+Open data
-Basic information
Entry | Database: PDB / ID: 5edx | ||||||
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Title | Crystal structure of swine CD8aa homodimer | ||||||
Components | CD8 alpha antigen | ||||||
Keywords | IMMUNE SYSTEM / swine / CD8alpha | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å | ||||||
Authors | Liu, Y.J. / Qi, J.X. / Zhang, N.Z. / Xia, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Rep / Year: 2016 Title: The structural basis of chicken, swine and bovine CD8 alpha alpha dimers provides insight into the co-evolution with MHC I in endotherm species. Authors: Liu, Y. / Li, X. / Qi, J. / Zhang, N. / Xia, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5edx.cif.gz | 116.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5edx.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 5edx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/5edx ftp://data.pdbj.org/pub/pdb/validation_reports/ed/5edx | HTTPS FTP |
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-Related structure data
Related structure data | 5eb9C 5ebgC 1cd8S 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: 13185.057 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-115 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: CD8A / Production host: Escherichia coli (E. coli) / References: UniProt: A0MNZ3 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.0 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 1% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 33859 / % possible obs: 99.9 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 30.235 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 5.476 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CD8 Resolution: 1.801→28.909 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 19.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.305 Å2 / ksol: 0.408 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.801→28.909 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 34.6344 Å / Origin y: -19.8132 Å / Origin z: 5.8652 Å
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Refinement TLS group | Selection details: all |