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Open data
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Basic information
Entry | Database: PDB / ID: 6a2b | ||||||
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Title | Crystal Structure of Xenopus laevis MHC I complex | ||||||
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![]() | IMMUNE SYSTEM / Xenopus laevis / MHC I / evolution | ||||||
Function / homology | ![]() antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / membrane => GO:0016020 / immune response / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ma, L.Z. / Xia, C. | ||||||
![]() | ![]() Title: A Glimpse of the Peptide Profile Presentation byXenopus laevisMHC Class I: Crystal Structure of pXela-UAA Reveals a Distinct Peptide-Binding Groove. Authors: Ma, L. / Zhang, N. / Qu, Z. / Liang, R. / Zhang, L. / Zhang, B. / Meng, G. / Dijkstra, J.M. / Li, S. / Xia, M.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 | ![]() | 90.2 KB | Display | ![]() |
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PDB format | ![]() | 67.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
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Full document | ![]() | 444.3 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4e0rS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31644.916 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 10942.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1232.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.65 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium malonate pH6.0, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Nov 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→15 Å / Num. obs: 29548 / % possible obs: 92.5 % / Redundancy: 2 % / CC1/2: 0.939 / Rmerge(I) obs: 0.188 / Net I/σ(I): 2.6 |
Reflection shell | Resolution: 2.8→2.83 Å / Num. unique obs: 4256 / CC1/2: 0.926 / % possible all: 91.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4E0R Resolution: 2.8→14.98 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.836 / SU B: 17.21 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.532 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.03 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→14.98 Å
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Refine LS restraints |
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