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Yorodumi- PDB-6frb: F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6frb | ||||||
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Title | F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T Cell Receptor / Human Leukocyte Antigen / Influenza Epitope / Haemagglutinin / 3D Structure | ||||||
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: 1.75 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 | 6frb.cif.gz | 188.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6frb.ent.gz | 150.7 KB | Display | PDB format |
PDBx/mmJSON format | 6frb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6frb_validation.pdf.gz | 436.4 KB | Display | wwPDB validaton report |
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Full document | 6frb_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 6frb_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 6frb_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/6frb ftp://data.pdbj.org/pub/pdb/validation_reports/fr/6frb | HTTPS FTP |
-Related structure data
Related structure data | 6eh4C 6eh5C 6eh6SC 6eh7C 6eh8C 6eh9C 6fr3C 6fr4C 6fr5C 6fr6C 6fr7C 6fr8C 6fr9C 6fraC 6frcC 6fumC 6funC 6fuoC 6fupC 6fuqC 6furC 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
#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) |
#3: Water | ChemComp-HOH / |
-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: 50.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M SPG Buffer, 25% PEG 1500 |
-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: 1.75→47.78 Å / Num. obs: 50657 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.064 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.161 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3716 / CC1/2: 0.711 / Rrim(I) all: 1.258 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EH6 Resolution: 1.75→47.78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.358 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 32.091 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→47.78 Å
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Refine LS restraints |
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