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Yorodumi- PDB-6eh6: F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eh6 | ||||||
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Title | F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101 | ||||||
Components | (Human T Cell Receptor ...T-cell receptor) x 2 | ||||||
Keywords | IMMUNE SYSTEM / T Cell Receptor / Human Leukocyte Antigen / Influenza Epitope / Haemagglutinin / 3D Structure | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Rizkallah, P.J. / Cole, D.K. | ||||||
Citation | Journal: Front Immunol / Year: 2018 Title: In Silicoand Structural Analyses Demonstrate That Intrinsic Protein Motions Guide T Cell Receptor Complementarity Determining Region Loop Flexibility. Authors: Holland, C.J. / MacLachlan, B.J. / Bianchi, V. / Hesketh, S.J. / Morgan, R. / Vickery, O. / Bulek, A.M. / Fuller, A. / Godkin, A. / Sewell, A.K. / Rizkallah, P.J. / Wells, S. / Cole, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eh6.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eh6.ent.gz | 153.9 KB | Display | PDB format |
PDBx/mmJSON format | 6eh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/6eh6 ftp://data.pdbj.org/pub/pdb/validation_reports/eh/6eh6 | HTTPS FTP |
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-Related structure data
Related structure data | 6eh4C 6eh5C 6eh7C 6eh8C 6eh9C 6fr3C 6fr4C 6fr5C 6fr6C 6fr7C 6fr8C 6fr9C 6fraC 6frbC 6frcC 6fumC 6funC 6fuoC 6fupC 6fuqC 6furC 4gkzS 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 on special symmetry positions |
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-Components
-Human T Cell Receptor ... , 2 types, 2 molecules AB
#1: Protein | Mass: 22438.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 27208.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Non-polymers , 4 types, 165 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-PEG / | #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: 2.5 Å3/Da / Density % sol: 50.79 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1.5K, 100mM MMT pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2012 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.78→50.72 Å / Num. obs: 48509 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.053 / Net I/σ(I): 22.5 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GKZ Resolution: 1.78→50.72 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.244 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.115 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 97.34 Å2 / Biso mean: 32.953 Å2 / Biso min: 16.19 Å2
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Refinement step | Cycle: final / Resolution: 1.78→50.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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