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Yorodumi- PDB-2pf2: THE CA+2 ION AND MEMBRANE BINDING STRUCTURE OF THE GLA DOMAIN OF ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pf2 | ||||||
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Title | THE CA+2 ION AND MEMBRANE BINDING STRUCTURE OF THE GLA DOMAIN OF CA-PROTHROMBIN FRAGMENT 1 | ||||||
Components | PROTHROMBIN FRAGMENT 1 | ||||||
Keywords | HYDROLASE(SERINE PROTEASE) | ||||||
Function / homology | Function and homology information fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Soriano-Garcia, M. / Padmanabhan, K. / De vos, A.M. / Tulinsky, A. | ||||||
Citation | Journal: Biochemistry / Year: 1992 Title: The Ca2+ ion and membrane binding structure of the Gla domain of Ca-prothrombin fragment 1. Authors: Soriano-Garcia, M. / Padmanabhan, K. / de Vos, A.M. / Tulinsky, A. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Structure of Bovine Prothrombin Fragment 1 Refined at 2.25 Angstroms Resolution Authors: Seshadri, T.P. / Tulinsky, A. / Skrzypczak-Jankun, E. / Park, C.H. #2: Journal: Biochemistry / Year: 1989 Title: Structure of Ca2+ Prothrombin Fragment 1 Including the Conformation of the Gla Domain Authors: Soriano-Garcia, M. / Park, C.H. / Tulinsky, A. / Ravichandran, K.G. / Skrzypczak-Jankun, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pf2.cif.gz | 45.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pf2.ent.gz | 35.1 KB | Display | PDB format |
PDBx/mmJSON format | 2pf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/2pf2 ftp://data.pdbj.org/pub/pdb/validation_reports/pf/2pf2 | 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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Atom site foot note | 1: RESIDUES PRO 54 AND PRO 95 ARE CIS PROLINES. |
-Components
#1: Protein | Mass: 18024.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00735 | ||
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#2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.75 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging dropDetails: taken from Soriano-Garacia, M. et al (1989), Biochemistry, 28, 6805-6810. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. all: 12662 / Num. obs: 8141 / % possible obs: 64 % |
-Processing
Software |
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Refinement | Resolution: 2.2→7 Å / Rfactor obs: 0.171 / σ(F): 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→7 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 7 Å / Num. reflection obs: 1024 / σ(F): 1 / Rfactor obs: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |