+Open data
-Basic information
Entry | Database: PDB / ID: 8f8v | ||||||||||||
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Title | Crystal structure of Nb.X0 | ||||||||||||
Components | Nb.X0 | ||||||||||||
Keywords | IMMUNE SYSTEM / nanobody / glycobiology / immunoglobulin | ||||||||||||
Biological species | Camelidae mixed library (mammal) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||||||||
Authors | Goldgur, Y. / Ravetch, J. / Gupta, A. / Kao, K. / Andi, B. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2023 Title: Mechanism of glycoform specificity and in vivo protection by an anti-afucosylated IgG nanobody. Authors: Gupta, A. / Kao, K.S. / Yamin, R. / Oren, D.A. / Goldgur, Y. / Du, J. / Lollar, P. / Sundberg, E.J. / Ravetch, J.V. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f8v.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f8v.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 8f8v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/8f8v ftp://data.pdbj.org/pub/pdb/validation_reports/f8/8f8v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 13105.541 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelidae mixed library (mammal) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) #2: 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: 2.97 Å3/Da / Density % sol: 58.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 % v/v PPGBA 400 + 15 % v/v 1-Propanol. Cryopreserved with 40% ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50.32 Å / Num. obs: 27855 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.045 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Num. unique obs: 1313 / CC1/2: 0.708 / Rpim(I) all: 0.339 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→50.32 Å / SU ML: 0.1849 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7857 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.99 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→50.32 Å
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Refine LS restraints |
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LS refinement shell |
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