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Yorodumi- PDB-6eh4: 003 Human T-Cell Receptor specific for HIV GAG epitope SLYNTVATL ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eh4 | ||||||
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Title | 003 Human T-Cell Receptor specific for HIV GAG epitope SLYNTVATL carried by Human Leukocyte Antigen HLA-A*0201 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Human T Cell Receptor / Human Leukocute Antigen / Influenza Haemagglutinin epitope / 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: 1.26 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 | 6eh4.cif.gz | 212.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eh4.ent.gz | 169.6 KB | Display | PDB format |
PDBx/mmJSON format | 6eh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eh4_validation.pdf.gz | 466.7 KB | Display | wwPDB validaton report |
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Full document | 6eh4_full_validation.pdf.gz | 478.1 KB | Display | |
Data in XML | 6eh4_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 6eh4_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/6eh4 ftp://data.pdbj.org/pub/pdb/validation_reports/eh/6eh4 | HTTPS FTP |
-Related structure data
Related structure data | 6eh5C 6eh6C 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
#1: Protein | Mass: 22413.729 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: 27449.461 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: Chemical | #4: Chemical | ChemComp-EDO / #5: 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: 2.29 Å3/Da / Density % sol: 46.31 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 4K, 15% Glycerol, 100mM TRIS pH 8.0 |
-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 6M / Detector: PIXEL / Date: Mar 17, 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: 1.26→43.23 Å / Num. obs: 106284 / Redundancy: 3.8 % / Biso Wilson estimate: 12.6 Å2 / Net I/σ(I): 15.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GKZ Resolution: 1.26→43.23 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.618 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.053 / 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: 18.743 Å2
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Refinement step | Cycle: 1 / Resolution: 1.26→43.23 Å
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Refine LS restraints |
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