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- PDB-1tfh: EXTRACELLULAR DOMAIN OF HUMAN TISSUE FACTOR -

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Basic information

Entry
Database: PDB / ID: 1tfh
TitleEXTRACELLULAR DOMAIN OF HUMAN TISSUE FACTOR
ComponentsHUMAN TISSUE FACTOR
KeywordsCOAGULATION FACTOR / BLOOD COAGULATION / TISSUE FACTOR / GLYCOPROTEIN
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 TOR signaling / positive regulation of endothelial cell proliferation ...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 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process / blood coagulation / collagen-containing extracellular matrix / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR, MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHuang, M. / Syed, R. / Stura, E.A. / Stone, M.J. / Stefanko, R.S. / Ruf, W. / Edgington, T.S. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF.G9 complex.
Authors: Huang, M. / Syed, R. / Stura, E.A. / Stone, M.J. / Stefanko, R.S. / Ruf, W. / Edgington, T.S. / Wilson, I.A.
History
DepositionApr 10, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 11, 2019Group: Database references / Derived calculations
Category: citation / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _citation.title
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN TISSUE FACTOR
B: HUMAN TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)49,6532
Polymers49,6532
Non-polymers00
Water25214
1
A: HUMAN TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)24,8271
Polymers24,8271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HUMAN TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)24,8271
Polymers24,8271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.393, 85.828, 112.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.011162, -0.309875, -0.950712), (0.252914, 0.918981, -0.302503), (0.967424, -0.243825, 0.068114)
Vector: 101.78719, -2.7234, -11.94945)
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO TISSUE FACTOR MOLECULES WITH CHAIN IDS OF A AND B. 14 WATER MOLECULES WERE IDENTIFIED AROUND MOLECULE A. MOLECULE B HAS ONLY A FEW CONTACTS (10 LESS THAN 5.0 ANGSTROMS) WITH ITS SYMMETRY-RELATED MOLECULES AND THUS HAS A MUCH HIGHER OVERALL B VALUE THAN MOLECULE A, WHICH HAS EXTENSIVE CONTACTS WITH ITS NEIGHBORING MOLECULES.

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Components

#1: Protein HUMAN TISSUE FACTOR / / TF / THROMBOPLASTIN / COAGULATION FACTOR III


Mass: 24826.512 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: HUMAN TISSUE FACTOR EXTRACELLU / Organ: BLOOD / Plasmid: PTRCHISC (INVITROGEN) / Species (production host): Escherichia coli / Cellular location (production host): INCLUSION BODIES
Gene (production host): HUMAN TISSUE FACTOR EXTRACELLULAR DOMAIN
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13726
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 278 K / pH: 7
Details: CRYSTAL CAN BE GROWN FROM 20MM PHOSPHATE BUFFER, PH 6.5, AT A 40MG/ML PROTEIN CONCENTRATION. THE CRYSTALS USED FOR DIFFRACTION STUDIES WERE IN FACT CRYSTALLIZED UNEXPECTEDLY IN 2 DAYS IN AN ...Details: CRYSTAL CAN BE GROWN FROM 20MM PHOSPHATE BUFFER, PH 6.5, AT A 40MG/ML PROTEIN CONCENTRATION. THE CRYSTALS USED FOR DIFFRACTION STUDIES WERE IN FACT CRYSTALLIZED UNEXPECTEDLY IN 2 DAYS IN AN NMR TUBE CONTAINING A SOLUTION OF APPROXIMATELY 3.5MM OF UNIFORMLY 15N-ENRICHED (~99 ATOM%) TISSUE FACTOR (AT ~85 MG/ML) IN 20MM KNA2PO4, 0.02%NAN3, 10% D2O AND 90% H2O, PH 7.0 AT 5 DEGREE., temperature 278K
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMphosphate11
240 mg/mlprotein11

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Dec 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.27→19 Å / Num. obs: 26432 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 50.1 Å2 / Rsym value: 0.073 / Net I/σ(I): 21
Reflection shellResolution: 2.27→2.42 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.436 / % possible all: 52.6
Reflection
*PLUS
Num. measured all: 64590 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 52.6 % / Rmerge(I) obs: 0.436

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
AMoREphasing
PHASESphasing
XTALVIEWrefinement
X-PLOR3.1refinement
XENGENdata scaling
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT
Starting model: C ALPHA COORDINATES OF PDB ENTRY 1BOY

1boy


Resolution: 2.4→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 2038 9.8 %RANDOM
Rwork0.217 ---
obs0.217 20860 85.6 %-
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20 Å2
2---0.39 Å20 Å2
3---1.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 0 14 3103
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.281.5
X-RAY DIFFRACTIONx_mcangle_it6.912
X-RAY DIFFRACTIONx_scbond_it6.832
X-RAY DIFFRACTIONx_scangle_it10.322.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION0.340.1
22X-RAY DIFFRACTION0.680.3
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 256 10.1 %
Rwork0.376 2287 -
obs--63.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55

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