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- PDB-6ilf: CRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.7 ANGSTROM -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ilf | ||||||
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Title | CRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.7 ANGSTROM | ||||||
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Function / homology | ![]() antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / host cell surface / symbiont entry into host cell ...antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / host cell surface / symbiont entry into host cell / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Qu, Z.H. / Zhang, N.Z. / Xia, C. | ||||||
![]() | ![]() Title: Structure and Peptidome of the Bat MHC Class I Molecule Reveal a Novel Mechanism Leading to High-Affinity Peptide Binding. Authors: Qu, Z. / Li, Z. / Ma, L. / Wei, X. / Zhang, L. / Liang, R. / Meng, G. / Zhang, N. / Xia, 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 | ![]() | 170.6 KB | Display | ![]() |
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PDB format | ![]() | 134.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ilcC ![]() 6ileC ![]() 6ilgC ![]() 3vfnS 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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Unit cell |
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Components
#1: Protein | Mass: 32345.482 Da / Num. of mol.: 1 / Fragment: UNP residues 25-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | ![]() Mass: 11474.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1048.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
Sequence details | NCBI Reference Sequence for Beta-2-microglobulin is XP_006920478.1. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.06 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH 6.5, 25%(w/v) Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 13, 2018 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.97→50 Å / Num. obs: 12065 / % possible obs: 75.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.213 / Net I/σ(I): 2.6 |
Reflection shell | Resolution: 1.97→2 Å / Rmerge(I) obs: 0.614 / Num. unique obs: 1349 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3VFN Resolution: 2.7→28.713 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→28.713 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: 82.1999 Å / Origin y: 28.9961 Å / Origin z: 17.776 Å
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Refinement TLS group |
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