HEADER HYDROLASE 12-DEC-13 4NZQ TITLE CRYSTAL STRUCTURE OF CA2+-FREE PROTHROMBIN DELETION MUTANT RESIDUES TITLE 2 146-167 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTHROMBIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.5; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F2; SOURCE 6 EXPRESSION_SYSTEM: CRICETINAE; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10026; SOURCE 8 EXPRESSION_SYSTEM_CELL: BABY HAMSTER KIDNEY (BHK) KEYWDS PROTHROMBIN, KRINGLE, SERINE PROTEASE, COAGULATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.POZZI,Z.CHEN,D.B.SHROPSHIRE,L.A.PELC,E.DI CERA REVDAT 6 06-DEC-23 4NZQ 1 REMARK REVDAT 5 20-SEP-23 4NZQ 1 HETSYN REVDAT 4 29-JUL-20 4NZQ 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 23-AUG-17 4NZQ 1 SOURCE REMARK REVDAT 2 25-JUN-14 4NZQ 1 JRNL REVDAT 1 21-MAY-14 4NZQ 0 JRNL AUTH N.POZZI,Z.CHEN,L.A.PELC,D.B.SHROPSHIRE,E.DI CERA JRNL TITL THE LINKER CONNECTING THE TWO KRINGLES PLAYS A KEY ROLE IN JRNL TITL 2 PROTHROMBIN ACTIVATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 111 7630 2014 JRNL REFN ISSN 0027-8424 JRNL PMID 24821807 JRNL DOI 10.1073/PNAS.1403779111 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.CHEN,L.A.PELC,E.DI CERA REMARK 1 TITL CRYSTAL STRUCTURE OF PRETHROMBIN-1 REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 107 19278 2010 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.P.SESHADRI,A.TULINSKY,E.SKRZYPCZAK-JANKUN,C.H.PARK REMARK 1 TITL STRUCTURE OF BOVINE PROTHROMBIN FRAGMENT 1 REFINED AT 2.25 A REMARK 1 TITL 2 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 220 481 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.81 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) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : -0.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 24937 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1330 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) : 2.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1775 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.3520 REMARK 3 BIN FREE R VALUE SET COUNT : 99 REMARK 3 BIN FREE R VALUE : 0.4330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4042 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.39000 REMARK 3 B33 (A**2) : -0.46000 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): 0.447 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.324 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.253 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.706 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.906 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.862 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4200 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5701 ; 1.743 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 506 ; 7.733 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 206 ;39.120 ;23.689 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 688 ;21.131 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;20.307 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 593 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3266 ; 0.007 ; 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): 2524 ; 0.914 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4065 ; 1.724 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1676 ; 2.001 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1636 ; 3.428 ; 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 : NULL 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 4NZQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000083859. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : 26373 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 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) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.47900 REMARK 200 R SYM FOR SHELL (I) : NULL 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: PHASER FROM CCP4 REMARK 200 STARTING MODEL: PDB ENTRIES 3NXP AND 2PF1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL, PH 8.5 AND 30% REMARK 280 PEG300, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 70.62600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.62600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 44.37700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 85.86950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 44.37700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 85.86950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 70.62600 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 44.37700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 85.86950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 70.62600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 44.37700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 85.86950 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 1 REMARK 465 ASN A 2 REMARK 465 THR A 3 REMARK 465 PHE A 4 REMARK 465 LEU A 5 REMARK 465 CGU A 6 REMARK 465 CGU A 7 REMARK 465 VAL A 8 REMARK 465 ARG A 9 REMARK 465 LYS A 10 REMARK 465 GLY A 11 REMARK 465 ASN A 12 REMARK 465 LEU A 13 REMARK 465 CGU A 14 REMARK 465 ARG A 15 REMARK 465 CGU A 16 REMARK 465 CYS A 17 REMARK 465 VAL A 18 REMARK 465 CGU A 19 REMARK 465 CGU A 20 REMARK 465 THR A 21 REMARK 465 CYS A 22 REMARK 465 SER A 23 REMARK 465 TYR A 24 REMARK 465 CGU A 25 REMARK 465 CGU A 26 REMARK 465 ALA A 27 REMARK 465 PHE A 28 REMARK 465 CGU A 29 REMARK 465 ALA A 30 REMARK 465 LEU A 31 REMARK 465 CGU A 32 REMARK 465 SER A 33 REMARK 465 ASP A 258 REMARK 465 GLY A 259 REMARK 465 LEU A 260 REMARK 465 ASP A 261 REMARK 465 GLU A 262 REMARK 465 ASP A 263 REMARK 465 SER A 264 REMARK 465 ASP A 265 REMARK 465 ARG A 266 REMARK 465 ALA A 267 REMARK 465 ILE A 268 REMARK 465 GLU A 269 REMARK 465 GLY A 270 REMARK 465 ARG A 271 REMARK 465 THR A 272 REMARK 465 ALA A 273 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 ARG A 382 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 382 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 CYS A 493 CB - CA - C ANGL. DEV. = 7.6 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 ARG A 51 -68.66 -130.79 REMARK 500 LEU A 69 37.51 -70.28 REMARK 500 THR A 71 0.06 -61.59 REMARK 500 ALA A 107 136.88 -39.11 REMARK 500 GLU A 111 -123.03 31.16 REMARK 500 THR A 121 8.05 -69.21 REMARK 500 TRP A 125 -159.38 -130.13 REMARK 500 THR A 129 1.20 -65.17 REMARK 500 CYS A 170 118.90 70.74 REMARK 500 LYS A 200 -69.73 -120.23 REMARK 500 LEU A 202 -20.61 -143.20 REMARK 500 GLU A 216 -115.80 40.09 REMARK 500 GLU A 254 51.89 -101.30 REMARK 500 THR A 256 -27.01 -164.62 REMARK 500 SER A 275 -91.58 -66.59 REMARK 500 PHE A 280 -50.63 -120.68 REMARK 500 PRO A 283 9.46 -60.01 REMARK 500 PHE A 299 -78.06 -125.35 REMARK 500 SER A 303 59.91 24.52 REMARK 500 ILE A 321 87.71 105.81 REMARK 500 ARG A 356 -25.64 -146.46 REMARK 500 ASN A 373 81.73 -171.82 REMARK 500 ILE A 395 -56.52 -121.04 REMARK 500 ASN A 415 52.23 -165.16 REMARK 500 ASN A 471 8.11 51.38 REMARK 500 VAL A 472 -12.93 -37.35 REMARK 500 ILE A 501 98.52 -66.10 REMARK 500 ASP A 503 5.62 -64.85 REMARK 500 PRO A 512 101.32 -41.77 REMARK 500 ARG A 517 -172.71 -66.64 REMARK 500 CYS A 521 66.17 -67.33 REMARK 500 PHE A 577 -81.80 -145.