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Yorodumi- PDB-2plf: The structure of aIF2gamma subunit from the archaeon Sulfolobus s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2plf | ||||||
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Title | The structure of aIF2gamma subunit from the archaeon Sulfolobus solfataricus in the nucleotide-free form. | ||||||
Components | Translation initiation factor 2 gamma subunit | ||||||
Keywords | TRANSLATION / aIF2 / Initiation factor 2 gamma subunit / Initiation of the translation / nucleotide binding | ||||||
Function / homology | Function and homology information selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / selenocysteine insertion sequence binding / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor activity / tRNA binding / GTPase activity / GTP binding ...selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / selenocysteine insertion sequence binding / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor activity / tRNA binding / GTPase activity / GTP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 2plf.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2plf.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 2plf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2plf_validation.pdf.gz | 427.3 KB | Display | wwPDB validaton report |
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Full document | 2plf_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 2plf_validation.xml.gz | 20 KB | Display | |
Data in CIF | 2plf_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pl/2plf ftp://data.pdbj.org/pub/pdb/validation_reports/pl/2plf | HTTPS FTP |
-Related structure data
Related structure data | 2pmdC 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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Unit cell |
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-Components
#1: Protein | Mass: 45718.035 Da / Num. of mol.: 1 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.72 Å3/Da / Density % sol: 73.96 % |
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Crystal grow | Temperature: 295 K / pH: 4.5 Details: natrium malonate dihydrate, glycine,CdCl2., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 4.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. obs: 19573 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rmerge(I) obs: 0.105 |
Reflection shell | Resolution: 2.9→3 Å / % possible all: 97 |
-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: 2.9→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 58.85 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
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