+Open data
-Basic information
Entry | Database: PDB / ID: 6med | |||||||||
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Title | Crystal structure of broadly neutralizing antibody HEPC3 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HCV glycoprotein / broadly neutralizing antibodies | |||||||||
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: 2.04 Å | |||||||||
Authors | Flyak, A.I. / Bjorkman, P.J. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Cell Host Microbe / Year: 2018 Title: HCV Broadly Neutralizing Antibodies Use a CDRH3 Disulfide Motif to Recognize an E2 Glycoprotein Site that Can Be Targeted for Vaccine Design. Authors: Flyak, A.I. / Ruiz, S. / Colbert, M.D. / Luong, T. / Crowe Jr., J.E. / Bailey, J.R. / Bjorkman, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6med.cif.gz | 486.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6med.ent.gz | 402.7 KB | Display | PDB format |
PDBx/mmJSON format | 6med.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6med_validation.pdf.gz | 470.4 KB | Display | wwPDB validaton report |
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Full document | 6med_full_validation.pdf.gz | 479.5 KB | Display | |
Data in XML | 6med_validation.xml.gz | 56.6 KB | Display | |
Data in CIF | 6med_validation.cif.gz | 82.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/6med ftp://data.pdbj.org/pub/pdb/validation_reports/me/6med | HTTPS FTP |
-Related structure data
Related structure data | 6meeC 6mefC 6megC 6mehC 6meiC 6mejC 6mekC 4mwfS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Antibody | Mass: 25418.410 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) #2: Antibody | Mass: 23384.883 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) #3: Chemical | ChemComp-SO4 / #4: 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: 3.15 Å3/Da / Density % sol: 60.91 % / Mosaicity: 0.33 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 2.0M ammonium sulfate, 0.3M sodium chloride, and 0.1M sodium cacodylate pH 6.3 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.2 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.04→85 Å / Num. obs: 114454 / % possible obs: 100 % / Redundancy: 4.4 % / Biso Wilson estimate: 32.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.054 / Rrim(I) all: 0.115 / Net I/σ(I): 9.2 / Num. measured all: 502647 / Scaling rejects: 224 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MWF Resolution: 2.04→39.583 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.05 / 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: 195.48 Å2 / Biso mean: 40.6303 Å2 / Biso min: 10.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.04→39.583 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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