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Yorodumi- PDB-6u43: Crystal structure of Methanoperedens nitroreducens elongation fac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u43 | ||||||
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Title | Crystal structure of Methanoperedens nitroreducens elongation factor 2 H595N bound to GMPPCP and magnesium (triclinic crystal form) | ||||||
Components | Elongation factor 2 | ||||||
Keywords | TRANSLATION / GTPase / ribosomal translocase / elongation | ||||||
Function / homology | Function and homology information translation elongation factor activity / cytosolic ribosome assembly / ribosome binding / ribonucleoprotein complex / GTPase activity / GTP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Candidatus Methanoperedens nitroreducens (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Fenwick, M.K. / Ealick, S.E. | ||||||
Citation | Journal: Curr Res Struct Biol / Year: 2020 Title: Structural basis of elongation factor 2 switching Authors: Fenwick, M.K. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u43.cif.gz | 351.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u43.ent.gz | 279.9 KB | Display | PDB format |
PDBx/mmJSON format | 6u43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/6u43 ftp://data.pdbj.org/pub/pdb/validation_reports/u4/6u43 | HTTPS FTP |
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-Related structure data
Related structure data | 6u44C 6u45C 1n0vS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 83304.219 Da / Num. of mol.: 1 / Mutation: H595N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Methanoperedens nitroreducens (archaea) Gene: fusA, ANME2D_00299 / Plasmid: pETDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A062V290 |
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-Non-polymers , 5 types, 812 molecules
#2: Chemical | ChemComp-GCP / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 2.4 Å3/Da / Density % sol: 48.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 100 mM HEPES, pH 7.1-7.6, 200 mM ammonium sulfate, 5-15 % (v/v) isopropanol, 16.5-20 % (w/v) polyethylene glycol (PEG) 4000, 9 mM GppCp, and 15 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→56.3 Å / Num. obs: 131884 / % possible obs: 90.3 % / Redundancy: 2.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.4→1.48 Å / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 17221 / CC1/2: 0.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Saccharomyces cerevisiae EF-2 (PDB entry 1N0V) Resolution: 1.4→54.264 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.77 / 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 max: 120.47 Å2 / Biso mean: 37.3984 Å2 / Biso min: 16.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→54.264 Å
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LS refinement shell |
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