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Yorodumi- PDB-1n0u: Crystal structure of yeast elongation factor 2 in complex with so... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n0u | ||||||
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Title | Crystal structure of yeast elongation factor 2 in complex with sordarin | ||||||
Components | Elongation factor 2 | ||||||
Keywords | TRANSLATION / G-protein / cis-proline | ||||||
Function / homology | Function and homology information Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / maintenance of translational fidelity / ribosome binding ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / maintenance of translational fidelity / ribosome binding / protein-folding chaperone binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å | ||||||
Authors | Joergensen, R. / Ortiz, P.A. / Carr-Schmid, A. / Nissen, P. / Kinzy, T.G. / Andersen, G.R. | ||||||
Citation | Journal: Nat. Struct. Biol. / Year: 2003 Title: Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase. Authors: Jorgensen, R. / Ortiz, P.A. / Carr-Schmid, A. / Nissen, P. / Kinzy, T.G. / Andersen, G.R. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Purification and Crystallization of the yeast elongation factor eEF2 Authors: Joergensen, R. / Carr-Schmid, A. / Ortiz, P.A. / Kinzy, T.G. / Andersen, G.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n0u.cif.gz | 182.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n0u.ent.gz | 142.9 KB | Display | PDB format |
PDBx/mmJSON format | 1n0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n0u_validation.pdf.gz | 756.2 KB | Display | wwPDB validaton report |
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Full document | 1n0u_full_validation.pdf.gz | 785.4 KB | Display | |
Data in XML | 1n0u_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 1n0u_validation.cif.gz | 57.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/1n0u ftp://data.pdbj.org/pub/pdb/validation_reports/n0/1n0u | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the molecule functions as a monomer |
-Components
#1: Protein | Mass: 93407.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32324 |
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#2: Chemical | ChemComp-SO1 / [ |
#3: 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: 3.15 Å3/Da / Density % sol: 60.97 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.2 Details: PEG8K, ethylene glycol, Hepes, KCl, magnesium chloride, edta, dtt, gdp, pH 7.2, VAPOR DIFFUSION, temperature 20K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, sitting dropDetails: Joergensen, R., (2002) Acta Crystallogr., Sect.D, 58, 712. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.811 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.811 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→31 Å / Num. all: 67778 / Num. obs: 66427 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.2 Å2 / Rsym value: 0.062 / Net I/σ(I): 34.3 |
Reflection shell | Resolution: 2.12→2.23 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.7 / % possible all: 94.1 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 98.3 % / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 94 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.12→31 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.12→31 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / Num. reflection obs: 64474 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.234 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.3 |