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Open data
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Basic information
Entry | Database: PDB / ID: 1ggy | ||||||
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Title | HUMAN FACTOR XIII WITH YTTERBIUM BOUND IN THE ION SITE | ||||||
![]() | PROTEIN (COAGULATION FACTOR XIII) | ||||||
![]() | TRANSFERASE / TRANSGLUTAMINASE / BLOOD COAGULATION / YTTERBIUM | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fox, B.A. / Yee, V.C. / Pederson, L.C. / Trong, I.L. / Bishop, P.D. / Stenkamp, R.E. / Teller, D.C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.9 KB | Display | ![]() |
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PDB format | ![]() | 236 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 385 KB | Display | ![]() |
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Full document | ![]() | 423.9 KB | Display | |
Data in XML | ![]() | 31.6 KB | Display | |
Data in CIF | ![]() | 49.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gguC ![]() 1qrkC ![]() 1fieS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: (-0.97149, -0.20231, -0.12363), Vector: |
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Components
#1: Protein | Mass: 83233.922 Da / Num. of mol.: 2 / Fragment: FULL LENGTH Source method: isolated from a genetically manipulated source Details: YTTERBIUM SOAKED INTO CRYSTAL / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00488, protein-glutamine gamma-glutamyltransferase #2: Chemical | ChemComp-YB / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 57 % | |||||||||||||||
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Crystal grow | pH: 6.2 / Details: pH 6.2 | |||||||||||||||
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: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
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: 49005 / % possible obs: 75.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 14.9 Å2 |
Reflection shell | Resolution: 2.5→2.65 Å / % possible all: 45 |
Reflection | *PLUS Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS Lowest resolution: 2.54 Å / % possible obs: 42 % / Mean I/σ(I) obs: 3.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FIE Resolution: 2.5→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 36.1 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: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.353 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.274 |