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Yorodumi- PDB-1kk1: Structure of the large gamma subunit of initiation factor eIF2 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kk1 | ||||||
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Title | Structure of the large gamma subunit of initiation factor eIF2 from Pyrococcus abyssi-G235D mutant complexed with GDPNP-Mg2+ | ||||||
Components | eIF2gamma | ||||||
Keywords | TRANSLATION / initiation of translation | ||||||
Function / homology | Function and homology information 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 | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / rigid body minimization / Resolution: 1.8 Å | ||||||
Authors | Schmitt, E. / Blanquet, S. / Mechulam, Y. | ||||||
Citation | Journal: EMBO J. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kk1.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kk1.ent.gz | 71.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kk1_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 1kk1_full_validation.pdf.gz | 466.6 KB | Display | |
Data in XML | 1kk1_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1kk1_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/1kk1 ftp://data.pdbj.org/pub/pdb/validation_reports/kk/1kk1 | HTTPS FTP |
-Related structure data
Related structure data | 1kjzSC 1kk0C 1kk2C 1kk3C 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: 44920.000 Da / Num. of mol.: 1 / Mutation: G235D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9V1G0 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GNP / |
#5: 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: 2.7 Å3/Da / Density % sol: 54.37 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: peg8000, 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 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: 1.8→45 Å / Num. all: 44188 / Num. obs: 44154 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.043 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 3.7 % / Num. unique all: 3255 / Rsym value: 0.304 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.304 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body minimization Starting model: 1kjz Resolution: 1.8→45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.81 Å
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.219 / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.219 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.3848 / Rfactor Rwork: 0.2899 |