+Open data
-Basic information
Entry | Database: PDB / ID: 8oul | ||||||
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Title | Arf GTPase from the asgard Hodarchaea : HodArfR1 bound to GDP | ||||||
Components | Arf GTPase | ||||||
Keywords | SIGNALING PROTEIN / GTPASE / GDP / ARF FAMILY / ASGARD ARCHAEA | ||||||
Function / homology | GUANOSINE-5'-DIPHOSPHATE Function and homology information | ||||||
Biological species | Asgard group (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Menetrey, J. / Jackson, C. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: Arf Family GTPases are present in Asgard archaea Authors: Menetrey, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oul.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oul.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 8oul.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/8oul ftp://data.pdbj.org/pub/pdb/validation_reports/ou/8oul | HTTPS FTP |
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-Related structure data
Related structure data | 8oukC 8oumC 8ounC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: Protein | Mass: 21796.906 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Asgard group (archaea) / Gene: OLS23013 / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.07 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→70.3 Å / Num. obs: 10627 / % possible obs: 99.9 % / Redundancy: 18.3 % / CC1/2: 0.994 / Rrim(I) all: 0.048 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 3.1→3.29 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1678 / CC1/2: 0.063 / Rrim(I) all: 0.269 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.47 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.864 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.635
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Displacement parameters | Biso mean: 60.99 Å2
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Refine analyze | Luzzati coordinate error obs: 0.45 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→48.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 23
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