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- PDB-4rd6: Structure of aIF2-gamma from Sulfolobus solfataricus bound to GDP -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rd6 | ||||||
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Title | Structure of aIF2-gamma from Sulfolobus solfataricus bound to GDP | ||||||
![]() | Translation initiation factor 2 subunit gamma | ||||||
![]() | TRANSLATION / Rossmann fold | ||||||
Function / homology | ![]() selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / selenocysteine insertion sequence binding / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor activity / tRNA binding / GTPase activity / GTP binding ...selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / selenocysteine insertion sequence binding / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor activity / tRNA binding / GTPase activity / GTP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dubiez, E. / Aleksandrov, A. / Lazennec-Schurdevin, C. / Mechulam, Y. / Schmitt, E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.5 KB | Display | ![]() |
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PDB format | ![]() | 76.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 800 KB | Display | ![]() |
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Full document | ![]() | 803.1 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rcyC ![]() 4rczC ![]() 4rd0C ![]() 4rd1C ![]() 4rd2C ![]() 4rd3C ![]() 4rd4C ![]() 2ahoS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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