HEADER COAGULATION FACTOR 08-SEP-95 2HFT TITLE THE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN TISSUE TITLE 2 FACTOR AT 1.7 ANGSTROMS RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN TISSUE FACTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: 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: 562 KEYWDS COAGULATION FACTOR EXPDTA X-RAY DIFFRACTION AUTHOR Y.A.MULLER,A.M.DE VOS REVDAT 3 06-NOV-24 2HFT 1 REMARK SEQADV REVDAT 2 24-FEB-09 2HFT 1 VERSN REVDAT 1 29-JAN-96 2HFT 0 SPRSDE 29-JAN-96 2HFT 1HFT JRNL AUTH Y.A.MULLER,M.H.ULTSCH,A.M.DE VOS JRNL TITL THE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN JRNL TITL 2 TISSUE FACTOR REFINED TO 1.7 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 256 144 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8609606 JRNL DOI 10.1006/JMBI.1996.0073 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.F.KELLEY,K.E.COSTAS,E.M.O'CONNELL,R.A.LAZARUS REMARK 1 TITL ANALYSIS OF THE FACTOR VIIA BINDING SITE ON HUMAN TISSUE REMARK 1 TITL 2 FACTOR: EFFECTS OF TISSUE FACTOR MUTATIONS ON THE KINETICS REMARK 1 TITL 3 AND THERMODYNAMICS OF BINDING REMARK 1 REF BIOCHEMISTRY V. 34 10383 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH Y.A.MULLER,M.H.ULTSCH,R.F.KELLEY,A.M.DE VOS REMARK 1 TITL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN TISSUE REMARK 1 TITL 2 FACTOR: LOCATION OF THE FACTOR VIIA BINDING SITE REMARK 1 REF BIOCHEMISTRY V. 33 10864 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 1.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 24199 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.500 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1645 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 235 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.012 ; NULL REMARK 3 ANGLE DISTANCE (A) : 1.840 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HFT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178187. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.908 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI FILM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24199 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 6.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 115.40000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.60000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.60000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.70000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.60000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.60000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 173.10000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.60000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.60000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 57.70000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.60000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.60000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 173.10000 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 115.40000 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 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 90.40000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 90.40000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 115.40000 REMARK 400 REMARK 400 COMPOUND REMARK 400 THE FACTOR VII BINDING SITE WAS IDENTIFIED BY REMARK 400 ALA-SCANNING MUTAGENESIS (KELLEY ET AL., 1995; SEE REMARK 400 REFERENCE 1 ABOVE). THIS SITE IS LISTED BELOW AND THE REMARK 400 SITE IDENTIFIER IS VII. 