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Yorodumi- PDB-2qn6: Structure of an archaeal heterotrimeric initiation factor 2 revea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qn6 | ||||||
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Title | Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states | ||||||
Components | (Translation initiation factor 2 ...) x 3 | ||||||
Keywords | TRANSLATION / initiation of translation / GTP-binding / Initiation factor / Nucleotide-binding / Protein biosynthesis / RNA-binding | ||||||
Function / homology | Function and homology information selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor binding / translational initiation / translation initiation factor activity ...selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor binding / translational initiation / translation initiation factor activity / ribosome binding / tRNA binding / GTPase activity / mRNA binding / GTP binding / RNA binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Mechulam, Y. / Yatime, L. / Blanquet, S. / Schmitt, E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states. Authors: Yatime, L. / Mechulam, Y. / Blanquet, S. / Schmitt, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qn6.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qn6.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 2qn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qn6_validation.pdf.gz | 798.7 KB | Display | wwPDB validaton report |
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Full document | 2qn6_full_validation.pdf.gz | 814.2 KB | Display | |
Data in XML | 2qn6_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 2qn6_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/2qn6 ftp://data.pdbj.org/pub/pdb/validation_reports/qn/2qn6 | HTTPS FTP |
-Related structure data
Related structure data | 2qmuC 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
-Translation initiation factor 2 ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 45718.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: eif2g / Plasmid: pET3alpa / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-De3 / References: UniProt: Q980A5 |
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#2: Protein | Mass: 10440.162 Da / Num. of mol.: 1 / Fragment: domain 3, res 175 to 265 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: eif2a / Plasmid: pET3alpa / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-De3 / References: UniProt: Q97Z79 |
#3: Protein/peptide | Mass: 2190.494 Da / Num. of mol.: 1 / Fragment: helix 1, res 2 to 19 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: eif2b / Plasmid: pET3alpa / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-De3 / References: UniProt: Q97W59 |
-Non-polymers , 3 types, 255 molecules
#4: Chemical | ChemComp-MG / |
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#5: Chemical | ChemComp-GDP / |
#6: 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: 2.66 Å3/Da / Density % sol: 53.72 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 16 % PEG 3350; 0.1 M Magnesium formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 6, 2006 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→100 Å / Num. all: 31835 / Num. obs: 31835 / % possible obs: 95.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 39.6 Å2 / Rsym value: 0.052 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4678 / Rsym value: 0.32 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: chain A from 2aho Resolution: 2.15→100 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: 46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.17 Å
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