+Open data
-Basic information
Entry | Database: PDB / ID: 1boy | ||||||
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Title | EXTRACELLULAR REGION OF HUMAN TISSUE FACTOR | ||||||
Components | HUMAN TISSUE FACTOR | ||||||
Keywords | CLASS 2 CYTOKINE RECEPTOR / INITIATOR OF BLOOD COAGULATION IN VERTEBRATES / COFACTOR FOR FACTOR VIIA / GLYCOPROTEIN / BLOOD COAGULATION | ||||||
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 / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of angiogenesis / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Boys, C.W.G. / Tuddenham, E.G.D. / Harlos, K. | ||||||
Citation | Journal: Nature / Year: 1994 Title: Crystal structure of the extracellular region of human tissue factor. Authors: Harlos, K. / Martin, D.M. / O'Brien, D.P. / Jones, E.Y. / Stuart, D.I. / Polikarpov, I. / Miller, A. / Tuddenham, E.G. / Boys, C.W. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization and Preliminary X-Ray Analysis of Human Tissue Factor Extracellular Domain Authors: Boys, C.W. / Miller, A. / Harlos, K. / Martin, D.M. / Tuddenham, E.G. / O'Brien, D.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1boy.cif.gz | 53.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1boy.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 1boy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/1boy ftp://data.pdbj.org/pub/pdb/validation_reports/bo/1boy | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24826.512 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 1 - 219 Source method: isolated from a genetically manipulated source Details: TYPE B CRYSTALS / Source: (gene. exp.) Homo sapiens (human) / Strain: W3110 Description: PURIFIED BY MONOCLONAL ANTIBODY AFFINITY, REVERSED PHASE HPLC AND ISO-ELECTRIC FOCUSSING Gene: HUMAN TISSUE FACTOR CDNA CODON / Organ: BLOOD / Variant: TONA / Plasmid: PHGH4L (GENE 55:189-196, 1987) Gene (production host): HUMAN TISSUE FACTOR CDNA CODONS 1-119 Production host: PERIPLASMIC SECRETION (U.S PAT 4963,495) / References: UniProt: P13726 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48 % Description: THE REDUNDANCY GIVEN ABOVE IS TO 2.2 ANGSTROMS RESOLUTION. | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97 |
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Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Mar 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Num. obs: 12666 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.065 |
Reflection | *PLUS Highest resolution: 2.2 Å |
-Processing
Software |
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Refinement | Resolution: 2.2→15 Å /
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 48.9 Å2 |