HEADER HYDROLASE/PEPTIDE 19-SEP-12 4H6S TITLE CRYSTAL STRUCTURE OF THROMBIN MUTANT E14EA/D14LA/E18A/S195A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 5 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT CHAIN, THROMBIN HEAVY COMPND 6 CHAIN; COMPND 7 EC: 3.4.21.5; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: PROTHROMBIN; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE FRAGMENT 1, COMPND 14 ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT CHAIN, THROMBIN HEAVY COMPND 15 CHAIN; COMPND 16 EC: 3.4.21.5; COMPND 17 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: F2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SERINE PROTEASE, PRETHROMBIN-2, AUTOACTIVATION, HYDROLASE, HYDROLASE- KEYWDS 2 PEPTIDE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.POZZI,Z.CHEN,F.ZAPATA,L.A.PELC,E.DI CERA REVDAT 3 20-SEP-23 4H6S 1 REMARK SEQADV LINK REVDAT 2 11-JUN-14 4H6S 1 JRNL REVDAT 1 13-MAR-13 4H6S 0 JRNL AUTH N.POZZI,Z.CHEN,F.ZAPATA,W.NIU,S.BARRANCO-MEDINA,L.A.PELC, JRNL AUTH 2 E.DI CERA JRNL TITL AUTOACTIVATION OF THROMBIN PRECURSORS. JRNL REF J.BIOL.CHEM. V. 288 11601 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23467412 JRNL DOI 10.1074/JBC.M113.451542 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.O.PINEDA,C.J.CARRELL,L.A.BUSH,S.PRASAD,S.CACCIA,Z.W.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 2 REMARK 2 RESOLUTION. 2.19 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 12369 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) : 0.196 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 646 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) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 810 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2275 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 103 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : -0.16000 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): 0.405 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.257 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.204 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.053 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2333 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3150 ; 1.486 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 279 ; 6.949 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;34.644 ;23.091 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 416 ;18.480 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.616 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 326 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1777 ; 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): 1401 ; 0.759 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2253 ; 1.432 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 932 ; 1.978 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 897 ; 3.311 ; 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 : 10 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 10 REMARK 3 ORIGIN FOR THE GROUP (A): -26.5730 24.2360 -6.3770 REMARK 3 T TENSOR REMARK 3 T11: 0.3634 T22: 0.2850 REMARK 3 T33: 0.0925 T12: 0.1552 REMARK 3 T13: 0.0777 T23: -0.0264 REMARK 3 L TENSOR REMARK 3 L11: 3.2699 L22: 16.3097 REMARK 3 L33: 2.0181 L12: -2.5797 REMARK 3 L13: -1.9936 L23: 4.9575 REMARK 3 S TENSOR REMARK 3 S11: -0.6080 S12: -0.7068 S13: 0.0942 REMARK 3 S21: 1.1011 S22: 0.3994 S23: 0.9817 REMARK 3 S31: 0.5272 S32: 0.3878 S33: 0.2086 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 11 A 15 REMARK 3 ORIGIN FOR THE GROUP (A): -29.4560 26.7100 -22.2410 REMARK 3 T TENSOR REMARK 3 T11: 0.1762 T22: 0.2775 REMARK 3 T33: 0.3000 T12: 0.0682 REMARK 3 T13: 0.0075 T23: -0.0044 REMARK 3 L TENSOR REMARK 3 L11: 1.0507 L22: 1.0381 REMARK 3 L33: 3.0030 L12: 1.0397 REMARK 3 L13: 1.4122 L23: 1.4031 REMARK 3 S TENSOR REMARK 3 S11: -0.1652 S12: -0.0255 S13: 0.2589 REMARK 3 S21: -0.1284 S22: -0.0608 S23: 0.2933 REMARK 3 S31: -0.0617 S32: -0.0808 S33: 0.2259 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 72 REMARK 3 ORIGIN FOR THE GROUP (A): -6.1480 18.4100 -10.2100 REMARK 3 T TENSOR REMARK 3 T11: 0.2397 T22: 0.2574 