HEADER HYDROLASE 22-SEP-09 3JZ2 TITLE CRYSTAL STRUCTURE OF HUMAN THROMBIN MUTANT N143P IN E* FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.5; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 9 CHAIN: B; COMPND 10 EC: 3.4.21.5; COMPND 11 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: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029; 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: CRICETULUS GRISEUS; SOURCE 15 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 10029 KEYWDS SERINE PROTEASE, ACUTE PHASE, BLOOD COAGULATION, CLEAVAGE ON PAIR OF KEYWDS 2 BASIC RESIDUES, DISEASE MUTATION, DISULFIDE BOND, GAMMA- KEYWDS 3 CARBOXYGLUTAMIC ACID, GLYCOPROTEIN, HYDROLASE, KRINGLE, PROTEASE, KEYWDS 4 SECRETED, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR W.NIU,Z.CHEN,L.A.BUSH-PELC,A.BAH,P.S.GANDHI,E.DI CERA REVDAT 6 06-SEP-23 3JZ2 1 REMARK REVDAT 5 13-OCT-21 3JZ2 1 SEQADV HETSYN REVDAT 4 29-JUL-20 3JZ2 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 13-JUL-11 3JZ2 1 VERSN REVDAT 2 12-JAN-10 3JZ2 1 JRNL REVDAT 1 20-OCT-09 3JZ2 0 JRNL AUTH W.NIU,Z.CHEN,L.A.BUSH-PELC,A.BAH,P.S.GANDHI,E.DI CERA JRNL TITL MUTANT N143P REVEALS HOW NA+ ACTIVATES THROMBIN JRNL REF J.BIOL.CHEM. V. 284 36175 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19846563 JRNL DOI 10.1074/JBC.M109.069500 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 2009 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 18250335 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.O.PINEDA,C.J.CARRELL,L.A.BUSH,S.PRASAD,S.CACCIA,Z.CHEN, REMARK 1 AUTH 2 F.S.MATHEWS,E.DI CERA REMARK 1 TITL MOLECULAR DISSECTION OF NA+ BINDING TO THROMBIN REMARK 1 REF J.BIOL.CHEM. V. 279 31842 2004 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 15152000 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : -3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 14167 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 747 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 851 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 48 REMARK 3 BIN FREE R VALUE : 0.4380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2234 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.338 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.250 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.171 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.999 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2318 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3122 ; 1.431 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 270 ; 6.566 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;34.677 ;23.148 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 406 ;16.764 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;16.319 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 324 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1754 ; 0.006 ; 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): 1364 ; 0.657 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2197 ; 1.251 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 954 ; 1.782 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 925 ; 2.949 ; 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 : 12 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 7 REMARK 3 ORIGIN FOR THE GROUP (A): 15.9655 3.7910 -9.9923 REMARK 3 T TENSOR REMARK 3 T11: 0.2108 T22: 0.1655 REMARK 3 T33: 0.2651 T12: 0.0191 REMARK 3 T13: -0.0776 T23: -0.0789 REMARK 3 L TENSOR REMARK 3 L11: 1.7723 L22: 9.3563 REMARK 3 L33: 5.2063 L12: 2.1533 REMARK 3 L13: -2.9187 L23: -2.0463 REMARK 3 S TENSOR REMARK 3 S11: -0.1189 S12: -0.1102 S13: -0.2285 REMARK 3 S21: -0.3399 S22: -0.0551 S23: -0.6877 REMARK 3 S31: 0.2389 S32: 0.2477 S33: 0.1740 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 8 A 14 REMARK 3 ORIGIN FOR THE GROUP (A): 6.1706 4.8887 -10.6939 REMARK 3 T TENSOR REMARK 3 T11: 0.0943 T22: 0.1246 REMARK 3 T33: 0.1150 T12: -0.0510 REMARK 3 T13: -0.0626 T23: -0.0172 REMARK 3 L TENSOR REMARK 3 L11: 3.0120 L22: 9.3923 REMARK 3 L33: 2.2080 L12: -1.2509 REMARK 3 L13: 0.2512 L23: -1.2112 REMARK 3 S TENSOR REMARK 3 S11: -0.0110 S12: 0.1305 S13: -0.4044 REMARK 3 S21: -0.4096 S22: 0.0350 S23: 0.4893 REMARK 3 S31: 0.2083 S32: -0.3074 S33: -0.0241 