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Yorodumi- PDB-2d74: Crystal structure of translation initiation factor aIF2betagamma ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d74 | ||||||
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Title | Crystal structure of translation initiation factor aIF2betagamma heterodimer | ||||||
Components |
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Keywords | TRANSLATION / PROTEIN COMPLEX | ||||||
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 / translation initiation factor activity / tRNA binding ...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 / translation initiation factor activity / tRNA binding / GTPase activity / mRNA binding / GTP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Sokabe, M. / Yao, M. / Sakai, N. / Toya, S. / Tanaka, I. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: Structure of archaeal translational initiation factor 2 betagamma-GDP reveals significant conformational change of the beta-subunit and switch 1 region. Authors: Sokabe, M. / Yao, M. / Sakai, N. / Toya, S. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d74.cif.gz | 122.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d74.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 2d74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d74_validation.pdf.gz | 443.9 KB | Display | wwPDB validaton report |
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Full document | 2d74_full_validation.pdf.gz | 491.4 KB | Display | |
Data in XML | 2d74_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 2d74_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/2d74 ftp://data.pdbj.org/pub/pdb/validation_reports/d7/2d74 | HTTPS FTP |
-Related structure data
Related structure data | 2dcuC 1kk1S 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: 46229.484 Da / Num. of mol.: 1 / Mutation: G236D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1717 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codonplus-RIL / References: UniProt: Q8U082 | ||
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#2: Protein | Mass: 17332.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF0481 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codonplus-RIL / References: UniProt: Q8U3I5 | ||
#3: Chemical | #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: 2.01 Å3/Da / Density % sol: 38.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 8000, 0.1M tris-HCl, 0.2M magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 13070 / Num. obs: 12894 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.2 / Redundancy: 5.3 % / Biso Wilson estimate: 62.02 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2 / Num. unique all: 1166 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KK1 Resolution: 2.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 61.94 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å
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