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Yorodumi- PDB-4rd6: Structure of aIF2-gamma from Sulfolobus solfataricus bound to GDP -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rd6 | ||||||
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Title | Structure of aIF2-gamma from Sulfolobus solfataricus bound to GDP | ||||||
Components | Translation initiation factor 2 subunit gammaInitiation factor | ||||||
Keywords | TRANSLATION / Rossmann fold | ||||||
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: 1.944 Å | ||||||
Authors | Dubiez, E. / Aleksandrov, A. / Lazennec-Schurdevin, C. / Mechulam, Y. / Schmitt, E. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2. Authors: Dubiez, E. / Aleksandrov, A. / Lazennec-Schurdevin, C. / Mechulam, Y. / Schmitt, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rd6.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rd6.ent.gz | 76.8 KB | Display | PDB format |
PDBx/mmJSON format | 4rd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/4rd6 ftp://data.pdbj.org/pub/pdb/validation_reports/rd/4rd6 | HTTPS FTP |
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-Related structure data
Related structure data | 4rcyC 4rczC 4rd0C 4rd1C 4rd2C 4rd3C 4rd4C 2ahoS C: citing same article (ref.) S: Starting model for refinement |
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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: 45849.230 Da / Num. of mol.: 1 / Fragment: aIF2-gamma subunit Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: eif2g, SSO0412, sulfolobus solfataricus / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 rosetta / References: UniProt: Q980A5 |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MG / |
#4: 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: 2.65 Å3/Da / Density % sol: 53.66 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 60%MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å |
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Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→48.82 Å / Num. all: 36258 / Num. obs: 36258 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.39 % / Biso Wilson estimate: 27.09 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 11.95 |
Reflection shell | Resolution: 1.94→2.06 Å / Redundancy: 4.44 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 1.95 / Num. unique all: 5648 / Rsym value: 0.755 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AHO Resolution: 1.944→48.817 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.39 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.944→48.817 Å
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Refine LS restraints |
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LS refinement shell |
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