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 : B 16 B 60 REMARK 3 ORIGIN FOR THE GROUP (A): 19.6565 12.6345 7.5358 REMARK 3 T TENSOR REMARK 3 T11: 0.0767 T22: 0.0998 REMARK 3 T33: 0.0631 T12: 0.0103 REMARK 3 T13: -0.0041 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 1.6836 L22: 2.4564 REMARK 3 L33: 1.8811 L12: 0.8191 REMARK 3 L13: 0.2452 L23: 0.6037 REMARK 3 S TENSOR REMARK 3 S11: 0.0071 S12: -0.2319 S13: -0.0454 REMARK 3 S21: 0.2595 S22: 0.0502 S23: -0.0723 REMARK 3 S31: 0.2430 S32: -0.0742 S33: -0.0573 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 61 B 82 REMARK 3 ORIGIN FOR THE GROUP (A): 18.6584 4.1757 11.1441 REMARK 3 T TENSOR REMARK 3 T11: 0.1849 T22: 0.1737 REMARK 3 T33: 0.1020 T12: 0.0323 REMARK 3 T13: -0.0377 T23: 0.0528 REMARK 3 L TENSOR REMARK 3 L11: 1.3842 L22: 3.9772 REMARK 3 L33: 1.9330 L12: 1.6910 REMARK 3 L13: 0.0487 L23: 0.6390 REMARK 3 S TENSOR REMARK 3 S11: -0.0113 S12: -0.2730 S13: -0.0290 REMARK 3 S21: 0.2725 S22: 0.0223 S23: -0.0575 REMARK 3 S31: 0.1256 S32: -0.1241 S33: -0.0109 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 83 B 121 REMARK 3 ORIGIN FOR THE GROUP (A): 28.0615 13.3530 3.8828 REMARK 3 T TENSOR REMARK 3 T11: 0.0350 T22: 0.1091 REMARK 3 T33: 0.0635 T12: 0.0274 REMARK 3 T13: 0.0098 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 2.1730 L22: 5.5204 REMARK 3 L33: 2.8909 L12: 1.4830 REMARK 3 L13: 0.5976 L23: 0.3186 REMARK 3 S TENSOR REMARK 3 S11: 0.0424 S12: -0.1943 S13: -0.0916 REMARK 3 S21: 0.1597 S22: 0.0767 S23: -0.4249 REMARK 3 S31: -0.0052 S32: 0.2849 S33: -0.1191 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 122 B 130 REMARK 3 ORIGIN FOR THE GROUP (A): 21.9467 19.0259 -14.6506 REMARK 3 T TENSOR REMARK 3 T11: 0.2054 T22: 0.1400 REMARK 3 T33: 0.0422 T12: -0.0304 REMARK 3 T13: -0.0100 T23: 0.0176 REMARK 3 L TENSOR REMARK 3 L11: 2.6770 L22: 4.6051 REMARK 3 L33: 2.3917 L12: 2.8120 REMARK 3 L13: -1.0836 L23: -1.6443 REMARK 3 S TENSOR REMARK 3 S11: -0.1804 S12: 0.2855 S13: 0.0280 REMARK 3 S21: -0.4022 S22: 0.2342 S23: 0.0075 REMARK 3 S31: 0.0987 S32: -0.0042 S33: -0.0537 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 131 B 175 REMARK 3 ORIGIN FOR THE GROUP (A): 12.0776 24.4083 -0.3828 REMARK 3 T TENSOR REMARK 3 T11: 0.2066 T22: 0.1214 REMARK 3 T33: 0.1268 T12: 0.0660 REMARK 3 T13: 0.0443 T23: -0.0372 REMARK 3 L TENSOR REMARK 3 L11: 1.8984 L22: 6.3119 REMARK 3 L33: 1.3948 L12: 1.0451 REMARK 3 L13: 0.9836 L23: 0.8471 REMARK 3 S TENSOR REMARK 3 S11: 0.0231 S12: -0.1396 S13: 0.1811 REMARK 3 S21: 0.4623 S22: 0.0892 S23: 0.1849 REMARK 3 S31: -0.3035 S32: -0.1286 S33: -0.1122 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 176 B 186 REMARK 3 ORIGIN FOR THE GROUP (A): 14.9316 30.4184 -2.7760 REMARK 3 T TENSOR REMARK 3 T11: 0.2427 T22: 0.1317 REMARK 3 T33: 0.1828 T12: 0.0593 REMARK 3 T13: 0.0653 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 9.1674 L22: 4.8049 REMARK 3 L33: 2.4865 L12: 2.7655 REMARK 3 L13: 1.6999 L23: 1.2082 REMARK 3 S TENSOR REMARK 3 S11: 0.2980 S12: -0.2928 S13: 1.0050 REMARK 3 S21: 0.3034 S22: -0.2840 S23: 0.4867 REMARK 3 S31: -0.4444 S32: -0.4912 S33: -0.0140 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 187 B 193 REMARK 3 ORIGIN FOR THE GROUP (A): 6.3480 24.4303 3.5146 REMARK 3 T TENSOR REMARK 3 T11: 0.4969 T22: 0.6795 REMARK 3 T33: 0.3890 T12: 0.3276 REMARK 3 T13: -0.1144 T23: -0.2570 REMARK 3 L TENSOR REMARK 3 L11: 0.7352 L22: 10.7002 REMARK 3 L33: 4.8708 L12: 1.3134 REMARK 3 L13: 0.1805 L23: 6.6179 REMARK 3 S TENSOR REMARK 3 S11: 0.0124 S12: -0.2793 S13: 0.4103 REMARK 3 S21: -0.9560 S22: -0.4912 S23: 1.1446 REMARK 3 S31: -0.8789 S32: -0.2696 S33: 0.4788 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 194 B 217 REMARK 3 ORIGIN FOR THE GROUP (A): 16.7784 16.6941 -5.2913 REMARK 3 T TENSOR REMARK 3 T11: 0.0842 T22: 0.0649 REMARK 3 T33: 0.0592 T12: -0.0101 REMARK 3 T13: 0.0083 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 1.4515 L22: 2.1674 REMARK 3 L33: 5.3733 L12: -0.0496 REMARK 3 L13: 1.3092 L23: 1.7013 REMARK 3 S TENSOR REMARK 3 S11: -0.0510 S12: 0.0269 S13: 0.0620 REMARK 3 S21: -0.1466 S22: -0.0024 S23: 0.0492 REMARK 3 S31: -0.1086 S32: 0.0742 S33: 0.0535 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 219 B 225 REMARK 3 ORIGIN FOR THE GROUP (A): 10.0946 30.4405 6.7321 REMARK 3 T TENSOR