+Open data
-Basic information
Entry | Database: PDB / ID: 1evu | ||||||
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Title | HUMAN FACTOR XIII WITH CALCIUM BOUND IN THE ION SITE | ||||||
Components | COAGULATION FACTOR XIIIFactor 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 / Resolution: 2.01 Å | ||||||
Authors | Garzon, R.J. / Pratt, K.P. / Bishop, P.D. / Le Trong, I. / Stenkamp, R.E. / Teller, D.C. | ||||||
Citation | Journal: To Be Published Title: Tryptophan 279 is Essential for the Transglutaminase Activity of Coagulation Factor XIII: Functional and Structural Characterization Authors: Garzon, R.J. / Pratt, K.P. / Bishop, P.D. / Le Trong, I. / Stenkamp, R.E. / Teller, D.C. #1: 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 | 1evu.cif.gz | 315.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1evu.ent.gz | 260.3 KB | Display | PDB format |
PDBx/mmJSON format | 1evu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/1evu ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1evu | HTTPS FTP |
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-Related 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: 83274.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): ZM118 References: UniProt: P00488, protein-glutamine gamma-glutamyltransferase #2: Chemical | #3: Chemical | ChemComp-PGO / | #4: 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: 2.73 Å3/Da / Density % sol: 55.03 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 6.2 Details: 24% 1,2-propanediol, 100 mM sodium potassium phosphate buffer. To incorporate Calcium, the crystals were transferred to 24% 1,2-propanediol and MES buffer and soaked for 1-2 days in 90 mM ...Details: 24% 1,2-propanediol, 100 mM sodium potassium phosphate buffer. To incorporate Calcium, the crystals were transferred to 24% 1,2-propanediol and MES buffer and soaked for 1-2 days in 90 mM CaCl2, pH 6.2, VAPOR DIFFUSION, temperature 294K |
-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: 23.3 Å2 / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.669 / % possible all: 76 |
-Processing
Software |
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Refinement | Resolution: 2.01→20.66 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2284378.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: maximum likelihood, Engh & Huber Details: This entry is the further refinement of the 1ggu PDB coordinates (Fox et al, 1999). The crystals of this zymogen contain 90 mM CaCl2 and diffract to 2.0 A resolution. The changes to the 1ggu ...Details: This entry is the further refinement of the 1ggu PDB coordinates (Fox et al, 1999). The crystals of this zymogen contain 90 mM CaCl2 and diffract to 2.0 A resolution. The changes to the 1ggu model include extension of the activation peptide of subunit 1 to the N-acetyl Ser at position 1, refitting of some residues, addition and deletion of water molecules, and insertion of alternate conformations for seven residues. The purpose for the further refinement is for comparison with the W279F mutant of factor XIII
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 69.9346 Å2 / ksol: 0.324987 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.01→20.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.14 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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