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- PDB-1a21: TISSUE FACTOR (TF) FROM RABBIT -

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Basic information

Entry
Database: PDB / ID: 1a21
TitleTISSUE FACTOR (TF) FROM RABBIT
ComponentsTISSUE FACTOR
KeywordsGLYCOPROTEIN / BLOOD COAGULATION FACTOR / FVIIA ACTIVATION / CYTOKINE RECEPTOR SUPERFAMILY / EXTRACELLULAR DOMAIN
Function / homology
Function and homology information


activation of plasma proteins involved in acute inflammatory response / positive regulation of platelet-derived growth factor receptor signaling pathway / extracellular matrix / positive regulation of endothelial cell proliferation / phospholipid binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of angiogenesis / blood coagulation / membrane => GO:0016020 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ...activation of plasma proteins involved in acute inflammatory response / positive regulation of platelet-derived growth factor receptor signaling pathway / extracellular matrix / positive regulation of endothelial cell proliferation / phospholipid binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of angiogenesis / blood coagulation / membrane => GO:0016020 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface / extracellular space
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 speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsMuller, Y.A. / De Vos, A.M.
CitationJournal: Protein Sci. / Year: 1998
Title: Hinge bending within the cytokine receptor superfamily revealed by the 2.4 A crystal structure of the extracellular domain of rabbit tissue factor.
Authors: Muller, Y.A. / Kelley, R.F. / de Vos, A.M.
History
DepositionJan 14, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 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

Downloads & links

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Assembly

Deposited unit
A: TISSUE FACTOR
B: TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)50,2122
Polymers50,2122
Non-polymers00
Water4,161231
1
A: TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)25,1061
Polymers25,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TISSUE FACTOR


Theoretical massNumber of molelcules
Total (without water)25,1061
Polymers25,1061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.540, 49.010, 65.010
Angle α, β, γ (deg.)96.06, 99.11, 91.14
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.98497, -0.0181, -0.17178), (-0.03601, 0.99416, 0.10173), (0.16894, 0.10639, -0.97987)9.96052, -23.50365, 39.08805
2given(-0.9877, 0.14736, -0.05231), (0.13584, 0.97428, 0.1798), (0.07746, 0.17048, -0.98231)3.03225, -26.61512, 38.77849

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Components

#1: Protein TISSUE FACTOR /


Mass: 25106.051 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 1 - 219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Organ: BLOOD / Production host: Escherichia coli (E. coli) / References: UniProt: P24055
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8
Details: SITTING DROP, 80 UL OF PROTEIN SOLUTION (10 MG/ML PROTEIN IN 50 MM TRIS*HCL,PH:8.0, 50 MM NACL, 75 MM LI2SO4, 12.5 % PEG 3350) EQUILIBRATED AGAINST 30 ML RESERVOIR SOLUTION (50 MM TRIS*HCL, ...Details: SITTING DROP, 80 UL OF PROTEIN SOLUTION (10 MG/ML PROTEIN IN 50 MM TRIS*HCL,PH:8.0, 50 MM NACL, 75 MM LI2SO4, 12.5 % PEG 3350) EQUILIBRATED AGAINST 30 ML RESERVOIR SOLUTION (50 MM TRIS*HCL, PH:8.0, 50 MM NACL, 150 MM LI2SO4, 25 % PEG3350), vapor diffusion - sitting drop
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMTris-HCl1drop
350 mM1dropNaCl
475 mM1dropLi2SO4
512.5 %PEG33501drop
650 mMTris-HCl1reservoir
750 mM1reservoirNaCl
8150 mM1reservoirLiSO4
925 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD / Date: Mar 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.35→60 Å / Num. obs: 20678 / % possible obs: 96.4 % / Redundancy: 3 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.075
Reflection shellResolution: 2.35→2.4 Å / Redundancy: 2 % / Rsym value: 0.07 / % possible all: 90.6
Reflection shell
*PLUS
% possible obs: 90.6 % / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HFT

2hft


Resolution: 2.35→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
Details: A BULK SOLVENT CORRECTION CALCULATED WITH PROGRAM X-PLOR WAS USED THROUGHOUT REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1953 9.7 %THIN RESOLUTION SHELLS
Rwork0.191 ---
obs0.191 20156 95.2 %-
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å26.3 Å2-8.5 Å2
2--4.56 Å27.94 Å2
3----7.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 0 231 3406
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.617
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.82
X-RAY DIFFRACTIONx_mcangle_it3.13
X-RAY DIFFRACTIONx_scbond_it4.84
X-RAY DIFFRACTIONx_scangle_it7.46
LS refinement shellResolution: 2.35→2.4 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.356 125 11.4 %
Rwork0.299 969 -
obs--78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5
LS refinement shell
*PLUS
Rfactor obs: 0.299

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