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Yorodumi- PDB-2pf1: STRUCTURE OF BOVINE PROTHROMBIN FRAGMENT 1 REFINED AT 2.25 ANGSTR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pf1 | ||||||
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Title | STRUCTURE OF BOVINE PROTHROMBIN FRAGMENT 1 REFINED AT 2.25 ANGSTROMS RESOLUTION | ||||||
Components | PROTHROMBIN FRAGMENT 1 | ||||||
Keywords | HYDROLASE(SERINE PROTEINASE) | ||||||
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: 2.8 Å | ||||||
Authors | Seshadri, T.P. / Tulinsky, A. / Skrzypczak-Jankun, E. / Park, C.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1991 Title: Structure of bovine prothrombin fragment 1 refined at 2.25 A resolution. Authors: Seshadri, T.P. / Tulinsky, A. / Skrzypczak-Jankun, E. / Park, C.H. #1: Journal: J.Mol.Biol. / Year: 1988 Title: Structure of Prothrombin Fragment 1 Refined at 2.8 Angstroms Resolution Authors: Tulinsky, A. / Park, C.H. / Skrzypczak-Jankun, E. #2: Journal: Biochemistry / Year: 1986 Title: Three-Dimensional Structure of the Kringle Sequence: Structure of Prothrombin Fragment 1 Authors: Park, C.H. / Tulinsky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pf1.cif.gz | 38 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pf1.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 2pf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/2pf1 ftp://data.pdbj.org/pub/pdb/validation_reports/pf/2pf1 | 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: RESIDUE PRO 95 IS A CIS PROLINE. |
-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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.43 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6.7 / Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.25 Å / Num. all: 10599 / Num. obs: 8365 / % possible obs: 76 % / Observed criterion σ(F): 3 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.8→5 Å / Rfactor obs: 0.175 / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→5 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 5 Å / Num. reflection all: 6364 / σ(F): 0 / Rfactor all: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |