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- PDB-4rcy: Structure of aIF2-gamma D19A variant from Sulfolobus solfataricus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4rcy | ||||||
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Title | Structure of aIF2-gamma D19A variant from Sulfolobus solfataricus bound to GTP | ||||||
![]() | Translation initiation factor 2 subunit gamma | ||||||
![]() | TRANSLATION / Rossmann fold | ||||||
Function / homology | ![]() protein-synthesizing GTPase / formation of translation preinitiation complex / translation elongation factor activity / membrane scission GTPase motor activity / translation initiation factor activity / tRNA binding / GTP binding / metal ion binding 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 | ![]() | 192.4 KB | Display | ![]() |
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PDB format | ![]() | 151.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 31 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4rczC ![]() 4rd0C ![]() 4rd1C ![]() 4rd2C ![]() 4rd3C ![]() 4rd4SC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45805.219 Da / Num. of mol.: 1 / Fragment: aIF2-gamma subunit / Mutation: D19A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 362 molecules 








#2: Chemical | ChemComp-GTP / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GDP / |
#5: Chemical | ChemComp-MPD / ( |
#6: Water | ChemComp-HOH / |
-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 70%MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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: 1.64→46.25 Å / Num. all: 50087 / Num. obs: 50087 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.12 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 15.39 |
Reflection shell | Resolution: 1.64→1.74 Å / Redundancy: 6.87 % / Rmerge(I) obs: 0.728 / Mean I/σ(I) obs: 2.64 / Num. unique all: 7829 / Rsym value: 0.728 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4RD4 Resolution: 1.65→46.252 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 18.7 / 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: 1.65→46.252 Å
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Refine LS restraints |
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LS refinement shell |
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