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Yorodumi- PDB-4m0l: Gamma subunit of the translation initiation factor 2 from Sulfolo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m0l | |||||||||
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Title | Gamma subunit of the translation initiation factor 2 from Sulfolobus solfataricus complexed with GDP | |||||||||
Components | Translation initiation factor 2 subunit gammaInitiation factor | |||||||||
Keywords | TRANSLATION / aIF2 / aIF2 gamma subunit / G-protein / translation initiation / protein biosynthesis / RNA-binding / GTP-binding / nucleotide-binding | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Nikonov, O.S. / Stolboushkina, E.A. / Arkhipova, V.I. / Gabdulkhakov, A.G. / Nikulin, A.D. / Lazopulo, A.M. / Lazopulo, S.M. / Garber, M.B. / Nikonov, S.V. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Conformational transitions in the gamma subunit of the archaeal translation initiation factor 2. Authors: Nikonov, O. / Stolboushkina, E. / Arkhipova, V. / Kravchenko, O. / Nikonov, S. / Garber, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m0l.cif.gz | 493.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m0l.ent.gz | 409 KB | Display | PDB format |
PDBx/mmJSON format | 4m0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/4m0l ftp://data.pdbj.org/pub/pdb/validation_reports/m0/4m0l | HTTPS FTP |
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-Related structure data
Related structure data | 4m2lC 4m4sC 4m53C 2qn6S 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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2 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 45849.230 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: eif2g / Production host: Escherichia coli (E. coli) / References: UniProt: Q980A5 #2: Chemical | ChemComp-GDP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-PO4 / | #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: 2.6 Å3/Da / Density % sol: 52.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM Tris-HCl, 50mM NaCl, 50mM KCl, 5mM MgCl2, 5mM 2-mercaptoethanol, 90mM KBr, 7.5% PEG 4000, 0.5mM GTP, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jan 18, 2012 |
Radiation | Monochromator: Montel 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19.811 Å / Num. all: 84101 / Num. obs: 84101 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.27 % / Biso Wilson estimate: 59.6 Å2 / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.4437 / Mean I/σ(I) obs: 1.93 / Num. unique all: 8374 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QN6 Resolution: 2.6→19.811 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 31.8 / 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: 170.31 Å2 / Biso mean: 54.6 Å2 / Biso min: 18.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→19.811 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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