REMARK 3 T33: 0.2257 T12: 0.0252 REMARK 3 T13: -0.0439 T23: -0.0072 REMARK 3 L TENSOR REMARK 3 L11: 0.6768 L22: 1.3850 REMARK 3 L33: 0.1228 L12: -0.3694 REMARK 3 L13: -0.1687 L23: -0.1432 REMARK 3 S TENSOR REMARK 3 S11: -0.0796 S12: -0.1214 S13: -0.0101 REMARK 3 S21: 0.1339 S22: 0.0655 S23: -0.1451 REMARK 3 S31: -0.0791 S32: 0.0017 S33: 0.0141 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 73 B 91 REMARK 3 ORIGIN FOR THE GROUP (A): -7.1860 20.7630 -2.6370 REMARK 3 T TENSOR REMARK 3 T11: 0.2859 T22: 0.2640 REMARK 3 T33: 0.1416 T12: 0.0546 REMARK 3 T13: -0.0125 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 1.4748 L22: 7.8488 REMARK 3 L33: 0.8014 L12: -1.3015 REMARK 3 L13: -0.3127 L23: 2.4862 REMARK 3 S TENSOR REMARK 3 S11: -0.0982 S12: -0.2927 S13: 0.1460 REMARK 3 S21: 0.1743 S22: 0.2237 S23: -0.5267 REMARK 3 S31: 0.0577 S32: 0.0589 S33: -0.1255 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 92 B 115 REMARK 3 ORIGIN FOR THE GROUP (A): -8.3880 8.2510 -12.6940 REMARK 3 T TENSOR REMARK 3 T11: 0.2517 T22: 0.2520 REMARK 3 T33: 0.2537 T12: 0.0094 REMARK 3 T13: -0.0039 T23: -0.0092 REMARK 3 L TENSOR REMARK 3 L11: 0.5064 L22: 1.3243 REMARK 3 L33: 1.9248 L12: -0.3728 REMARK 3 L13: -0.9323 L23: 0.6596 REMARK 3 S TENSOR REMARK 3 S11: -0.0795 S12: -0.0711 S13: -0.1434 REMARK 3 S21: 0.1234 S22: -0.0642 S23: -0.0706 REMARK 3 S31: -0.0679 S32: 0.1447 S33: 0.1437 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 116 B 146 REMARK 3 ORIGIN FOR THE GROUP (A): -19.7130 19.1430 -17.9760 REMARK 3 T TENSOR REMARK 3 T11: 0.1965 T22: 0.2588 REMARK 3 T33: 0.2224 T12: 0.0594 REMARK 3 T13: -0.0095 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 0.5509 L22: 0.9611 REMARK 3 L33: 0.8776 L12: -0.0503 REMARK 3 L13: 0.5502 L23: -0.4522 REMARK 3 S TENSOR REMARK 3 S11: -0.0750 S12: 0.0850 S13: -0.0054 REMARK 3 S21: 0.1045 S22: 0.1228 S23: -0.0181 REMARK 3 S31: 0.0119 S32: -0.0447 S33: -0.0478 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 150 B 164 REMARK 3 ORIGIN FOR THE GROUP (A): -13.3540 25.8110 -22.5580 REMARK 3 T TENSOR REMARK 3 T11: 0.2188 T22: 0.1980 REMARK 3 T33: 0.2092 T12: 0.0113 REMARK 3 T13: 0.0190 T23: 0.0122 REMARK 3 L TENSOR REMARK 3 L11: 1.9181 L22: 5.6729 REMARK 3 L33: 4.1133 L12: 2.2658 REMARK 3 L13: 1.5820 L23: 3.8776 REMARK 3 S TENSOR REMARK 3 S11: 0.0592 S12: 0.0759 S13: -0.0934 REMARK 3 S21: -0.1457 S22: 0.1029 S23: -0.2785 REMARK 3 S31: -0.4404 S32: -0.1386 S33: -0.1620 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 165 B 175 REMARK 3 ORIGIN FOR THE GROUP (A): -11.0310 9.4710 -36.0040 REMARK 3 T TENSOR REMARK 3 T11: 0.2094 T22: 0.2311 REMARK 3 T33: 0.2454 T12: 0.0187 REMARK 3 T13: -0.0678 T23: -0.0432 REMARK 3 L TENSOR REMARK 3 L11: 12.3814 L22: 3.6231 REMARK 3 L33: 3.6193 L12: -5.1691 REMARK 3 L13: 4.0139 L23: -3.5160 REMARK 3 S TENSOR REMARK 3 S11: 0.5194 S12: 0.0620 S13: -0.2334 REMARK 3 S21: -0.4731 S22: -0.0732 S23: 0.3884 REMARK 3 S31: 0.4786 S32: 0.1210 S33: -0.4462 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 176 B 232 REMARK 3 ORIGIN FOR THE GROUP (A): -15.6620 17.9950 -25.0450 REMARK 3 T TENSOR REMARK 3 T11: 0.1950 T22: 0.2536 REMARK 3 T33: 0.2326 T12: 0.0246 REMARK 3 T13: -0.0113 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.6822 L22: 0.7943 REMARK 3 L33: 0.4746 L12: 0.1719 REMARK 3 L13: -0.0683 L23: -0.0620 REMARK 3 S TENSOR REMARK 3 S11: -0.0046 S12: 0.0157 S13: -0.0670 REMARK 3 S21: -0.0232 S22: 0.0164 S23: -0.0172 REMARK 3 S31: -0.0794 S32: -0.0462 S33: -0.0118 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 233 B 247 REMARK 3 ORIGIN FOR THE GROUP (A): -16.6190 2.0340 -8.9920 REMARK 3 T TENSOR REMARK 3 T11: 0.1681 T22: 0.2697 REMARK 3 T33: 0.3076 T12: -0.0052 REMARK 3 T13: 0.0662 T23: 0.1087 REMARK 3 L TENSOR REMARK 3 L11: 0.0709 L22: 6.5008 REMARK 3 L33: 8.5202 L12: -0.1825 REMARK 3 L13: 0.7210 L23: -0.2025 REMARK 3 S TENSOR REMARK 3 S11: -0.0020 S12: -0.0250 S13: -0.0425 REMARK 3 S21: 0.3481 S22: -0.0293 S23: 0.4480 REMARK 3 S31: 0.4702 S32: -0.2092 S33: 0.0314 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 4H6S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000075090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 