A 11 5 5 HELIX 2 2 THR A 14B TYR A 14J 1 9 HELIX 3 3 ALA B 55 CYS B 58 5 4 HELIX 4 4 PRO B 60B ASP B 60E 5 4 HELIX 5 5 THR B 60I ASN B 62 5 3 HELIX 6 6 ASP B 125 LEU B 130 1 9 HELIX 7 7 GLU B 164 SER B 171 1 8 HELIX 8 8 LEU B 234 ASP B 243 1 10 SHEET 1 A 7 SER B 20 ASP B 21 0 SHEET 2 A 7 GLN B 156 PRO B 161 -1 O VAL B 157 N SER B 20 SHEET 3 A 7 LYS B 135 GLY B 140 -1 N VAL B 138 O VAL B 158 SHEET 4 A 7 PRO B 198 LYS B 202 -1 O VAL B 200 N ARG B 137 SHEET 5 A 7 TRP B 207 VAL B 213 -1 O TYR B 208 N MET B 201 SHEET 6 A 7 GLY B 226 HIS B 230 -1 O THR B 229 N ILE B 212 SHEET 7 A 7 MET B 180 ALA B 183 -1 N PHE B 181 O TYR B 228 SHEET 1 B 7 GLN B 30 ARG B 35 0 SHEET 2 B 7 GLU B 39 LEU B 46 -1 O CYS B 42 N LEU B 33 SHEET 3 B 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 4 B 7 ALA B 104 LEU B 108 -1 O MET B 106 N VAL B 52 SHEET 5 B 7 LYS B 81 ILE B 90 -1 N GLU B 86 O LYS B 107 SHEET 6 B 7 LEU B 64 ILE B 68 -1 N ILE B 68 O LYS B 81 SHEET 7 B 7 GLN B 30 ARG B 35 -1 N PHE B 34 O LEU B 65 SHEET 1 C 2 LEU B 60 TYR B 60A 0 SHEET 2 C 2 LYS B 60F ASN B 60G-1 O LYS B 60F N TYR B 60A SSBOND 1 CYS A 1 CYS B 122 1555 1555 2.06 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.02 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.04 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.05 LINK ND2 ASN B 60G C1 NAG B 400 1555 1555 1.44 CISPEP 1 SER B 36A PRO B 37 0 -9.49 CRYST1 57.620 57.620 119.914 90.00 90.00 90.00 P 43 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 0.017355 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017355 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008339 0.00000