+Open data
-Basic information
Entry | Database: PDB / ID: 3qjh | ||||||
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Title | The crystal structure of the 5c.c7 TCR | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin domain / T cell receptor | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Ely, L.K. / Newell, E.W. / Davis, M.M. / Garcia, K.C. | ||||||
Citation | Journal: J.Immunol. / Year: 2011 Title: Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k). Authors: Newell, E.W. / Ely, L.K. / Kruse, A.C. / Reay, P.A. / Rodriguez, S.N. / Lin, A.E. / Kuhns, M.S. / Garcia, K.C. / Davis, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qjh.cif.gz | 185.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qjh.ent.gz | 151.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qjh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qjh_validation.pdf.gz | 447.4 KB | Display | wwPDB validaton report |
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Full document | 3qjh_full_validation.pdf.gz | 457.1 KB | Display | |
Data in XML | 3qjh_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 3qjh_validation.cif.gz | 50.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/3qjh ftp://data.pdbj.org/pub/pdb/validation_reports/qj/3qjh | HTTPS FTP |
-Related 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: 22765.146 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 27613.924 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) #3: Water | ChemComp-HOH / | |
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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: 2.86 Å3/Da / Density % sol: 56.93 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.7 Details: 20 % PEG3350, 0.1 M calcium chloride and Tris, pH 7.7, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 19, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→96.31 Å / Num. all: 91312 / Num. obs: 91312 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 20.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.323 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8153 / SU ML: 0.26 / σ(F): 1.07 / Phase error: 25.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.874 Å2 / ksol: 0.388 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.36 Å2 / Biso mean: 32.1987 Å2 / Biso min: 14.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→46.323 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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