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 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 : 13133 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : 0.10700 REMARK 200 FOR THE DATA SET : 10.5000 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) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.44400 REMARK 200 R SYM FOR SHELL (I) : 0.44400 REMARK 200 FOR SHELL : 2.500 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 1SHH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NH4CL AND 20% PEG 3350, PH 6.3, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 31.95200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.41400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.95200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.41400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 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 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 ASP A 1A 45.17 -94.95 REMARK 500 PHE A 7 -85.84 -122.83 REMARK 500 TYR B 60A 88.98 -152.53 REMARK 500 ARG B 75 119.51 -167.78 REMARK 500 ASN B 78 8.73 59.54 REMARK 500 ILE B 79 -61.12 -120.43 REMARK 500 GLU B 97A -84.40 -118.36 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 ASN B 143 -147.66 REMARK 500 REMARK 500 REMARK: NULL 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 B 301 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 221A O REMARK 620 2 LYS B 224 O 87.0 REMARK 620 3 HOH B 401 O 77.6 89.2 REMARK 620 4 HOH B 405 O 147.2 71.7 77.4 REMARK 620 5 HOH B 457 O 96.4 73.3 161.9 100.9 REMARK 620 6 HOH B 473 O 104.1 157.8 74.9 89.5 123.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 301 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: 4H6T RELATED DB: PDB DBREF 4H6S A 1C 15 UNP P00734 THRB_HUMAN 333 363 DBREF 4H6S B 16 247 UNP P00734 THRB_HUMAN 364 622 SEQADV 4H6S ALA A 14E UNP P00734 GLU 354 ENGINEERED MUTATION SEQADV 4H6S ALA A 14L UNP P00734 ASP 361 ENGINEERED MUTATION SEQADV 4H6S ALA B 18 UNP P00734 GLU 366 ENGINEERED MUTATION SEQADV 4H6S ALA B 195 UNP P00734 SER 568 ENGINEERED MUTATION SEQRES 1 A 31 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 2 A 31 SER LEU GLU ASP LYS THR GLU ARG ALA LEU LEU GLU SER SEQRES 3 A 31 TYR ILE ALA GLY ARG SEQRES 1 B 259 ILE VAL ALA 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 ALA 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 HET NA B 301 1 HETNAM NA SODIUM ION FORMUL 3 NA NA 1+ FORMUL 4 HOH *103(H2 O) HELIX 1 1 PHE A 7 SER A 11 5 5 HELIX 2 2 GLU A 14C ILE A 14K 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 ASP B 125 LEU B 130 1 9 HELIX 6 6 GLU B 164 SER B 171 1 8 HELIX 7 7 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 TRP B 215 -1 O TYR B 208 N MET B 201 SHEET 6 A 7 GLY B 226 HIS B 230 -1 O PHE B 227 N TRP B 215 SHEET 7 A 7 MET B 180 ALA B 183 -1 N PHE B 181 O TYR B 228 SHEET 1 B 7 LYS B 81 SER B 83 0 SHEET 2 B 7 LEU B 64 ILE B 68 -1 N VAL B 66 O SER B 83 SHEET 3 B 7 GLN B 30 ARG B 35 -1 N PHE B 34 O LEU B 65 SHEET 4 B 7 GLU B 39 LEU B 46 -1 O LEU B 41 N LEU B 33 SHEET 5 B 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 6 B 7 ALA B 104 LEU B 108 -1 O MET B 106 N VAL B 52 SHEET 7 B 7 LEU B 85 ILE B 90 -1 N TYR B 89 O LEU B 105 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 2.05 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.06 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.03 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.08 LINK O ARG B 221A NA NA B 301 1555 1555 2.47 LINK O LYS B 224 NA NA B 301 1555 1555 2.41 LINK NA NA B 301 O HOH B 401 1555 1555 2.55 LINK NA NA B 301 O HOH B 405 1555 1555 2.44 LINK NA NA B 301 O HOH B 457 1555 1555 2.38 LINK NA NA B 301 O HOH B 473 1555 1555 2.37 CISPEP 1 SER B 36A PRO B 37 0 -11.04 SITE 1 AC1 6 ARG B 221A LYS B 224 HOH B 401 HOH B 405 SITE 2 AC1 6 HOH B 457 HOH B 473 CRYST1 63.904 70.828 56.103 90.00 90.00 90.00 P 21 21 2 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 0.015648 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014119 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017824 0.00000