+Open data
-Basic information
Entry | Database: PDB / ID: 3vxq | ||||||
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Title | H27-14 TCR specific for HLA-A24-Nef134-10 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HIV-1 / NEF / T CELL RECEPTOR / IMMUNOGLOBURIN DOMAIN / TCR / IMMUNE RESPONSE | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shimizu, A. / Fukai, S. / Yamagata, A. / Iwamoto, A. | ||||||
Citation | Journal: SCI REP / Year: 2013 Title: Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection Authors: Shimizu, A. / Kawana-Tachikawa, A. / Yamagata, A. / Han, C. / Zhu, D. / Sato, Y. / Nakamura, H. / Koibuchi, T. / Carlson, J. / Martin, E. / Brumme, C.J. / Shi, Y. / Gao, G.F. / Brumme, Z.L. ...Authors: Shimizu, A. / Kawana-Tachikawa, A. / Yamagata, A. / Han, C. / Zhu, D. / Sato, Y. / Nakamura, H. / Koibuchi, T. / Carlson, J. / Martin, E. / Brumme, C.J. / Shi, Y. / Gao, G.F. / Brumme, Z.L. / Fukai, S. / Iwamoto, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vxq.cif.gz | 198 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vxq.ent.gz | 156.5 KB | Display | PDB format |
PDBx/mmJSON format | 3vxq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/3vxq ftp://data.pdbj.org/pub/pdb/validation_reports/vx/3vxq | HTTPS FTP |
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-Related structure data
Related structure data | 3vxmC 3vxnC 3vxoC 3vxpC 3vxrC 3vxsC 3vxtC 3vxuC 3w0wC 2bnuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22607.123 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 #2: Protein | Mass: 27949.979 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21D(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE DATABASE REFERENCE FOR BOTH ENTITIES DO NOT CURRENTLY EXIST. | |
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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: 2.29 Å3/Da / Density % sol: 46.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M Bis-Tris, 20% PEG8000, 0.5M magnesium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 59865 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 0.233 % / Rmerge(I) obs: 0.233 / Num. unique all: 5913 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BNU Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.891 / SU B: 4.731 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 26.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.997→2.049 Å / Total num. of bins used: 20
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