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Yorodumi- PDB-2pmd: The structures of aIF2gamma subunit from the archaeon Sulfolobus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pmd | ||||||
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Title | The structures of aIF2gamma subunit from the archaeon Sulfolobus solfataricus in the GDP-bound form. | ||||||
Components | Translation initiation factor 2 gamma subunit | ||||||
Keywords | TRANSLATION / aIF2 / Initiation factor 2 gamma subunit / Initiation of the translation / nucleotide binding / GDPNP / GDP / pyrophosphate | ||||||
Function / homology | Function and homology information protein-synthesizing GTPase / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor activity / tRNA binding / GTPase activity / GTP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Nikonov, O.S. / Stolboushkina, E.A. / Nikulin, A.D. / Hasenohrl, D. / Blaesi, U. / Manstein, D.J. / Fedorov, R.V. / Garber, M.B. / Nikonov, S.V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: New Insights into the Interactions of the Translation Initiation Factor 2 from Archaea with Guanine Nucleotides and Initiator tRNA. Authors: Nikonov, O. / Stolboushkina, E. / Nikulin, A. / Hasenohrl, D. / Blasi, U. / Manstein, D.J. / Fedorov, R. / Garber, M. / Nikonov, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pmd.cif.gz | 178.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pmd.ent.gz | 140.9 KB | Display | PDB format |
PDBx/mmJSON format | 2pmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/2pmd ftp://data.pdbj.org/pub/pdb/validation_reports/pm/2pmd | HTTPS FTP |
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-Related structure data
Related structure data | 2plfC 2ahoS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45849.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2g / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q980A5 #2: Chemical | #3: Chemical | ChemComp-GNP / | #4: Chemical | ChemComp-PPV / #5: 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: 4.71 Å3/Da / Density % sol: 73.89 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: natrium malonate dihydrate, glycine,CdCl2, GDPNP., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→19.85 Å / Num. all: 48398 / Num. obs: 45642 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.076 |
Reflection shell | Resolution: 2.65→2.81 Å / Mean I/σ(I) obs: 2.58 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: gamma subunit form the aIF2 alpha-gamma dimer. PDB ENTRY: 2AHO Resolution: 2.65→19.85 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2.65→19.85 Å
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