+Open data
-Basic information
Entry | Database: PDB / ID: 6fr5 | ||||||
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Title | HA1.7 TCR Study of CDR Loop Flexibility | ||||||
Components | (TCR HA1.7 specific for FLU epitope PKYVKQNTLKLAT, ...) x 2 | ||||||
Keywords | IMMUNE SYSTEM / 003 TCR / CDR Flexibility / 3D Structure / MHC Class II | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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. #1: Journal: To Be Published Title: Flexibility Study of CDRs in 003 TCR Authors: Rizkallah, P.J. / 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 | 6fr5.cif.gz | 207.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fr5.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fr5_validation.pdf.gz | 478 KB | Display | wwPDB validaton report |
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Full document | 6fr5_full_validation.pdf.gz | 486 KB | Display | |
Data in XML | 6fr5_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 6fr5_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/6fr5 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/6fr5 | HTTPS FTP |
-Related structure data
Related structure data | 6eh4SC 6eh5C 6eh6C 6eh7C 6eh8C 6eh9C 6fr3C 6fr4C 6fr6C 6fr7C 6fr8C 6fr9C 6fraC 6frbC 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
-TCR HA1.7 specific for FLU epitope PKYVKQNTLKLAT, ... , 2 types, 2 molecules AB
#1: Protein | Mass: 22241.654 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: 27451.434 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, 401 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACT / | #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: 2.28 Å3/Da / Density % sol: 46.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M Na Citrate, 0.1M TrisHCl, 30% PEG 400 |
-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 6M / Detector: PIXEL / Date: Mar 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→40.59 Å / Num. obs: 91903 / % possible obs: 98.4 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.057 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.37→1.41 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6599 / CC1/2: 0.736 / Rrim(I) all: 0.638 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EH4 Resolution: 1.37→40.59 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.976 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.059 / 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: 19.183 Å2
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Refinement step | Cycle: 1 / Resolution: 1.37→40.59 Å
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Refine LS restraints |
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