HEADER HYDROLASE 16-NOV-10 3PMB TITLE 2.9 ANGSTROM CRYSTAL STRUCTURE OF BOVINE THROMBIN IN TETRAGONAL TITLE 2 SPACEGROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: BOVINE THROMBIN LIGHT CHAIN RESIDUES 336-364; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 8 CHAIN: B, D; COMPND 9 EC: 3.4.21.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 7 ORGANISM_COMMON: BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW; SOURCE 8 ORGANISM_TAXID: 9913 KEYWDS PROTEASE, THROMBOSIS, FIBRINOLOSYS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.T.WRIGHT,J.N.SCARSDALE,B.J.DESAI REVDAT 2 24-AUG-11 3PMB 1 JRNL REVDAT 1 20-JUL-11 3PMB 0 JRNL AUTH B.J.DESAI,R.S.BOOTHELLO,A.Y.MEHTA,J.N.SCARSDALE,H.T.WRIGHT, JRNL AUTH 2 U.R.DESAI JRNL TITL INTERACTION OF THROMBIN WITH SUCROSE OCTASULFATE. JRNL REF BIOCHEMISTRY V. 50 6973 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21736375 JRNL DOI 10.1021/BI2004526 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.6 REMARK 3 NUMBER OF REFLECTIONS : 14714 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) : 0.245 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 746 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1113 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4255 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.07000 REMARK 3 B22 (A**2) : -1.07000 REMARK 3 B33 (A**2) : 2.15000 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): 0.523 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.349 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 40.628 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.878 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.805 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4379 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5954 ; 1.230 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 542 ; 4.831 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 198 ;34.331 ;23.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 697 ;19.733 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;19.952 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 640 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3361 ; 0.004 ; 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): 2722 ; 0.246 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4344 ; 0.459 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1657 ; 0.504 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1610 ; 0.891 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : B D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 0 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 B (A): 816 ; 0.08 ; 0.05 REMARK 3 LOOSE POSITIONAL 1 B (A): 745 ; 0.20 ; 5.00 REMARK 3 TIGHT THERMAL 1 B (A**2): 816 ; 0.08 ; 0.50 REMARK 3 LOOSE THERMAL 1 B (A**2): 745 ; 0.08 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 15 REMARK 3 RESIDUE RANGE : B 16 B 243 REMARK 3 ORIGIN FOR THE GROUP (A): -4.2715 -21.5149 31.8908 REMARK 3 T TENSOR REMARK 3 T11: 0.0775 T22: 0.1399 REMARK 3 T33: 0.1110 T12: 0.0229 REMARK 3 T13: -0.0335 T23: -0.1109 REMARK 3 L TENSOR REMARK 3 L11: 2.2771 L22: 3.1490 REMARK 3 L33: 1.3772 L12: 0.6205 REMARK 3 L13: -0.5027 L23: 0.6255 REMARK 3 S TENSOR REMARK 3 S11: -0.0571 S12: 0.2796 S13: -0.2299 REMARK 3 S21: 0.0707 S22: 0.0100 S23: -0.1764 REMARK 3 S31: 0.1146 S32: 0.0115 S33: 0.0470 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 15 REMARK 3 RESIDUE RANGE : D 16 D 243 REMARK 3 ORIGIN FOR THE GROUP (A): 1.9984 -66.8338 31.3999 REMARK 3 T TENSOR REMARK 3 T11: 0.0212 T22: 0.1343 REMARK 3 T33: 0.0591 T12: -0.0029 REMARK 3 T13: -0.0057 T23: 0.0811 REMARK 3 L TENSOR REMARK 3 L11: 2.2758 L22: 2.0296 REMARK 3 L33: 1.7771 L12: 0.4965 REMARK 3 L13: 0.2356 L23: -0.4809 REMARK 3 S TENSOR REMARK 3 S11: -0.0603 S12: 0.3369 S13: 0.1504 REMARK 3 S21: -0.0992 S22: -0.0392 S23: 0.0420 REMARK 3 S31: -0.0343 S32: 0.0759 S33: 0.0995 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 3PMB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-10. REMARK 100 THE RCSB ID CODE IS RCSB062548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 104 REMARK 200 PH : 6.2 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : RIGAKU VARIMAX CONFOCAL OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16696 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 39.