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Yorodumi- PDB-3oby: Crystal structure of Archaeoglobus fulgidus Pelota reveals inter-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3oby | ||||||
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Title | Crystal structure of Archaeoglobus fulgidus Pelota reveals inter-domain structural plasticity | ||||||
Components | Protein pelota homolog | ||||||
Keywords | HYDROLASE / Sm fold | ||||||
Function / homology | Function and homology information RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Lee, H.H. / Jang, J.Y. / Yoon, H.-J. / Kim, S.J. / Suh, S.W. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2010 Title: Crystal structures of two archaeal Pelotas reveal inter-domain structural plasticity Authors: Lee, H.H. / Jang, J.Y. / Yoon, H.-J. / Kim, S.J. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oby.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oby.ent.gz | 112.1 KB | Display | PDB format |
PDBx/mmJSON format | 3oby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/3oby ftp://data.pdbj.org/pub/pdb/validation_reports/ob/3oby | 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
#1: Protein | Mass: 40273.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) References: UniProt: O29421, Hydrolases; Acting on ester bonds #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.56 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100mM imidazole pH 6.0, 200mM MgCl2, 8%(w/v) polyethylene glycol 8000, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.9→15 Å / Num. all: 18733 / Num. obs: 17950 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||||||||
Reflection shell | Resolution: 2.9→3 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 37.5956 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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