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Yorodumi- PDB-8r2c: Crystal structure of the Vint domain from Tetrahymena thermophila -
+Open data
-Basic information
Entry | Database: PDB / ID: 8r2c | |||||||||||||||||||||
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Title | Crystal structure of the Vint domain from Tetrahymena thermophila | |||||||||||||||||||||
Components | von willebrand factor type A (VWA) domain was originally protein | |||||||||||||||||||||
Keywords | UNKNOWN FUNCTION / hedgehog / Vint / intein / HINT / von Willebrand factor type A domain | |||||||||||||||||||||
Function / homology | Function and homology information | |||||||||||||||||||||
Biological species | Tetrahymena thermophila SB210 (eukaryote) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||||||||||||||
Authors | Iwai, H. / Beyer, H.M. / Johannson, J.E. / Li, M. / Wlodawer, A. | |||||||||||||||||||||
Funding support | Finland, Denmark, United States, 6items
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Citation | Journal: Febs Lett. / Year: 2024 Title: The three-dimensional structure of the Vint domain from Tetrahymena thermophila suggests a ligand-regulated cleavage mechanism by the HINT fold. Authors: Iwai, H. / Beyer, H.M. / Johansson, J.E.M. / Li, M. / Wlodawer, A. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r2c.cif.gz | 95 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r2c.ent.gz | 59.8 KB | Display | PDB format |
PDBx/mmJSON format | 8r2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/8r2c ftp://data.pdbj.org/pub/pdb/validation_reports/r2/8r2c | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 19149.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena thermophila SB210 (eukaryote) Gene: TTHERM_00471620 / Plasmid: pBHRSF123 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: I7M030 | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.5 Å3/Da / Density % sol: 50.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 100 nL concentrated protein (14.6 mg/mL) with 100 nL mother liquid (2% PEG 400, 2.4 M ammonium sulfate, 0.1 M HEPES) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 18445 / % possible obs: 97.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 20.63 Å2 / Rmerge(I) obs: 0.0157 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.8→1.864 Å / Rmerge(I) obs: 0.1109 / Num. unique obs: 1737 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43 Å / SU ML: 0.2045 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4094 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 27.44 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→43 Å
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Refine LS restraints |
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LS refinement shell |
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