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Yorodumi- PDB-2jor: NMR Solution Structure, Stability, and Interaction of the Recombi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jor | ||||||
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Title | NMR Solution Structure, Stability, and Interaction of the Recombinant Bovine Fibrinogen alphaC-Domain Fragment | ||||||
Components | Fibrinogen alpha chain | ||||||
Keywords | BLOOD CLOTTING / Protein | ||||||
Function / homology | Function and homology information blood coagulation, common pathway / fibrinogen complex / positive regulation of heterotypic cell-cell adhesion / extracellular matrix structural constituent / positive regulation of peptide hormone secretion / protein polymerization / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / platelet aggregation ...blood coagulation, common pathway / fibrinogen complex / positive regulation of heterotypic cell-cell adhesion / extracellular matrix structural constituent / positive regulation of peptide hormone secretion / protein polymerization / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / platelet aggregation / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / innate immune response / signaling receptor binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing | ||||||
Authors | Burton, R.A. / Tsurupa, G. / Roy, H. / Nico, T. / Leonid, M. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: NMR Solution Structure, Stability, and Interaction of the Recombinant Bovine Fibrinogen alphaC-Domain Fragment Authors: Burton, R.A. / Tsurupa, G. / Hantgan, R.R. / Tjandra, N. / Medved, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jor.cif.gz | 470.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jor.ent.gz | 389.7 KB | Display | PDB format |
PDBx/mmJSON format | 2jor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jor_validation.pdf.gz | 345.1 KB | Display | wwPDB validaton report |
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Full document | 2jor_full_validation.pdf.gz | 515.8 KB | Display | |
Data in XML | 2jor_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 2jor_validation.cif.gz | 52.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/2jor ftp://data.pdbj.org/pub/pdb/validation_reports/jo/2jor | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8974.674 Da / Num. of mol.: 1 / Fragment: ALPHA-C DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: FGA / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P02672 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 150 uM [U-99% 13C; U-99% 15N] protein, 10 mM KPO4 pH 6.5, 150 mM NaCl, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 150 uM / Component: entity_1 / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Ionic strength: 150 / pH: 6.0 / Pressure: ambient / Temperature: 282 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz |
-Processing
NMR software | Name: X-PLOR NIH / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement |
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Refinement | Method: distance geometry, simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 500 / Conformers submitted total number: 20 |