+Open data
-Basic information
Entry | Database: PDB / ID: 5nmd | ||||||
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Title | 868 TCR Specific for HLA A02 presenting HIV Epitope SLYNTVATL | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC / TCR / CD8+ | ||||||
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: 2.07 Å | ||||||
Authors | Rizkallah, P.J. / Cole, D.K. / Fuller, A. / Sewell, A.K. | ||||||
Citation | Journal: Front Immunol / Year: 2017 Title: Dual Molecular Mechanisms Govern Escape at Immunodominant HLA A2-Restricted HIV Epitope. Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. ...Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. / Beck, K. / Evavold, B.D. / Rizkallah, P.J. / Sewell, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nmd.cif.gz | 366.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nmd.ent.gz | 300.8 KB | Display | PDB format |
PDBx/mmJSON format | 5nmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nmd_validation.pdf.gz | 477.3 KB | Display | wwPDB validaton report |
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Full document | 5nmd_full_validation.pdf.gz | 494 KB | Display | |
Data in XML | 5nmd_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 5nmd_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/5nmd ftp://data.pdbj.org/pub/pdb/validation_reports/nm/5nmd | HTTPS FTP |
-Related structure data
Related structure data | 5nmeC 5nmfC 5nmgC 5nmhC 5nmkC 2bnuS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 22224.604 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 27440.178 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / #5: 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: 2.55 Å3/Da / Density % sol: 51.72 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium Cacodylate, pH 6.5, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→43.81 Å / Num. obs: 60507 / % possible obs: 98.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.07→2.13 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4492 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BNU Resolution: 2.07→43.81 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 11.417 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.168 / 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: 56.984 Å2
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Refinement step | Cycle: 1 / Resolution: 2.07→43.81 Å
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Refine LS restraints |
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