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Yorodumi- PDB-5lyg: CRYSTAL STRUCTURE OF INTRACELLULAR B30.2 DOMAIN OF BTN3A1 BOUND T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lyg | ||||||
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Title | CRYSTAL STRUCTURE OF INTRACELLULAR B30.2 DOMAIN OF BTN3A1 BOUND TO MALONATE | ||||||
Components | Butyrophilin subfamily 3 member A1 | ||||||
Keywords | SIGNALING PROTEIN / B30.2 / butyrophilin | ||||||
Function / homology | Function and homology information Butyrophilin (BTN) family interactions / activated T cell proliferation / regulation of cytokine production / positive regulation of cytokine production / positive regulation of type II interferon production / T cell receptor signaling pathway / adaptive immune response / external side of plasma membrane / signaling receptor binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Mohammed, F. / Baker, A.T. / Salim, M. / Willcox, B.E. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: BTN3A1 Discriminates gamma delta T Cell Phosphoantigens from Nonantigenic Small Molecules via a Conformational Sensor in Its B30.2 Domain. Authors: Salim, M. / Knowles, T.J. / Baker, A.T. / Davey, M.S. / Jeeves, M. / Sridhar, P. / Wilkie, J. / Willcox, C.R. / Kadri, H. / Taher, T.E. / Vantourout, P. / Hayday, A. / Mehellou, Y. / Mohammed, F. / Willcox, B.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lyg.cif.gz | 93.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lyg.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 5lyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/5lyg ftp://data.pdbj.org/pub/pdb/validation_reports/ly/5lyg | HTTPS FTP |
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-Related 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: 21489.451 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A1, BTF5 / Plasmid: pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: O00481 | ||||
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#2: Chemical | #3: Chemical | ChemComp-MLI / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350 and 0.2M Sodium malonate dibasic monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.52→39.4 Å / Num. obs: 67598 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 29.811 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.29 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→39.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.218 / SU ML: 0.051 / SU R Cruickshank DPI: 0.1032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.079 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 54.45 Å2 / Biso mean: 23.514 Å2 / Biso min: 14.73 Å2
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Refinement step | Cycle: final / Resolution: 1.6→39.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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