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Yorodumi- PDB-5ioo: Accommodation of massive sequence variation in Nanoarchaeota by t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ioo | ||||||
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Title | Accommodation of massive sequence variation in Nanoarchaeota by the C-type lectin fold | ||||||
Components | AvpA | ||||||
Keywords | UNKNOWN FUNCTION / Massive Protein Diversification / CLec fold / Archaea / SUGAR BINDING PROTEIN | ||||||
Function / homology | AvpA Function and homology information | ||||||
Biological species | Nanoarchaeota archaeon JGI OTU-1 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.521 Å | ||||||
Authors | Handa, S. / Paul, B. / Miller, J. / Valentine, D. / Ghosh, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Bmc Struct.Biol. / Year: 2016 Title: Conservation of the C-type lectin fold for accommodating massive sequence variation in archaeal diversity-generating retroelements. Authors: Handa, S. / Paul, B.G. / Miller, J.F. / Valentine, D.L. / Ghosh, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ioo.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ioo.ent.gz | 76.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ioo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/5ioo ftp://data.pdbj.org/pub/pdb/validation_reports/io/5ioo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28703.021 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nanoarchaeota archaeon JGI OTU-1 (archaea) Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: A0A1L1QK08*PLUS #2: Chemical | ChemComp-MG / #3: 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: 3.09 Å3/Da / Density % sol: 60.19 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES (pH 7.5), 50 mM magnesium chloride, 30% PEG monoethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→71.999 Å / Num. obs: 46142 / % possible obs: 99.8 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.25 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.52→2.61 Å / Rmerge(I) obs: 1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.521→71.999 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.521→71.999 Å
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Refine LS restraints |
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LS refinement shell |
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