PDB Short entry for 2WPH HEADER BLOOD CLOTTING 06-AUG-09 2WPH TITLE FACTOR IXA SUPERACTIVE TRIPLE MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAGULATION FACTOR IXA LIGHT CHAIN; COMPND 3 CHAIN: E; COMPND 4 FRAGMENT: EGF2 DOMAIN, RESIDUES 133-191; COMPND 5 SYNONYM: HUMAN COAGULATION FACTOR IXA, CHRISTMAS FACTOR, PLASMA COMPND 6 THROMBOPLASTIN COMPONENT, PTC; COMPND 7 EC: 3.4.21.22; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: D-PHE-PRO-ARG-CHLOROMETHYL KETONE; COMPND 11 CHAIN: L; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: COAGULATION FACTOR IXA HEAVY CHAIN; COMPND 15 CHAIN: S; COMPND 16 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 227-461; COMPND 17 SYNONYM: HUMAN COAGULATION FACTOR IXA, CHRISTMAS FACTOR, PLASMA COMPND 18 THROMBOPLASTIN COMPONENT, PTC; COMPND 19 EC: 3.4.21.22; COMPND 20 ENGINEERED: YES; COMPND 21 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET22D; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-FIXA-3X; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 21 EXPRESSION_SYSTEM_VECTOR: PET22D; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PET-FIXA-3X KEYWDS BLOOD CLOTTING, HYDROLASE, GLYCOPROTEIN, HEMOSTASIS EXPDTA X-RAY DIFFRACTION AUTHOR T.ZOGG,H.BRANDSTETTER REVDAT 6 20-DEC-23 2WPH 1 REMARK LINK REVDAT 5 05-JUL-17 2WPH 1 REMARK REVDAT 4 21-DEC-16 2WPH 1 SOURCE REVDAT 3 23-OCT-13 2WPH 1 KEYWDS REMARK VERSN REVDAT 2 11-MAY-11 2WPH 1 JRNL REMARK SHEET REVDAT 1 22-DEC-09 2WPH 0 JRNL AUTH T.ZOGG,H.BRANDSTETTER JRNL TITL STRUCTURAL BASIS OF THE COFACTOR- AND SUBSTRATE-ASSISTED JRNL TITL 2 ACTIVATION OF HUMAN COAGULATION FACTOR IXA JRNL REF STRUCTURE V. 17 1669 2009 JRNL REFN ISSN 0969-2126 JRNL PMID 20004170 JRNL DOI 10.1016/J.STR.2009.10.011 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.21 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 44244 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 SET) : 0.240 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.900 REMARK 3 FREE R VALUE TEST SET COUNT : 884 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2314 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 524 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : 0.39000 REMARK 3 B33 (A**2) : -0.16000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.840 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 58.07 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : PEG_5P.XPAR REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : PEG_5P.XTOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2WPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1290040673. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44244 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 7.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1RFN REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22 % PEG 3000, 100 MM BIS/TRIS, PH REMARK 280 6.85, PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.14500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.81000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.24500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.81000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.14500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.24500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, L, S 