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Yorodumi- PDB-4qhy: The structure of aIF2gamma subunit H20F/D152A from archaeon Sulfo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qhy | ||||||
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Title | The structure of aIF2gamma subunit H20F/D152A from archaeon Sulfolobus solfataricus complexed with GDPCP | ||||||
Components | Translation initiation factor 2 subunit gammaInitiation factor | ||||||
Keywords | TRANSLATION / 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: 3.29 Å | ||||||
Authors | Kravchenko, O.V. / Nikonov, O.S. / Arhipova, V.I. / Stolboushkina, E.A. / Gabdulkhakov, A.G. / Nikulin, A.D. / Garber, M.B. / Nikonov, S.V. | ||||||
Citation | Journal: To be Published Title: Binding mRNA on the archaeal translation initiation factor 2 gamma-subunit Authors: Kravchenko, O.V. / Nikonov, O.S. / Arhipova, V.I. / Stolboushkina, E.A. / Gabdulkhakov, A.G. / Nikulin, A.D. / Garber, M.B. / Nikonov, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qhy.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qhy.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/4qhy ftp://data.pdbj.org/pub/pdb/validation_reports/qh/4qhy | HTTPS FTP |
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-Related structure data
Related structure data | 4nbsS 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: 45814.246 Da / Num. of mol.: 1 / Mutation: H20F, D152A 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 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q980A5 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GCP / |
#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: 6.01 Å3/Da / Density % sol: 79.54 % |
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 4M sodium formiate, 0.1M sodium cacodylate, 1% MMEPEG 5K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K |
-Data collection
Diffraction | Mean temperature: 100 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: May 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 3.29→41.97 Å / Num. all: 16879 / Num. obs: 16853 / % possible obs: 99.84 % / Rmerge(I) obs: 0.0924 / Net I/σ(I): 10.89 |
Reflection shell | Resolution: 3.29→3.39 Å / Rmerge(I) obs: 0.4513 / Mean I/σ(I) obs: 1.87 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 4NBS Resolution: 3.29→41.969 Å / SU ML: 0.44 / Isotropic thermal model: 52 / σ(F): 1.33 / Phase error: 30.65 / 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: 3.29→41.969 Å
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Refine LS restraints |
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LS refinement shell |
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