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- PDB-2hft: THE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN TISSUE... -

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Basic information

Entry
Database: PDB / ID: 2hft
TitleTHE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF HUMAN TISSUE FACTOR AT 1.7 ANGSTROMS RESOLUTION
ComponentsHUMAN TISSUE FACTOR
KeywordsCOAGULATION FACTOR
Function / homology
Function and homology information


activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of endothelial cell apoptotic process / positive regulation of TOR signaling ...activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / cytokine receptor activity / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of endothelial cell apoptotic process / positive regulation of TOR signaling / positive regulation of endothelial cell proliferation / positive regulation of interleukin-8 production / phospholipid binding / protein processing / cytokine-mediated signaling pathway / positive regulation of angiogenesis / blood coagulation / : / protease binding / positive regulation of cell migration / external side of plasma membrane / positive regulation of gene expression / cell surface / extracellular space / membrane / plasma membrane
Similarity search - Function
Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold ...Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.69 Å
AuthorsMuller, Y.A. / De Vos, A.M.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The crystal structure of the extracellular domain of human tissue factor refined to 1.7 A resolution.
Authors: Muller, Y.A. / Ultsch, M.H. / de Vos, A.M.
#1: Journal: Biochemistry / Year: 1995
Title: Analysis of the Factor Viia Binding Site on Human Tissue Factor: Effects of Tissue Factor Mutations on the Kinetics and Thermodynamics of Binding
Authors: Kelley, R.F. / Costas, K.E. / O'Connell, E.M. / Lazarus, R.A.
#2: Journal: Biochemistry / Year: 1994
Title: Structure of the Extracellular Domain of Human Tissue Factor: Location of the Factor Viia Binding Site
Authors: Muller, Y.A. / Ultsch, M.H. / Kelley, R.F. / De Vos, A.M.
History
DepositionSep 8, 1995Processing site: BNL
SupersessionJan 29, 1996ID: 1HFT
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN TISSUE FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7932
Polymers24,6971
Non-polymers961
Water4,234235
1
A: HUMAN TISSUE FACTOR
hetero molecules

A: HUMAN TISSUE FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5874
Polymers49,3952
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Unit cell
Length a, b, c (Å)45.200, 45.200, 230.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: CIS PROLINE - PRO 27

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Components

#1: Protein HUMAN TISSUE FACTOR


Mass: 24697.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P13726
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE FACTOR VII BINDING SITE WAS IDENTIFIED BY ALA-SCANNING MUTAGENESIS (KELLEY ET AL., 1995; SEE ...THE FACTOR VII BINDING SITE WAS IDENTIFIED BY ALA-SCANNING MUTAGENESIS (KELLEY ET AL., 1995; SEE REFERENCE 1 ABOVE). THIS SITE IS LISTED BELOW AND THE SITE IDENTIFIER IS VII.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Density % sol: 49 %
Crystal grow
*PLUS
Temperature: 100 K / Method: vapor diffusion, sitting drop
Details: drop contains 0.05 ml of protein solution and 0.01 ml of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
123 mg/mlprotein1drop
20.1 Msodium chloride1drop
31 mMPMSF1drop
420 mMTris-HCl1drop
550 %satammonium sulfate1reservoir
60.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 0.908 Å
DetectorType: FUJI FILM / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.69→6 Å / Num. obs: 24199 / % possible obs: 97 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.058
Reflection
*PLUS
Rmerge(I) obs: 0.058

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Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.69→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.254 -8.5 %
obs0.204 24199 97 %
Displacement parametersBiso mean: 27.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.69→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 5 235 1936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d1.84
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ/X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.84
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg24.92
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.44

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