+Open data
-Basic information
Entry | Database: PDB / ID: 1ggu | ||||||
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Title | HUMAN FACTOR XIII WITH CALCIUM BOUND IN THE ION SITE | ||||||
Components | PROTEIN (COAGULATION FACTOR XIII) | ||||||
Keywords | TRANSFERASE / TRANSGLUTAMINASE / BLOOD COAGULATION / CALCIUM | ||||||
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 / Interleukin-4 and Interleukin-13 signaling ...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 / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / blood microparticle / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Fox, B.A. / Yee, V.C. / Pederson, L.C. / Trong, I.L. / 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 | 1ggu.cif.gz | 310.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ggu.ent.gz | 248.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ggu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gg/1ggu ftp://data.pdbj.org/pub/pdb/validation_reports/gg/1ggu | HTTPS FTP |
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-Related structure data
Related structure data | 1ggyC 1qrkC 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9706, -0.20087, -0.13264), Vector: |
-Components
#1: Protein | Mass: 83233.922 Da / Num. of mol.: 2 / Fragment: FULL LENGTH Source method: isolated from a genetically manipulated source Details: CALCIUM 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 / | |
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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: 55 % | |||||||||||||||
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Crystal grow | pH: 6.2 / Details: pH 6.20 | |||||||||||||||
Crystal grow | *PLUS pH: 6.2 / Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→20.66 Å / Num. obs: 111498 / % possible obs: 91.5 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.669 / % possible all: 76 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 20.66 Å / % possible obs: 93 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 24.9 Å2 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.15 Å / % possible obs: 86 % / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FIE Resolution: 2.1→20 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 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 38.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.399 / Rfactor Rwork: 0.364 |