+Open data
-Basic information
Entry | Database: PDB / ID: 5z11 | ||||||
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Title | Crystal Structure of Grass Carp CD8 alpha alpha Homodimers | ||||||
Components | CD8 alpha chain | ||||||
Keywords | IMMUNE SYSTEM / Grass carp / CD8 alpha / crystal structure / MHC / evolution. | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ctenopharyngodon idella (grass carp) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.35 Å | ||||||
Authors | Wang, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the Grass Carp CD8 alpha alpha Homodimers Indicates a Dramatic Evolution of CD8 from Ectotherms to Endotherms. Authors: Wang, J. / Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z11.cif.gz | 51 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z11.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 5z11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/5z11 ftp://data.pdbj.org/pub/pdb/validation_reports/z1/5z11 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14164.089 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ctenopharyngodon idella (grass carp) / Production host: Escherichia coli (E. coli) / References: UniProt: C7FF18 #2: 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: 2.46 Å3/Da / Density % sol: 50.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M Ammonium phosphate monobasic, 20%(w/v) Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 0.987 Å |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Jul 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. obs: 12041 / % possible obs: 99.8 % / Redundancy: 12.4 % / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.35→2.48 Å / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→47 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.422 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.229 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.679 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→47 Å
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Refine LS restraints |
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