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Open data
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Basic information
Entry | Database: PDB / ID: 3vxq | ||||||
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Title | H27-14 TCR specific for HLA-A24-Nef134-10 | ||||||
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![]() | IMMUNE SYSTEM / HIV-1 / NEF / T CELL RECEPTOR / IMMUNOGLOBURIN DOMAIN / TCR / IMMUNE RESPONSE | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shimizu, A. / Fukai, S. / Yamagata, A. / Iwamoto, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198 KB | Display | ![]() |
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PDB format | ![]() | 156.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.8 KB | Display | ![]() |
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Full document | ![]() | 465.8 KB | Display | |
Data in XML | ![]() | 39.9 KB | Display | |
Data in CIF | ![]() | 57.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vxmC ![]() 3vxnC ![]() 3vxoC ![]() 3vxpC ![]() 3vxrC ![]() 3vxsC ![]() 3vxtC ![]() 3vxuC ![]() 3w0wC ![]() 2bnuS C: citing same article ( 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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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.) ![]() ![]() ![]() #2: Protein | Mass: 27949.979 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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