+Open data
-Basic information
Entry | Database: PDB / ID: 1a21 | ||||||
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Title | TISSUE FACTOR (TF) FROM RABBIT | ||||||
Components | TISSUE FACTOR | ||||||
Keywords | GLYCOPROTEIN / 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 / positive regulation of endothelial cell proliferation / extracellular matrix / 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 / positive regulation of endothelial cell proliferation / extracellular matrix / 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 | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Muller, Y.A. / De Vos, A.M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a21.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a21.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a21_validation.pdf.gz | 419.6 KB | Display | wwPDB validaton report |
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Full document | 1a21_full_validation.pdf.gz | 424.1 KB | Display | |
Data in XML | 1a21_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1a21_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a2/1a21 ftp://data.pdbj.org/pub/pdb/validation_reports/a2/1a21 | HTTPS FTP |
-Related structure data
Related structure data | 2hftS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Mar 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 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.
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Displacement parameters | Biso mean: 34.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.4 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 15
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.299 |