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- PDB-4rd3: Structure of aIF2-gamma H97A variant from Sulfolobus solfataricus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rd3 | ||||||
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Title | Structure of aIF2-gamma H97A variant from Sulfolobus solfataricus bound to GDP and Pi | ||||||
![]() | 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 | ![]() | 186.2 KB | Display | ![]() |
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PDB format | ![]() | 145.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rcyC ![]() 4rczC ![]() 4rd0C ![]() 4rd1SC ![]() 4rd2C ![]() 4rd4C ![]() 4rd6C 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: 45782.160 Da / Num. of mol.: 1 / Fragment: aIF2-gamma subunit / Mutation: H97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-PO4 / | ||||
#3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.24 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 60%MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2013 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→46.36 Å / Num. all: 46188 / Num. obs: 46188 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.44 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 12.85 |
Reflection shell | Resolution: 1.68→1.78 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.74 / Num. unique all: 6968 / Rsym value: 0.56 / % possible all: 91.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RD1 Resolution: 1.69→46.363 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.05 / 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: 1.69→46.363 Å
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Refine LS restraints |
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LS refinement shell |
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