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NXP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PRETHROMBIN-1 REMARK 900 RELATED ID: 2PF1 RELATED DB: PDB REMARK 900 STRUCTURE OF BOVINE PROTHROMBIN FRAGMENT 1 REFINED AT 2.25 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 4O03 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE COORDS CONTAIN DELETION OF RESIDUES 146-167, CORRESPONDING TO REMARK 999 UNP RESIDUES 189-210 DBREF 4NZQ A 1 145 UNP P00734 THRB_HUMAN 44 188 DBREF 4NZQ A 168 579 UNP P00734 THRB_HUMAN 211 622 SEQRES 1 A 557 ALA ASN THR PHE LEU CGU CGU VAL ARG LYS GLY ASN LEU SEQRES 2 A 557 CGU ARG CGU CYS VAL CGU CGU THR CYS SER TYR CGU CGU SEQRES 3 A 557 ALA PHE CGU ALA LEU CGU SER SER THR ALA THR ASP VAL SEQRES 4 A 557 PHE TRP ALA LYS TYR THR ALA CYS GLU THR ALA ARG THR SEQRES 5 A 557 PRO ARG ASP LYS LEU ALA ALA CYS LEU GLU GLY ASN CYS SEQRES 6 A 557 ALA GLU GLY LEU GLY THR ASN TYR ARG GLY HIS VAL ASN SEQRES 7 A 557 ILE THR ARG SER GLY ILE GLU CYS GLN LEU TRP ARG SER SEQRES 8 A 557 ARG TYR PRO HIS LYS PRO GLU ILE ASN SER THR THR HIS SEQRES 9 A 557 PRO GLY ALA ASP LEU GLN GLU ASN PHE CYS ARG ASN PRO SEQRES 10 A 557 ASP SER SER THR THR GLY PRO TRP CYS TYR THR THR ASP SEQRES 11 A 557 PRO THR VAL ARG ARG GLN GLU CYS SER ILE PRO VAL CYS SEQRES 12 A 557 GLY GLN GLU GLN CYS VAL PRO ASP ARG GLY GLN GLN TYR SEQRES 13 A 557 GLN GLY ARG LEU ALA VAL THR THR HIS GLY LEU PRO CYS SEQRES 14 A 557 LEU ALA TRP ALA SER ALA GLN ALA LYS ALA LEU SER LYS SEQRES 15 A 557 HIS GLN ASP PHE ASN SER ALA VAL GLN LEU VAL GLU ASN SEQRES 16 A 557 PHE CYS ARG ASN PRO ASP GLY ASP GLU GLU GLY VAL TRP SEQRES 17 A 557 CYS TYR VAL ALA GLY LYS PRO GLY ASP PHE GLY TYR CYS SEQRES 18 A 557 ASP LEU ASN TYR CYS GLU GLU ALA VAL GLU GLU GLU THR SEQRES 19 A 557 GLY ASP GLY LEU ASP GLU ASP SER ASP ARG ALA ILE GLU SEQRES 20 A 557 GLY ARG THR ALA THR SER GLU TYR GLN THR PHE PHE ASN SEQRES 21 A 557 PRO ARG THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU SEQRES 22 A 557 ARG PRO LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR SEQRES 23 A 557 GLU ARG GLU LEU LEU GLU SER TYR ILE ASP GLY ARG ILE SEQRES 24 A 557 VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO TRP SEQRES 25 A 557 GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU LEU SEQRES 26 A 557 CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU THR SEQRES 27 A 557 ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS ASN SEQRES 28 A 557 PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS HIS SEQRES 29 A 557 SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SER SEQRES 30 A 557 MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN TRP SEQRES 31 A 557 ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS LEU SEQRES 32 A 557 LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO VAL SEQRES 33 A 557 CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU GLN SEQRES 34 A 557 ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN