+Open data
-Basic information
Entry | Database: PDB / ID: 5aoy | ||||||
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Title | Structure of mouse Endonuclease V | ||||||
Components | ENDONUCLEASE V | ||||||
Keywords | HYDROLASE / ENDONUCLEASE / ENDONUCLEASE V | ||||||
Function / homology | Function and homology information RNA endonuclease activity, producing 5'-phosphomonoesters / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / cytoplasmic stress granule / single-stranded RNA binding / DNA repair / nucleolus / magnesium ion binding / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Vik, E.S. / Nawaz, M.S. / Ronander, M.E. / Solvoll, A.M. / Strom-Andersen, P. / Bjoras, M. / Alseth, I. / Dalhus, B. | ||||||
Citation | Journal: Sci.Rep. / Year: 2016 Title: Crystal Structure and Md Simulation of Mouse Endov Reveal Wedge Motif Plasticity in This Inosine-Specific Endonuclease. Authors: Nawaz, M.S. / Vik, E.S. / Ronander, M.E. / Solvoll, A.M. / Blicher, P. / Bjoras, M. / Alseth, I. / Dalhus, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aoy.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aoy.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 5aoy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/5aoy ftp://data.pdbj.org/pub/pdb/validation_reports/ao/5aoy | HTTPS FTP |
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-Related structure data
Related structure data | 4b20S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27706.111 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PETM41 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS RIPL References: UniProt: Q8C9A2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters |
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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: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→32.47 Å / Num. obs: 32035 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4B20 Resolution: 1.75→32.474 Å / SU ML: 0.1 / σ(F): 0.03 / Phase error: 16.81 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→32.474 Å
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Refine LS restraints |
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LS refinement shell |
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