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Yorodumi- PDB-5ecy: Structure of the Shigella flexneri VapC mutant D98N crystal form 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ecy | ||||||
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Title | Structure of the Shigella flexneri VapC mutant D98N crystal form 2 | ||||||
Components | tRNA(fMet)-specific endonuclease VapC | ||||||
Keywords | HYDROLASE / Toxin / PIN-domain | ||||||
Function / homology | Function and homology information RNA nuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding Similarity search - Function | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Xu, K. / Dedic, E. / Brodersen, D.E. | ||||||
Funding support | China, 1items
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Citation | Journal: to be published Title: Structural analysis on the active site architecture of an activated VapC toxin from Shigella flexneri Authors: Xu, K. / Dedic, E. / Brodersen, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ecy.cif.gz | 236.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ecy.ent.gz | 197.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ecy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/5ecy ftp://data.pdbj.org/pub/pdb/validation_reports/ec/5ecy | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 15663.973 Da / Num. of mol.: 8 / Mutation: D98N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: vapC, mvpA, stborf2, CP0245 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O06662, 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.46 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.8 M sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.67 Å / Num. obs: 8429 / % possible obs: 100 % / Redundancy: 9.76 % / Net I/σ(I): 8.71 |
-Processing
Software |
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Refinement | Resolution: 2→47.67 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.65 / Phase error: 20.08 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→47.67 Å
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Refine LS restraints |
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LS refinement shell |
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