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Yorodumi- PDB-4o03: Crystal structure of Ca2+ bound prothrombin deletion mutant resid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o03 | ||||||
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Title | Crystal structure of Ca2+ bound prothrombin deletion mutant residues 146-167 | ||||||
Components | Prothrombin | ||||||
Keywords | HYDROLASE / PROTHROMBIN / KRINGLE / SERINE PROTEASE / COAGULATION | ||||||
Function / homology | Function and homology information positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.38 Å | ||||||
Authors | Pozzi, N. / Chen, Z. / Shropshire, D.B. / Pelc, L.A. / Di Cera, E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: The linker connecting the two kringles plays a key role in prothrombin activation. Authors: Pozzi, N. / Chen, Z. / Pelc, L.A. / Shropshire, D.B. / Di Cera, E. #1: Journal: Nat.Struct.Mol.Biol. / Year: 2003 Title: Structural basis of membrane binding by GLA domains of vitamin K-Dependent proteins. Authors: Huang, M. / Rigby, A.C. / Morelli, X. / Grant, M.A. / Huang, G. / Furie, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o03.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o03.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 4o03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/4o03 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/4o03 | HTTPS FTP |
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-Related structure data
Related structure data | 4nzqSC 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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Unit cell |
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-Components
#1: Protein | Mass: 63557.668 Da / Num. of mol.: 1 / Mutation: deletion mutant residues 146-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell (production host): Baby Hamster Kidney (BHK) / Production host: Cricetinae (hamsters) / References: UniProt: P00734, thrombin | ||||
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#2: Chemical | ChemComp-CA / #3: Sugar | Sequence details | THE COORDS CONTAIN DELETION OF RESIDUES 146-167, CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.92 Å3/Da / Density % sol: 75.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES, pH 7.5, 10% PEG 4000 and 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 28, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.38→40 Å / Num. all: 17364 / Num. obs: 16635 / % possible obs: 95.8 % / Observed criterion σ(F): -0.7 / Observed criterion σ(I): -0.7 / Redundancy: 2.9 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 6.9 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4NZQ Resolution: 3.38→39.75 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.813 / SU B: 26.65 / SU ML: 0.43 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -0.7 / σ(I): -0.7 / ESU R Free: 0.515 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.096 Å2
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Refinement step | Cycle: LAST / Resolution: 3.38→39.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.38→3.462 Å / Total num. of bins used: 20
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