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE BIVALIRUDIN C-TERMINUS FRAGMENT IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 THROMBIN INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: BIVALIRUDIN C-TERMINUS FRAGMENT REMARK 400 CHAIN: L REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLN E 139 REMARK 475 THR E 140 REMARK 475 SER E 141 REMARK 475 LYS E 142 REMARK 475 LEU E 143 REMARK 475 THR E 144 REMARK 475 ARG E 145 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR E 87 N CB OG1 CG2 REMARK 480 LYS E 91 CD CE NZ REMARK 480 LYS E 100 CE NZ REMARK 480 ASP E 104 CG OD1 OD2 REMARK 480 ASN E 105 CB CG OD1 ND2 REMARK 480 LYS E 106 CG CD CE NZ REMARK 480 LYS E 122 CG CD CE NZ REMARK 480 GLU S 20 CG REMARK 480 LYS S 23 CG CD CE NZ REMARK 480 LYS S 62 CD CE NZ REMARK 480 GLU S 74 CD OE1 OE2 REMARK 480 ARG S 87 CZ NH1 NH2 REMARK 480 GLU S 110 OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 C ARG L 3 OG SER S 195 1.40 REMARK 500 OXT ARG L 3 NE2 HIS S 57 1.51 REMARK 500 O HOH S 2025 O HOH S 2028 2.11 REMARK 500 O LEU S 244 O HOH S 2398 2.16 REMARK 500 O HOH S 2067 O HOH S 2068 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 ARG L 3 C ARG L 3 O 0.179 REMARK 500 ARG L 3 C ARG L 3 OXT 0.305 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 ARG L 3 CA - C - O ANGL. DEV. = -13.0 DEGREES REMARK 500 CYS S 182 CA - CB - SG ANGL. DEV. = 8.1 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 GLN E 97 -81.39 -118.33 REMARK 500 SER E 102 -113.41 -106.75 REMARK 500 ALA E 118 -172.21 -67.95 REMARK 500 SER E 138 -36.82 71.14 REMARK 500 GLN E 139 156.26 89.18 REMARK 500 THR E 140 161.70 54.17 REMARK 500 LYS E 142 69.04 -169.53 REMARK 500 GLU S 60 102.10 -42.67 REMARK 500 THR S 61 106.95 -30.67 REMARK 500 HIS S 71 -62.23 -134.23 REMARK 500 SER S 214 -62.18 -121.16 REMARK 500 GLU S 219 -155.99 59.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH E2052 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH E2063 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH E2067 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH E2071 DISTANCE = 7.59 ANGSTROMS REMARK 525 HOH E2081 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH E2085 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH S2019 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH S2134 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH S2141 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH S2192 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH S2194 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH S2221 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH S2223 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH S2224 DISTANCE = 7.38 ANGSTROMS REMARK 525 HOH S2239 DISTANCE = 7.42 ANGSTROMS REMARK 525 HOH S2241 DISTANCE = 6.08 ANGSTROMS 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 CA S1246 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU S 70 OE1 REMARK 620 2 ASN S 72 O 84.5 REMARK 620 3 GLU S 75 O 156.7 84.0 REMARK 620 4 GLU S 77 OE1 78.7 92.8 122.0 REMARK 620 5 GLU S 77 OE2 127.2 89.6 72.8 49.2 REMARK 620 6 GLU S 80 OE2 96.7 174.6 96.7 82.3 85.4 REMARK 620 7 HOH S2088 O 80.7 95.6 80.4 156.9 152.1 89.9 REMARK 620 N 1 2 3 4 5 6 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "SA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "SB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA S 1246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE S 1247 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE S 1248 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EDM RELATED DB: PDB REMARK 900 EPIDERMAL GROWTH FACTOR-LIKE DOMAIN FROM HUMAN FACTOR IX REMARK 900 RELATED ID: 1CFH RELATED DB: PDB REMARK 900 COAGULATION FACTOR IX (THE GLA AND AROMATIC AMINO ACID STACK REMARK 900 DOMAINS FROM RESIDUES 1 - 47) (NMR, 15 STRUCTURES) REMARK 900 RELATED ID: 1MGX RELATED DB: PDB REMARK 900 COAGULATION FACTOR, MG(II), NMR, 7 STRUCTURES (BACKBONE ATOMS ONLY) REMARK 900 RELATED ID: 2WPM RELATED DB: PDB REMARK 900 FACTOR IXA SUPERACTIVE MUTANT, EGR-CMK INHIBITED REMARK 900 RELATED ID: 2WPI RELATED DB: PDB REMARK 900 FACTOR IXA SUPERACTIVE DOUBLE MUTANT REMARK 900 RELATED ID: 2WPL RELATED DB: PDB REMARK 900 FACTOR IXA SUPERACTIVE TRIPLE MUTANT, EDTA-SOAKED REMARK 900 RELATED ID: 1CFI RELATED DB: PDB REMARK 900 NMR STRUCTURE OF CALCIUM ION-BOUND GAMMA- CARBOXY-GLUTAMIC ACID- REMARK 900 RICH DOMAIN OF FACTOR IX REMARK 900 RELATED ID: 2WPJ RELATED DB: PDB REMARK 900 FACTOR IXA SUPERACTIVE TRIPLE MUTANT, NACL-SOAKED REMARK 900 RELATED ID: 1IXA RELATED DB: PDB REMARK 900 EGF-LIKE MODULE OF HUMAN FACTOR IX (NMR, MINIMIZED AVERAGE REMARK 900 STRUCTURE) REMARK 900 RELATED ID: 2WPK RELATED DB: PDB REMARK 900 FACTOR IXA SUPERACTIVE TRIPLE MUTANT, ETHYLENE GLYCOL-SOAKED REMARK 900 RELATED ID: 1RFN RELATED DB: PDB REMARK 900 HUMAN COAGULATION FACTOR IXA IN COMPLEX WITH P-AMINO BENZAMIDINE REMARK 900 RELATED ID: 1NL0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN FACTOR IX GLA DOMAIN IN COMPLEXOF AN REMARK 900 INHIBITORY ANTIBODY, 10C12 DBREF 2WPH E 87 145 UNP P00740 FA9_HUMAN 133 191 DBREF 2WPH L 1 3 PDB 2WPH 2WPH 1 3 DBREF 2WPH S 16 245 UNP P00740 FA9_HUMAN 227 461 SEQADV 2WPH PHE S 94 UNP P00740 TYR 305 ENGINEERED MUTATION SEQADV 2WPH THR S 98B UNP P00740 LYS 311 ENGINEERED MUTATION SEQADV 2WPH THR S 177 UNP P00740 TYR 391 ENGINEERED MUTATION SEQRES 1 E 59 THR CYS ASN ILE LYS ASN GLY ARG CYS GLU GLN PHE CYS SEQRES 2 E 59 LYS ASN SER ALA ASP ASN LYS VAL VAL CYS SER CYS THR SEQRES 3 E 59 GLU GLY TYR ARG LEU ALA GLU ASN GLN LYS SER CYS GLU SEQRES 4 E 59 PRO ALA VAL PRO PHE PRO CYS GLY ARG VAL SER VAL SER SEQRES 5 E 59 GLN THR SER LYS LEU THR ARG SEQRES 1 L 3 DPN PRO ARG SEQRES 1 S 235 VAL VAL GLY GLY GLU ASP ALA LYS PRO GLY GLN PHE PRO SEQRES 2 S 235 TRP GLN VAL VAL LEU ASN GLY LYS VAL ASP ALA PHE CYS SEQRES 3 S 235 GLY GLY SER ILE VAL ASN GLU LYS TRP ILE VAL THR ALA SEQRES 4 S 235 ALA HIS CYS VAL GLU THR GLY VAL LYS ILE THR VAL VAL SEQRES 5 S 235 ALA GLY GLU HIS ASN ILE GLU GLU THR GLU HIS THR GLU SEQRES 6 S 235 GLN LYS ARG ASN VAL ILE ARG ILE ILE PRO HIS HIS ASN SEQRES 7 S 235 PHE ASN ALA ALA ILE ASN THR TYR ASN HIS ASP ILE ALA SEQRES 8 S 235 LEU LEU GLU LEU ASP GLU PRO LEU VAL LEU ASN SER TYR SEQRES 9 S 235 VAL THR PRO ILE CYS ILE ALA ASP LYS GLU TYR THR ASN SEQRES 10 S 235 ILE PHE LEU LYS PHE GLY SER GLY TYR VAL SER GLY TRP SEQRES 11 S 235 GLY ARG VAL PHE HIS LYS GLY ARG SER ALA LEU VAL LEU SEQRES 12 S 235 GLN TYR LEU ARG VAL PRO LEU VAL ASP ARG ALA THR CYS SEQRES 13 S 235 LEU ARG SER THR LYS PHE THR ILE THR ASN ASN MET PHE SEQRES 14 S 235 CYS ALA GLY PHE HIS GLU GLY GLY ARG ASP SER CYS GLN SEQRES 15 S 235 GLY ASP SER GLY GLY PRO HIS VAL THR GLU VAL GLU GLY SEQRES 16 S 235 THR SER PHE LEU THR GLY ILE ILE SER TRP GLY GLU GLU SEQRES 17 S 235 CYS ALA MET LYS GLY LYS TYR GLY ILE TYR THR LYS VAL SEQRES 18 S 235 SER ARG TYR VAL ASN TRP ILE LYS GLU LYS THR LYS LEU SEQRES 19 S 235 THR HET DPN L 1 11 HET CA S1246 1 HET 1PE S1247 16 HET 1PE S1248 16 HETNAM DPN D-PHENYLALANINE HETNAM CA CALCIUM ION HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 2 DPN C9 H11 N O2 FORMUL 4 CA CA 2+ FORMUL 5 1PE 2(C10 H22 O6) FORMUL 7 HOH *524(H2 O) HELIX 1 1 ILE E 90 CYS E 95 5 6 HELIX 2 2 ALA S 55 VAL S 59 5 5 HELIX 3 3 ASP S 125 PHE S 133 1 11 HELIX 4 4 ASP S 164 SER S 171 1 8 HELIX 5 5 TYR S 234 THR S 242 1 9 SHEET 1 EA 2 PHE E 98 ASN E 101 0 SHEET 2 EA 2 VAL E 107 SER E 110 -1 O VAL E 108 N LYS E 100 SHEET 1 EB 2 TYR E 115 LEU E 117 0 SHEET 2 EB 2 CYS E 124 PRO E 126 -1 O GLU E 125 N ARG E 116 SHEET 1 SA 8 GLU S 20 ASP S 21 0 SHEET 2 SA 8 GLN S 156 VAL S 163 -1 O TYR S 157 N GLU S 20 SHEET 3 SA 8 MET S 180 ALA S 183 -1 O CYS S 182 N VAL S 163 SHEET 4 SA 8 GLY S 226 LYS S 230 -1 O GLY S 226 N ALA S 183 SHEET 5 SA 8 THR S 206 TRP S 215 -1 O ILE S 212 N THR S 229 SHEET 6 SA 8 PRO S 198 VAL S 203 -1 O HIS S 199 N THR S 210 SHEET 7 SA 8 SER S 135 GLY S 140 -1 O TYR S 137 N VAL S 200 SHEET 8 SA 8 GLU S 20 ASP S 21 0 SHEET 1 SB 7 GLN S 30 ASN S 34 0 SHEET 2 SB 7 CYS S 42 ASN S 48 -1 O CYS S 42 N LEU S 33 SHEET 3 SB 7 TRP S 51 THR S 54 -1 O TRP S 51 N VAL S 47 SHEET 4 SB 7 ALA S 104 LEU S 108 -1 O ALA S 104 N THR S 54 SHEET 5 SB 7 GLN S 81 PRO S 90 -1 N ILE S 86 O GLU S 107 SHEET 6 SB 7 THR S 64 ALA S 66 -1 O VAL S 65 N ARG S 83 SHEET 7 SB 7 GLN S 30 ASN S 34 -1 O VAL S 32 N VAL S 65A SSBOND 1 CYS E 88 CYS E 99 1555 1555 2.03 SSBOND 2 CYS E 95 CYS E 109 1555 1555 2.02 SSBOND 3 CYS E 111 CYS E 124 1555 1555 2.04 SSBOND 4 CYS E 132 CYS S 122 1555 1555 2.04 SSBOND 5 CYS S 42 CYS S 58 1555 1555 2.07 SSBOND 6 CYS S 168 CYS S 182 1555 1555 2.02 SSBOND 7 CYS S 191 CYS S 220 1555 1555 2.04 LINK C DPN L 1 N PRO L 2 1555 1555 1.34 LINK OE1 GLU S 70 CA CA S1246 1555 1555 2.32 LINK O ASN S 72 CA CA S1246 1555 1555 2.38 LINK O GLU S 75 CA CA S1246 1555 1555 2.31 LINK OE1 GLU S 77 CA CA S1246 1555 1555 2.50 LINK OE2 GLU S 77 CA CA S1246 1555 1555 2.71 LINK OE2 GLU S 80 CA CA S1246 1555 1555 2.29 LINK CA CA S1246 O HOH S2088 1555 1555 2.51 SITE 1 AC1 6 GLU S 70 ASN S 72 GLU S 75 GLU S 77 SITE 2 AC1 6 GLU S 80 HOH S2088 SITE 1 AC2 10 HOH E2040 GLU S 186 ARG S 188A HOH S2327 SITE 2 AC2 10 HOH S2402 HOH S2404 HOH S2405 HOH S2406 SITE 3 AC2 10 HOH S2407 HOH S2408 SITE 1 AC3 12 THR S 76 HIS S 78 PRO S 90 HIS S 92 SITE 2 AC3 12 LYS S 148 HOH S2130 HOH S2138 HOH S2205 SITE 3 AC3 12 HOH S2410 HOH S2411 HOH S2412 HOH S2413 CRYST1 44.290 66.490 97.620 90.00 90.00 90.00 P 21 21 21 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 0.022578 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010244 0.00000