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- PDB-1kjz: Structure of the large gamma subunit of initiation factor eIF2 fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kjz | ||||||
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Title | Structure of the large gamma subunit of initiation factor eIF2 from Pyrococcus abyssi-G235D mutant | ||||||
![]() | eIF2gamma | ||||||
![]() | TRANSLATION / initiation of translation | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Schmitt, E. / Blanquet, S. / Mechulam, Y. | ||||||
![]() | ![]() Title: The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors. Authors: Schmitt, E. / Blanquet, S. / Mechulam, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.5 KB | Display | ![]() |
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PDB format | ![]() | 70.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 369.9 KB | Display | ![]() |
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Full document | ![]() | 373.8 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 15.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 44920.000 Da / Num. of mol.: 1 / Mutation: G235D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.51 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: peg8000, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.7 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 31, 2001 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→34 Å / Num. all: 40474 / Num. obs: 40474 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 30.3 Å2 / Rsym value: 0.049 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2309 / Rsym value: 0.324 / % possible all: 98.4 |
Reflection | *PLUS Lowest resolution: 34 Å / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 98.4 % / Rmerge(I) obs: 0.324 |
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Processing
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Refinement | Method to determine structure: ![]() ![]()
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.85→34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.86 Å /
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.225 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.225 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.38 / Rfactor Rwork: 0.281 |