[English] 日本語
Yorodumi- PDB-6i5m: Gamma subunit of the translation initiation factor 2 from Sulfolo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i5m | ||||||
---|---|---|---|---|---|---|---|
Title | Gamma subunit of the translation initiation factor 2 from Sulfolobus solfataricus in complex with GDP and formate ion | ||||||
Components | Translation initiation factor 2 subunit gamma | ||||||
Keywords | TRANSLATION / GAMMA SUBUNIT / G-PROTEIN / TRANSLATION INITIATION / BIOSYNTHESIS / RNA-BINDING / GTP-BINDING / NUCLEOTIDE-BINDING / BIOSYNTHETIC PROTEIN | ||||||
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 | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Kravchenko, O. / Nikonov, O. / Gabdulkhakov, A. / Stolboushkina, E. / Arkhipova, V. / Garber, M. / Nikonov, S. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: The third structural switch in the archaeal translation initiation factor 2 (aIF2) molecule and its possible role in the initiation of GTP hydrolysis and the removal of aIF2 from the ribosome. Authors: Nikonov, O. / Kravchenko, O. / Nevskaya, N. / Stolboushkina, E. / Garber, M. / Nikonov, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6i5m.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6i5m.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 6i5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i5m_validation.pdf.gz | 788.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6i5m_full_validation.pdf.gz | 788.4 KB | Display | |
Data in XML | 6i5m_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 6i5m_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/6i5m ftp://data.pdbj.org/pub/pdb/validation_reports/i5/6i5m | HTTPS FTP |
-Related structure data
Related structure data | 6h6kC 4m4sS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45849.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2g, SSO0412 / Production host: Escherichia coli (E. coli) / References: UniProt: Q980A5 |
---|
-Non-polymers , 5 types, 471 molecules
#2: Chemical | ChemComp-GDP / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-FMT / #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 73.46 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2,85mM GTP, 1,33M sodium formiate, 37mM sodium cacodylate pH 6.5, 13 mM TrisHCl pH 7.5, 130 mM NaCl, 1,3 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Apr 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→27.243 Å / Num. obs: 33014 / % possible obs: 98.7 % / Redundancy: 2.91 % / Rsym value: 0.0837 / Net I/σ(I): 10.28 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 2.81 % / Mean I/σ(I) obs: 2.16 / Num. unique obs: 3784 / Rsym value: 0.3362 / % possible all: 99.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M4S Resolution: 2.4→27.243 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.58
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→27.243 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|