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Yorodumi- PDB-6u50: Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u50 | ||||||||||||
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Title | Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB) | ||||||||||||
Components | Anti-Sudan ebolavirus Nucleoprotein Single Domain Antibody Sudan B (SB) | ||||||||||||
Keywords | IMMUNE SYSTEM / Antibody / nanobody / Ebola / filovirus | ||||||||||||
Biological species | Lama glama (llama) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | Taylor, A.B. / Sherwood, L.J. / Hart, P.J. / Hayhurst, A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2019 Title: Paratope Duality and Gullying are Among the Atypical Recognition Mechanisms Used by a Trio of Nanobodies to Differentiate Ebolavirus Nucleoproteins. Authors: Sherwood, L.J. / Taylor, A.B. / Hart, P.J. / Hayhurst, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u50.cif.gz | 64.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u50.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 6u50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/6u50 ftp://data.pdbj.org/pub/pdb/validation_reports/u5/6u50 | HTTPS FTP |
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-Related structure data
Related structure data | 6u51SC 6u52C 6u53C 6u54C 6u55C 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: Antibody | Mass: 13056.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Semi-synthetic single pot library Nomad 1 based upon Lama glama Source: (gene. exp.) Lama glama (llama) / Plasmid: pecan219 / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-MPD / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-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: 46.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 37.5% precipitant mix (2-methyl-2,4-pentanediol, polyethylene glycol [PEG] 1000, PEG 3350), 0.1 M amino acids mix (glutamate, alanine, glycine, lysine, serine), 0.1 M HEPES/MOPS pH 7.5 ...Details: 37.5% precipitant mix (2-methyl-2,4-pentanediol, polyethylene glycol [PEG] 1000, PEG 3350), 0.1 M amino acids mix (glutamate, alanine, glycine, lysine, serine), 0.1 M HEPES/MOPS pH 7.5 {Molecular Dimensions Morpheus HT-96 Condition H8} |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 31, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→42.69 Å / Num. obs: 15558 / % possible obs: 99.4 % / Redundancy: 9.7 % / Biso Wilson estimate: 17.62 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.045 / Rrim(I) all: 0.142 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.6→1.68 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2140 / CC1/2: 0.367 / Rpim(I) all: 0.605 / Rrim(I) all: 1.82 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6U51 Resolution: 1.6→37.27 Å / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.2285
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→37.27 Å
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Refine LS restraints |
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LS refinement shell |
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