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Yorodumi- PDB-8ht3: Crystal structure of immunoglobulin new antigen receptor variable... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ht3 | ||||||
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Title | Crystal structure of immunoglobulin new antigen receptor variable domain from Okamejei kenojei | ||||||
Components | New Antigen Receptor variable domain | ||||||
Keywords | IMMUNE SYSTEM / Nanobody / Ray vNAR. | ||||||
Biological species | Okamejei kenojei (ocellate spot skate) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Wen, J. / Li, P. / Bi, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Front Mar Sci / Year: 2023 Title: Identification and characterization of IgNAR and VNAR repertoire from the ocellate spot skate (Okamejei kenojei) Authors: Wen, J. / Gong, J. / Li, P. / Deng, P. / Sun, M. / Wu, Y. / Tian, C. / Wang, H. / Bi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ht3.cif.gz | 34.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ht3.ent.gz | 21.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ht3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/8ht3 ftp://data.pdbj.org/pub/pdb/validation_reports/ht/8ht3 | HTTPS FTP |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11533.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Okamejei kenojei (ocellate spot skate) / Production host: Escherichia coli (E. coli) |
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#2: 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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium sulfate monohydrate/0.1 M Tris pH 8.0/26% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54184 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 14, 2022 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→14.05 Å / Num. obs: 4028 / % possible obs: 98.92 % / Redundancy: 5.2 % / CC1/2: 1 / Rmerge(I) obs: 0.02776 / Rpim(I) all: 0.01293 / Rrim(I) all: 0.03077 / Net I/σ(I): 61.28 |
Reflection shell | Resolution: 2.5→2.589 Å / Num. unique obs: 1866 / CC1/2: 0.997 / % possible all: 97.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→14.05 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 0 / Phase error: 22.03 / 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 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→14.05 Å
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Refine LS restraints |
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LS refinement shell |
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