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Yorodumi- PDB-5f6i: Crystal Structure of Tier 2 Neutralizing Antibody DH428 from a Rh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f6i | ||||||
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Title | Crystal Structure of Tier 2 Neutralizing Antibody DH428 from a Rhesus Macaque | ||||||
Components |
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Keywords | IMMUNE SYSTEM / FAB FRAGMENT / HIV-1 / ANTIBODY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Macaca mulatta (Rhesus monkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Fera, D. / Harrison, S.C. | ||||||
Citation | Journal: Cell Rep / Year: 2016 Title: Structural Constraints of Vaccine-Induced Tier-2 Autologous HIV Neutralizing Antibodies Targeting the Receptor-Binding Site. Authors: Bradley, T. / Fera, D. / Bhiman, J. / Eslamizar, L. / Lu, X. / Anasti, K. / Zhang, R. / Sutherland, L.L. / Scearce, R.M. / Bowman, C.M. / Stolarchuk, C. / Lloyd, K.E. / Parks, R. / Eaton, A. ...Authors: Bradley, T. / Fera, D. / Bhiman, J. / Eslamizar, L. / Lu, X. / Anasti, K. / Zhang, R. / Sutherland, L.L. / Scearce, R.M. / Bowman, C.M. / Stolarchuk, C. / Lloyd, K.E. / Parks, R. / Eaton, A. / Foulger, A. / Nie, X. / Karim, S.S. / Barnett, S. / Kelsoe, G. / Kepler, T.B. / Alam, S.M. / Montefiori, D.C. / Moody, M.A. / Liao, H.X. / Morris, L. / Santra, S. / Harrison, S.C. / Haynes, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f6i.cif.gz | 175.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f6i.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 5f6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/5f6i ftp://data.pdbj.org/pub/pdb/validation_reports/f6/5f6i | HTTPS FTP |
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-Related structure data
Related structure data | 5f6hC 5f6jC 4qhlS C: citing same article (ref.) S: Starting model for refinement |
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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: Antibody | Mass: 24293.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 22926.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human) |
#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: 3.08 Å3/Da / Density % sol: 60.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 40% PEG 400 and 100 mM sodium citrate, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97916 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→60.36 Å / Num. obs: 22905 / % possible obs: 91.72 % / Redundancy: 4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.43 |
Reflection shell | Resolution: 2.32→2.4 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.2 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: separated Fv and Fc regions of I3.2 Fab from PDB Entry 4QHL Resolution: 2.32→60.356 Å / FOM work R set: 0.8008 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.72 Å2 / Biso mean: 48.6 Å2 / Biso min: 23.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.32→60.356 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 3.0516 Å / Origin y: -18.8539 Å / Origin z: -21.5289 Å
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Refinement TLS group |
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