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 85.9 REMARK 200 DATA REDUNDANCY : 4.190 REMARK 200 R MERGE (I) : 0.16700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.62 REMARK 200 R MERGE FOR SHELL (I) : 0.33500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX.REFINE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3 MICROLITERS BOVINE THROMBIN, 7 MG/ML REMARK 280 IN 0.01M TRIS-HCL, PH 8.0, 0.05M NACL, 0.1M SODIUM CITRATE, 20% REMARK 280 W/V PEG3350, 15% V/V 2-PROPANOL, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 97.25700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 43.82200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.82200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 145.88550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.82200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 43.82200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 48.62850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.82200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.82200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 145.88550 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 43.82200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.82200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.62850 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 97.25700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 2540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 HIS B 70A REMARK 465 SER B 70B REMARK 465 ARG B 70C REMARK 465 THR B 70D REMARK 465 ARG B 70E REMARK 465 TYR B 70F REMARK 465 GLU B 70G REMARK 465 ARG B 70H REMARK 465 LYS B 70I REMARK 465 THR B 146A REMARK 465 TRP B 146B REMARK 465 THR B 146C REMARK 465 THR B 146D REMARK 465 SER B 146E REMARK 465 VAL B 146F REMARK 465 ALA B 146G REMARK 465 GLU B 146H REMARK 465 VAL B 146I REMARK 465 ARG B 244 REMARK 465 LEU B 245 REMARK 465 GLY B 246 REMARK 465 SER B 247 REMARK 465 ARG D 74A REMARK 465 TYR D 74B REMARK 465 GLU D 74C REMARK 465 ARG D 244 REMARK 465 LEU D 245 REMARK 465 GLY D 246 REMARK 465 SER D 247 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG B 50 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 VAL B 79 CG1 CG2 REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 MET B 84 CG SD CE REMARK 470 LYS B 87 CG CD CE NZ REMARK 470 GLU B 97A CG CD OE1 OE2 REMARK 470 LYS B 107 CG CD CE NZ REMARK 470 LYS B 109 CG CD CE NZ REMARK 470 ILE B 112 CG1 CG2 CD1 REMARK 470 GLN B 127 CG CD OE1 NE2 REMARK 470 LYS B 129B CG CD CE NZ REMARK 470 ARG B 145 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 186D CG CD CE NZ REMARK 470 GLU B 192 CG CD OE1 OE2 REMARK 470 TYR B 204A CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 206 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 236 CG CD CE NZ REMARK 470 LYS B 240 CG CD CE NZ REMARK 470 GLN C 11 CG CD OE1 NE2 REMARK 470 LYS C 14D CG CD CE NZ REMARK 470 ILE C 14K CG1 CG2 CD1 REMARK 470 ARG D 73 CG CD NE CZ NH1 NH2 REMARK 470 THR D 74 OG1 CG2 REMARK 470 ARG D 77A CG CD NE CZ NH1 NH2 REMARK 470 LYS D 78 CG CD CE NZ REMARK 470 LYS D 81 CG CD CE NZ REMARK 470 MET D 84 CG SD CE REMARK 470 LYS D 87 CG CD CE NZ REMARK 470 LYS D 109 CG CD CE NZ REMARK 470 ILE D 112 CG1 CG2 CD1 REMARK 470 LYS D 126 CG CD CE NZ REMARK 470 GLN D 127 CG CD OE1 NE2 REMARK 470 LYS D 129B CG CD CE NZ REMARK 470 ARG D 145 CG CD NE CZ NH1 NH2 REMARK 470 THR D 149 OG1 CG2 REMARK 470 THR D 149A OG1 CG2 REMARK 470 VAL D 149C CG1 CG2 REMARK 470 SER D 153 OG REMARK 470 GLU D 192 CG CD OE1 OE2 REMARK 470 TYR D 204A CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS D 236 CG CD CE NZ REMARK 470 LYS D 240 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ALA B 129A N ALA B 129A CA -0.124 REMARK 500 TRP B 141 CG TRP B 141 CD1 -0.123 REMARK 500 TRP B 141 CD2 TRP B 141 CE3 -0.090 REMARK 500 TRP D 141 CG TRP D 141 CD1 -0.125 REMARK 500 TRP D 141 CD2 TRP D 141 CE3 -0.091 REMARK 500 REMARK 500 REMARK: NULL 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 ALA B 129 CA - C - N ANGL. DEV. = -15.1 DEGREES REMARK 500 ASP D 86 CB - CG - OD2 ANGL. DEV. = 5.5 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 PHE A 7 -74.34 -133.46 REMARK 500 GLN A 11 18.71 57.66 REMARK 500 SER B 36A 113.72 -160.98 REMARK 500 ASP B 60E 30.48 71.33 REMARK 500 GLU B 97A -64.85 -103.37 REMARK 500 ALA B 129 -74.42 -72.99 REMARK 500 ARG B 187 -159.32 -123.26 REMARK 500 PHE C 7 -82.65 -139.17 REMARK 500 TYR D 60A 86.32 -159.69 REMARK 500 LYS D 78 -33.50 -144.17 REMARK 500 GLU D 97A -65.82 -106.48 REMARK 500 THR D 149A -24.04 -141.02 REMARK 500 SER D 214 -64.93 -108.70 REMARK 500 ILE D 242 -111.88 -111.88 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 2 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 224 O REMARK 620 2 ARG B 221A O 72.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA D 1 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG D 221A O REMARK 620 2 HOH D 10 O 68.6 REMARK 620 3 HOH D 261 O 86.3 152.9 REMARK 620 4 LYS D 224 O 72.8 67.1 116.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA D 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PMA RELATED DB: PDB DBREF 3PMB A 1C 14L UNP P00735 THRB_BOVIN 336 364 DBREF 3PMB B 16 247 UNP P00735 THRB_BOVIN 367 625 DBREF 3PMB C 1C 14L UNP P00735 THRB_BOVIN 336 364 DBREF 3PMB D 16 247 UNP P00735 THRB_BOVIN 367 625 SEQRES 1 A 29 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 2 A 29 GLN VAL GLN ASP GLN THR GLU LYS GLU LEU PHE GLU SER SEQRES 3 A 29 TYR ILE GLU SEQRES 1 B 259 ILE VAL GLU GLY GLN ASP ALA GLU VAL GLY LEU 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 VAL ASP ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 259 HIS SER ARG THR ARG TYR GLU ARG LYS VAL GLU LYS ILE SEQRES 7 B 259 SER MET LEU ASP LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 B 259 TRP LYS GLU ASN LEU ASP ARG ASP ILE ALA LEU LEU LYS SEQRES 9 B 259 LEU LYS ARG PRO ILE GLU LEU SER ASP TYR ILE HIS PRO SEQRES 10 B 259 VAL CYS LEU PRO ASP LYS GLN THR ALA ALA LYS LEU LEU SEQRES 11 B 259 HIS ALA GLY PHE LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 259 ARG ARG GLU THR TRP THR THR SER VAL ALA GLU VAL GLN SEQRES 13 B 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO LEU VAL GLU SEQRES 14 B 259 ARG PRO VAL CYS LYS ALA SER THR ARG ILE ARG ILE THR SEQRES 15 B 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO GLY 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 TYR 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 ARG LEU GLY SER SEQRES 1 C 29 GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE GLU LYS LYS SEQRES 2 C 29 GLN VAL GLN ASP GLN THR GLU LYS GLU LEU PHE GLU SER SEQRES 3 C 29 TYR ILE GLU SEQRES 1 D 259 ILE VAL GLU GLY GLN ASP ALA GLU VAL GLY LEU SER PRO SEQRES 2 D 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 D 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 D 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 D 259 ASN PHE THR VAL ASP ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 D 259 HIS SER ARG THR ARG TYR GLU ARG LYS VAL GLU LYS ILE SEQRES 7 D 