LEU SEQRES 35 A 557 LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN PRO SEQRES 36 A 557 SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU ARG SEQRES 37 A 557 PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR ASP SEQRES 38 A 557 ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY LYS SEQRES 39 A 557 ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO PHE SEQRES 40 A 557 VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN MET SEQRES 41 A 557 GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP GLY SEQRES 42 A 557 LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS LYS SEQRES 43 A 557 TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU MODRES 4NZQ ASN A 100 ASN GLYCOSYLATION SITE MODRES 4NZQ ASN A 78 ASN GLYCOSYLATION SITE MODRES 4NZQ ASN A 373 ASN GLYCOSYLATION SITE HET NAG A 701 14 HET NAG A 702 14 HET NAG A 703 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 FORMUL 2 NAG 3(C8 H15 N O6) HELIX 1 1 SER A 34 CYS A 47 1 14 HELIX 2 2 PRO A 53 GLU A 62 1 10 HELIX 3 3 PRO A 172 GLN A 176 5 5 HELIX 4 4 SER A 196 ALA A 201 1 6 HELIX 5 5 ALA A 251 GLU A 255 5 5 HELIX 6 6 GLY A 289 CYS A 293 5 5 HELIX 7 7 THR A 308 GLU A 314 1 7 HELIX 8 8 ALA A 361 CYS A 364 5 4 HELIX 9 9 PRO A 368 ASP A 371 5 4 HELIX 10 10 THR A 375 ASN A 377 5 3 HELIX 11 11 ASP A 442 ALA A 452 1 11 HELIX 12 12 GLY A 462 THR A 469 1 8 HELIX 13 13 GLU A 489 THR A 497 1 9 HELIX 14 14 GLY A 548 ASP A 552 5 5 HELIX 15 15 LEU A 566 GLN A 576 1 11 SHEET 1 A 2 TRP A 125 TYR A 127 0 SHEET 2 A 2 ARG A 135 GLU A 137 -1 O GLN A 136 N CYS A 126 SHEET 1 B 2 TRP A 230 TYR A 232 0 SHEET 2 B 2 PHE A 240 TYR A 242 -1 O GLY A 241 N CYS A 231 SHEET 1 C 3 SER A 325 ASP A 326 0 SHEET 2 C 3 GLN A 481 PRO A 486 -1 O VAL A 482 N SER A 325 SHEET 3 C 3 LYS A 455 GLY A 460 -1 N GLY A 460 O GLN A 481 SHEET 1 D 7 LYS A 397 SER A 399 0 SHEET 2 D 7 LEU A 379 ILE A 383 -1 N ILE A 383 O LYS A 397 SHEET 3 D 7 GLN A 335 ARG A 340 -1 N PHE A 339 O LEU A 380 SHEET 4 D 7 GLU A 345 LEU A 352 -1 O GLU A 345 N ARG A 340 SHEET 5 D 7 TRP A 357 THR A 360 -1 O LEU A 359 N SER A 351 SHEET 6 D 7 ALA A 421 LEU A 425 -1 O ALA A 421 N THR A 360 SHEET 7 D 7 LEU A 401 ILE A 406 -1 N TYR A 405 O LEU A 422 SHEET 1 E 2 LEU A 366 TYR A 367 0 SHEET 2 E 2 LYS A 372 ASN A 373 -1 O LYS A 372 N TYR A 367 SHEET 1 F 4 MET A 505 ALA A 508 0 SHEET 2 F 4 GLY A 558 HIS A 562 -1 O GLY A 558 N ALA A 508 SHEET 3 F 4 TRP A 539 VAL A 545 -1 N ILE A 544 O THR A 561 SHEET 4 F 4 PRO A 528 LYS A 532 -1 N MET A 531 O TYR A 540 SSBOND 1 CYS A 47 CYS A 60 1555 1555 2.07 SSBOND 2 CYS A 65 CYS A 143 1555 1555 2.06 SSBOND 3 CYS A 86 CYS A 126 1555 1555 2.01 SSBOND 4 CYS A 114 CYS A 138 1555 1555 2.06 SSBOND 5 CYS A 170 CYS A 248 1555 1555 2.10 SSBOND 6 CYS A 191 CYS A 231 1555 1555 2.03 SSBOND 7 CYS A 219 CYS A 243 1555 1555 2.03 SSBOND 8 CYS A 293 CYS A 439 1555 1555 2.07 SSBOND 9 CYS A 348 CYS A 364 1555 1555 2.03 SSBOND 10 CYS A 493 CYS A 507 1555 1555 2.09 SSBOND 11 CYS A 521 CYS A 551 1555 1555 2.11 LINK ND2 ASN A 78 C1 NAG A 702 1555 1555 1.44 LINK ND2 ASN A 100 C1 NAG A 703 1555 1555 1.42 LINK ND2 ASN A 373 C1 NAG A 701 1555 1555 1.46 CISPEP 1 TYR A 93 PRO A 94 0 -0.91 CISPEP 2 SER A 342 PRO A 343 0 -2.09 CRYST1 88.754 171.739 141.252 90.00 90.00 90.00 C 2 2 21 8 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 0.011267 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007080 0.00000