+Open data
-Basic information
Entry | Database: PDB / ID: 6ovo | ||||||
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Title | Crystal structure of the unliganded PG10 TCR | ||||||
Components |
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Keywords | IMMUNE SYSTEM / alpha beta / T-cell receptor / receptor | ||||||
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: 2.49 Å | ||||||
Authors | Shahine, A. / Rossjohn, J. | ||||||
Citation | Journal: J Immunol. / Year: 2019 Title: A TCR beta-Chain Motif Biases toward Recognition of Human CD1 Proteins. Authors: Reinink, P. / Shahine, A. / Gras, S. / Cheng, T.Y. / Farquhar, R. / Lopez, K. / Suliman, S.A. / Reijneveld, J.F. / Le Nours, J. / Tan, L.L. / Leon, S.R. / Jimenez, J. / Calderon, R. / Lecca, ...Authors: Reinink, P. / Shahine, A. / Gras, S. / Cheng, T.Y. / Farquhar, R. / Lopez, K. / Suliman, S.A. / Reijneveld, J.F. / Le Nours, J. / Tan, L.L. / Leon, S.R. / Jimenez, J. / Calderon, R. / Lecca, L. / Murray, M.B. / Rossjohn, J. / Moody, D.B. / Van Rhijn, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ovo.cif.gz | 191.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ovo.ent.gz | 150.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ovo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ovo_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 6ovo_full_validation.pdf.gz | 459.8 KB | Display | |
Data in XML | 6ovo_validation.xml.gz | 19 KB | Display | |
Data in CIF | 6ovo_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/6ovo ftp://data.pdbj.org/pub/pdb/validation_reports/ov/6ovo | HTTPS FTP |
-Related structure data
Related structure data | 6ovnC 5wjoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 22873.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV (TCRA) / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Protein | Mass: 27975.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV (TCRB) / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) |
-Non-polymers , 4 types, 121 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | #6: 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: 3.62 Å3/Da / Density % sol: 66.03 % / Description: Rod morphology |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2015 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→74.81 Å / Num. obs: 25252 / % possible obs: 99.6 % / Redundancy: 10.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.048 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.49→2.62 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2502 / CC1/2: 0.537 / Rpim(I) all: 0.402 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WJO Resolution: 2.49→44.826 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.94 Å2 / Biso mean: 58.7487 Å2 / Biso min: 22.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.49→44.826 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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