REMARK 3 T11: 0.4878 T22: 0.3971 REMARK 3 T33: 0.2688 T12: 0.1194 REMARK 3 T13: 0.1471 T23: -0.0918 REMARK 3 L TENSOR REMARK 3 L11: 1.3774 L22: 9.6686 REMARK 3 L33: 6.9423 L12: -1.2053 REMARK 3 L13: 2.7206 L23: -6.0564 REMARK 3 S TENSOR REMARK 3 S11: -0.2466 S12: -0.3996 S13: 0.1651 REMARK 3 S21: 1.0051 S22: 0.3027 S23: 0.7494 REMARK 3 S31: -0.8392 S32: -0.7722 S33: -0.0561 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 226 B 245 REMARK 3 ORIGIN FOR THE GROUP (A): 29.9247 18.7533 -4.4102 REMARK 3 T TENSOR REMARK 3 T11: 0.0808 T22: 0.1582 REMARK 3 T33: 0.1747 T12: -0.0016 REMARK 3 T13: 0.0372 T23: -0.0090 REMARK 3 L TENSOR REMARK 3 L11: 3.8054 L22: 4.3172 REMARK 3 L33: 3.7393 L12: 0.2887 REMARK 3 L13: -2.4455 L23: -0.1827 REMARK 3 S TENSOR REMARK 3 S11: 0.0532 S12: 0.0973 S13: 0.1492 REMARK 3 S21: -0.2749 S22: -0.0483 S23: -0.7310 REMARK 3 S31: -0.0325 S32: 0.4002 S33: -0.0049 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: NULL REMARK 4 REMARK 4 3JZ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055339. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-09 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 : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14942 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.40800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: PEB ENTRY 3BEI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M IMIDAZOLE AND 7% PEG 8000, PH REMARK 280 8.0, 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 59.88500 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 89.82750 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 29.94250 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: 3670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 THR A -3 REMARK 465 PHE A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 ASP A 14L REMARK 465 GLY A 14M REMARK 465 ARG A 15 REMARK 465 LYS B 145 REMARK 465 GLU B 146 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 GLY B 246 REMARK 465 GLU B 247 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 VAL B 31 O - C - N ANGL. DEV. = -9.7 DEGREES 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 GLU A 1C -35.91 140.05 REMARK 500 PHE A 7 -83.36 -125.03 REMARK 500 ASN B 60G 71.75 -154.24 REMARK 500 GLU B 97A -72.79 -112.02 REMARK 500 PRO B 186 -10.16 -44.91 REMARK 500 ASP B 186A -94.76 -64.22 REMARK 500 GLU B 186B 124.18 160.18 REMARK 500 LYS B 186D -179.49 118.72 REMARK 500 ARG B 187 34.78 -154.56 REMARK 500 ASP B 189 144.88 -178.31 REMARK 500 SER B 214 -148.13 -94.90 REMARK 500 ASP B 222 77.02 38.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY B 142 PRO B 143 -149.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SHH RELATED DB: PDB REMARK 900 SLOW FORM OF THROMBIN BOUND WITH PPACK 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: 3JZ1 RELATED DB: PDB DBREF 3JZ2 A -3 15 UNP P00734 THRB_HUMAN 328 363 DBREF 3JZ2 B 16 247 UNP P00734 THRB_HUMAN 364 622 SEQADV 3JZ2 PRO B 143 UNP P00734 ASN 506 ENGINEERED MUTATION SEQRES 1 A 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 A 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 A 36 GLU 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 PRO 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 TYR 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 3JZ2 ASN B 60G ASN GLYCOSYLATION SITE HET NAG B 301 14 HET GOL B 401 6 HET GOL B 402 6 HET GOL B 403 6 HET GOL B 404 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 4(C3 H8 O3) FORMUL 8 HOH *116(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 CYS B 191 SER B 195 5 5 HELIX 9 9 LEU B 234 PHE B 245 1 12 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 GLY B 211 N PHE B 199 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 LEU B 41 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 2.02 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.04 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.03 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.04 LINK ND2 ASN B 60G C1 NAG B 301 1555 1555 1.44 CISPEP 1 SER B 36A PRO B 37 0 -7.61 CRYST1 57.890 57.890 119.770 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 0.017274 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017274 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008349 0.00000