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Yorodumi- PDB-1czv: CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V:... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1czv | ||||||
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Title | CRYSTAL STRUCTURE OF THE C2 DOMAIN OF HUMAN COAGULATION FACTOR V: DIMERIC CRYSTAL FORM | ||||||
Components | PROTEIN (COAGULATION FACTOR V) | ||||||
Keywords | BLOOD CLOTTING / COAGULATION / MEMBRANE-BINDING / DISCOIDIN FAMILY / CALCIUM-INDEPENDENT | ||||||
Function / homology | Function and homology information response to vitamin K / platelet alpha granule / Cargo concentration in the ER / blood circulation / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Common Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation ...response to vitamin K / platelet alpha granule / Cargo concentration in the ER / blood circulation / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / Common Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / extracellular vesicle / blood coagulation / Platelet degranulation / signaling receptor activity / copper ion binding / endoplasmic reticulum lumen / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Macedo-Ribeiro, S. / Bode, W. / Huber, R. / Kane, W.H. / Fuentes-Prior, P. | ||||||
Citation | Journal: Nature / Year: 1999 Title: Crystal structures of the membrane-binding C2 domain of human coagulation factor V. Authors: Macedo-Ribeiro, S. / Bode, W. / Huber, R. / Quinn-Allen, M.A. / Kim, S.W. / Ortel, T.L. / Bourenkov, G.P. / Bartunik, H.D. / Stubbs, M.T. / Kane, W.H. / Fuentes-Prior, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1czv.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1czv.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 1czv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1czv_validation.pdf.gz | 371.9 KB | Display | wwPDB validaton report |
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Full document | 1czv_full_validation.pdf.gz | 379 KB | Display | |
Data in XML | 1czv_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 1czv_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/1czv ftp://data.pdbj.org/pub/pdb/validation_reports/cz/1czv | HTTPS FTP |
-Related structure data
Related structure data | 1czsSC 1cztC S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 18611.420 Da / Num. of mol.: 2 / Fragment: C2 DISCOIDIN-LIKE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P12259 #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: 2.48 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 10 / Details: pH 10.00 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion / PH range low: 10 / PH range high: 9.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 7, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→24.6 Å / Num. obs: 14635 / % possible obs: 96.8 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.094 |
Reflection shell | Resolution: 2.4→2.51 Å / Rmerge(I) obs: 0.399 / % possible all: 90.7 |
Reflection shell | *PLUS % possible obs: 90.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CZS Resolution: 2.4→8 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |