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- PDB-5ecd: Structure of the Shigella flexneri VapC mutant D98N crystal form 1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ecd | |||||||||
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Title | Structure of the Shigella flexneri VapC mutant D98N crystal form 1 | |||||||||
![]() | tRNA(fMet)-specific endonuclease VapC | |||||||||
![]() | HYDROLASE / Toxin / PIN-domain / Hepes | |||||||||
Function / homology | ![]() RNA nuclease activity / endonuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Xu, K. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri. Authors: Xu, K. / Dedic, E. / Brodersen, D.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.9 KB | Display | ![]() |
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PDB format | ![]() | 102.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.3 KB | Display | ![]() |
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Full document | ![]() | 446.9 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 22.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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.: 2 / Mutation: D98N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O06662, Hydrolases; Acting on ester bonds #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.53 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 3350, 0.2M sodium malonate, NaOH-Hepes, pH7.0 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.75→25.41 Å / Num. obs: 2917 / % possible obs: 99.9 % / Redundancy: 3.84 % / Net I/σ(I): 15.69 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.75→25.41 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -24.1057 Å / Origin y: -7.8213 Å / Origin z: 20.3833 Å
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Refinement TLS group | Selection details: all |