+Open data
-Basic information
Entry | Database: PDB / ID: 1qrk | |||||||||
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Title | HUMAN FACTOR XIII WITH STRONTIUM BOUND IN THE ION SITE | |||||||||
Components | PROTEIN (COAGULATION FACTOR XIII) | |||||||||
Keywords | TRANSFERASE / TRANSGLUTAMINASE / BLOOD COAGULATION / CALCIUM / STRONTIUM | |||||||||
Function / homology | Function and homology information protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / blood microparticle / Interleukin-4 and Interleukin-13 signaling / extracellular space / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Fox, B.A. / Yee, V.C. / Pederson, L.C. / Le Trong, I. / Bishop, P.D. / Stenkamp, R.E. / Teller, D.C. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Identification of the calcium binding site and a novel ytterbium site in blood coagulation factor XIII by x-ray crystallography. Authors: Fox, B.A. / Yee, V.C. / Pedersen, L.C. / Le Trong, I. / Bishop, P.D. / Stenkamp, R.E. / Teller, D.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qrk.cif.gz | 289.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qrk.ent.gz | 233.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qrk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/1qrk ftp://data.pdbj.org/pub/pdb/validation_reports/qr/1qrk | HTTPS FTP |
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-Related structure data
Related structure data | 1gguC 1ggyC 1fieS 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: 83233.922 Da / Num. of mol.: 2 / Fragment: FULL LENGTH DIMER Source method: isolated from a genetically manipulated source Details: STRONTIUM BOUND IN THE ION SITE / Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P00488, protein-glutamine gamma-glutamyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | RESIDUES NOT VISIBLE IN ELECTRON DENSITY MAPS: CHAIN A 1-8, 31-44, 512-516, 728-731 CHAIN B 1-9, 36- ...RESIDUES NOT VISIBLE IN ELECTRON DENSITY MAPS: CHAIN A 1-8, 31-44, 512-516, 728-731 CHAIN B 1-9, 36-40, 508-515, 728-731 | |
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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: 2.7 Å3/Da / Density % sol: 57 % | |||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 1,2-PROPANEDIOL (24%) AND NAKPO4 (100MM) PH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 25K | |||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 1, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 50777 / % possible obs: 78.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 17.6 Å2 |
Reflection shell | Resolution: 2.5→2.65 Å / % possible all: 55.1 |
Reflection shell | *PLUS % possible obs: 51 % / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FIE Resolution: 2.5→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.342 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.27 |