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 GLY A 87 REMARK 465 SER A 88 REMARK 465 ALA A 89 REMARK 465 GLY A 90 REMARK 465 SER A 160A REMARK 465 SER A 160B REMARK 465 GLN A 160C REMARK 465 GLU A 160D REMARK 465 LYS A 160E REMARK 465 GLY A 160F REMARK 465 GLU A 160G REMARK 465 PHE A 160H REMARK 465 ARG A 160I 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 THR A 3 166.51 63.59 REMARK 500 PHE A 19 -8.03 74.44 REMARK 500 TYR A 51 63.63 32.93 REMARK 500 ASN A 137 -125.15 63.83 REMARK 500 ASN A 138 46.08 -109.98 REMARK 500 THR A 172 -161.26 -119.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: VII REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: FACTOR VII BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 850 DBREF 2HFT A 1 211 UNP P13726 TF_HUMAN 33 243 SEQADV 2HFT GLN A 160C UNP P13726 INSERTION SEQADV 2HFT GLU A 160D UNP P13726 INSERTION SEQADV 2HFT LYS A 160E UNP P13726 INSERTION SEQADV 2HFT GLY A 160F UNP P13726 INSERTION SEQADV 2HFT GLU A 160G UNP P13726 INSERTION SEQADV 2HFT PHE A 160H UNP P13726 INSERTION SEQADV 2HFT ARG A 160I UNP P13726 INSERTION SEQRES 1 A 218 SER GLY THR THR ASN THR VAL ALA ALA TYR ASN LEU THR SEQRES 2 A 218 TRP LYS SER THR ASN PHE LYS THR ILE LEU GLU TRP GLU SEQRES 3 A 218 PRO LYS PRO VAL ASN GLN VAL TYR THR VAL GLN ILE SER SEQRES 4 A 218 THR LYS SER GLY ASP TRP LYS SER LYS CYS PHE TYR THR SEQRES 5 A 218 THR ASP THR GLU CYS ASP LEU THR ASP GLU ILE VAL LYS SEQRES 6 A 218 ASP VAL LYS GLN THR TYR LEU ALA ARG VAL PHE SER TYR SEQRES 7 A 218 PRO ALA GLY ASN VAL GLU SER THR GLY SER ALA GLY GLU SEQRES 8 A 218 PRO LEU TYR GLU ASN SER PRO GLU PHE THR PRO TYR LEU SEQRES 9 A 218 GLU THR ASN LEU GLY GLN PRO THR ILE GLN SER PHE GLU SEQRES 10 A 218 GLN VAL GLY THR LYS VAL ASN VAL THR VAL GLU ASP GLU SEQRES 11 A 218 ARG THR LEU VAL ARG ARG ASN ASN THR PHE LEU SER LEU SEQRES 12 A 218 ARG ASP VAL PHE GLY LYS ASP LEU ILE TYR THR LEU TYR SEQRES 13 A 218 TYR TRP LYS SER SER SER GLN GLU LYS GLY GLU PHE ARG SEQRES 14 A 218 SER GLY LYS LYS THR ALA LYS THR ASN THR ASN GLU PHE SEQRES 15 A 218 LEU ILE ASP VAL ASP LYS GLY GLU ASN TYR CYS PHE SER SEQRES 16 A 218 VAL GLN ALA VAL ILE PRO SER ARG THR VAL ASN ARG LYS SEQRES 17 A 218 SER THR ASP SER PRO VAL GLU CYS MET GLY HET SO4 A 850 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *235(H2 O) HELIX 1 1 THR A 60 ASP A 66 1 7 HELIX 2 2 PRO A 102 GLU A 105 1 4 HELIX 3 3 LEU A 143 ASP A 150 1 8 SHEET 1 A 3 THR A 13 THR A 17 0 SHEET 2 A 3 LYS A 20 GLU A 24 -1 N GLU A 24 O THR A 13 SHEET 3 A 3 GLU A 56 ASP A 58 -1 N CYS A 57 O LEU A 23 SHEET 1 B 4 TYR A 94 ASN A 96 0 SHEET 2 B 4 TYR A 71 PRO A 79 -1 N VAL A 75 O GLU A 95 SHEET 3 B 4 GLN A 32 THR A 40 -1 N SER A 39 O LEU A 72 SHEET 4 B 4 LYS A 46 CYS A 49 -1 N CYS A 49 O VAL A 36 SHEET 1 C 3 GLU A 174 ASP A 178 0 SHEET 2 C 3 LYS A 122 VAL A 127 -1 N VAL A 125 O PHE A 175 SHEET 3 C 3 ILE A 113 VAL A 119 -1 N VAL A 119 O LYS A 122 SHEET 1 D 3 CYS A 186 VAL A 192 0 SHEET 2 D 3 ILE A 152 TRP A 158 -1 N TRP A 158 O CYS A 186 SHEET 3 D 3 LYS A 166 THR A 170 -1 N THR A 170 O TYR A 153 SSBOND 1 CYS A 49 CYS A 57 1555 1555 2.04 SSBOND 2 CYS A 186 CYS A 209 1555 1555 2.06 CISPEP 1 GLU A 26 PRO A 27 0 1.72 SITE 1 VII 5 LYS A 20 TRP A 45 ASP A 58 TYR A 94 SITE 2 VII 5 PHE A 140 SITE 1 AC1 8 THR A 3 THR A 4 ASN A 5 THR A 6 SITE 2 AC1 8 PRO A 79 SER A 85 THR A 86 HOH A 463 CRYST1 45.200 45.200 230.800 90.00 90.00 90.00 P 41 21 2 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 0.022124 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004333 0.00000