259 SER MET LEU ASP LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 D 259 TRP LYS GLU ASN LEU ASP ARG ASP ILE ALA LEU LEU LYS SEQRES 9 D 259 LEU LYS ARG PRO ILE GLU LEU SER ASP TYR ILE HIS PRO SEQRES 10 D 259 VAL CYS LEU PRO ASP LYS GLN THR ALA ALA LYS LEU LEU SEQRES 11 D 259 HIS ALA GLY PHE LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 D 259 ARG ARG GLU THR TRP THR THR SER VAL ALA GLU VAL GLN SEQRES 13 D 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO LEU VAL GLU SEQRES 14 D 259 ARG PRO VAL CYS LYS ALA SER THR ARG ILE ARG ILE THR SEQRES 15 D 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO GLY GLU GLY SEQRES 16 D 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 D 259 PHE VAL MET LYS SER PRO TYR ASN ASN ARG TRP TYR GLN SEQRES 18 D 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 D 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 D 259 LYS TRP ILE GLN LYS VAL ILE ASP ARG LEU GLY SER HET NA B 2 1 HET NA D 1 1 HETNAM NA SODIUM ION FORMUL 5 NA 2(NA 1+) FORMUL 7 HOH *74(H2 O) HELIX 1 1 THR A 14B ILE A 14K 1 10 HELIX 2 2 ALA B 55 CYS B 58 5 4 HELIX 3 3 PRO B 60B ASP B 60E 5 4 HELIX 4 4 ASP B 125 LEU B 130 1 9 HELIX 5 5 GLU B 164 SER B 171 1 8 HELIX 6 6 LEU B 234 ASP B 243 1 10 HELIX 7 7 PHE C 7 GLN C 11 5 5 HELIX 8 8 THR C 14B ILE C 14K 1 10 HELIX 9 9 ALA D 55 CYS D 58 5 4 HELIX 10 10 PRO D 60B ASP D 60E 5 4 HELIX 11 11 ASP D 125 LEU D 130 1 9 HELIX 12 12 SER D 149B VAL D 150 5 5 HELIX 13 13 GLU D 164 SER D 171 1 8 HELIX 14 14 LEU D 234 VAL D 241 1 8 SHEET 1 A 7 GLN B 20 ASP B 21 0 SHEET 2 A 7 GLN B 156 PRO B 161 -1 O VAL B 157 N GLN 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 ILE B 68 O LYS B 81 SHEET 3 B 7 GLN B 30 ARG B 35 -1 N PHE B 34 O LEU B 65 SHEET 4 B 7 LEU B 40 LEU B 46 -1 O CYS B 42 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 LEU B 106 N VAL B 52 SHEET 7 B 7 LEU B 85 ILE B 90 -1 N ASP B 86 O LYS B 107 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 SHEET 1 D 7 GLN D 20 ASP D 21 0 SHEET 2 D 7 GLN D 156 PRO D 161 -1 O VAL D 157 N GLN D 20 SHEET 3 D 7 LYS D 135 GLY D 140 -1 N VAL D 138 O VAL D 158 SHEET 4 D 7 PRO D 198 LYS D 202 -1 O VAL D 200 N ARG D 137 SHEET 5 D 7 TRP D 207 TRP D 215 -1 O TYR D 208 N MET D 201 SHEET 6 D 7 GLY D 226 HIS D 230 -1 O PHE D 227 N TRP D 215 SHEET 7 D 7 MET D 180 ALA D 183 -1 N PHE D 181 O TYR D 228 SHEET 1 E 6 LEU D 64 ILE D 68 0 SHEET 2 E 6 GLN D 30 ARG D 35 -1 N MET D 32 O ARG D 67 SHEET 3 E 6 LEU D 40 LEU D 46 -1 O CYS D 42 N LEU D 33 SHEET 4 E 6 TRP D 51 THR D 54 -1 O LEU D 53 N SER D 45 SHEET 5 E 6 ALA D 104 LEU D 108 -1 O LEU D 106 N VAL D 52 SHEET 6 E 6 LEU D 85 ILE D 90 -1 N ASP D 86 O LYS D 107 SHEET 1 F 2 LEU D 60 TYR D 60A 0 SHEET 2 F 2 LYS D 60F ASN D 60G-1 O LYS D 60F N TYR D 60A SSBOND 1 CYS A 1 CYS B 122 1555 1555 2.05 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.03 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.04 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.04 SSBOND 5 CYS C 1 CYS D 122 1555 1555 2.04 SSBOND 6 CYS D 42 CYS D 58 1555 1555 2.03 SSBOND 7 CYS D 168 CYS D 182 1555 1555 2.04 SSBOND 8 CYS D 191 CYS D 220 1555 1555 2.04 LINK O LYS B 224 NA NA B 2 1555 1555 2.64 LINK O ARG D 221A NA NA D 1 1555 1555 2.67 LINK NA NA D 1 O HOH D 10 1555 1555 2.68 LINK O ARG B 221A NA NA B 2 1555 1555 2.92 LINK NA NA D 1 O HOH D 261 1555 1555 2.95 LINK O LYS D 224 NA NA D 1 1555 1555 2.97 CISPEP 1 SER B 36A PRO B 37 0 -4.76 CISPEP 2 SER D 36A PRO D 37 0 -7.27 SITE 1 AC1 4 HOH D 10 ARG D 221A LYS D 224 HOH D 261 SITE 1 AC2 2 ARG B 221A LYS B 224 CRYST1 87.644 87.644 194.514 90.00 90.00 90.00 P 43 21 2 16 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 0.011410 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011410 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005141 0.00000