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Yorodumi- PDB-4nbs: The structure of aIF2gamma subunit H20F from archaeon Sulfolobus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nbs | ||||||
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Title | The structure of aIF2gamma subunit H20F from archaeon Sulfolobus solfataricus complexed with GDPCP | ||||||
Components | Translation initiation factor 2 subunit gamma | ||||||
Keywords | TRANSLATION / TRANSLATION INITIATION / RNA-BINDING / GTP-BINDING | ||||||
Function / homology | Function and homology information protein-synthesizing GTPase / formation of translation preinitiation complex / translation elongation factor activity / translation initiation factor activity / tRNA binding / GTPase activity / GTP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 Å | ||||||
Authors | Kravchenko, O.V. / Nikonov, O.S. / Arhipova, V.I. / Stolboushkina, E.A. / Gabdulkhakov, A.G. / Nikulin, A.D. / Garber, M.B. / Nikonov, S.V. | ||||||
Citation | Journal: To be Published Title: The structure of aIF2gamma subunit H20F from archaeon Sulfolobus solfataricus complexed with GDPCP Authors: Kravchenko, O.V. / Nikonov, O.S. / Arhipova, V.I. / Stolboushkina, E.A. / Gabdulkhakov, A.G. / Nikulin, A.D. / Garber, M.B. / Nikonov, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nbs.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nbs.ent.gz | 79.2 KB | Display | PDB format |
PDBx/mmJSON format | 4nbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nbs_validation.pdf.gz | 756.7 KB | Display | wwPDB validaton report |
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Full document | 4nbs_full_validation.pdf.gz | 758.2 KB | Display | |
Data in XML | 4nbs_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 4nbs_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/4nbs ftp://data.pdbj.org/pub/pdb/validation_reports/nb/4nbs | HTTPS FTP |
-Related structure data
Related structure data | 3sjy S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45858.254 Da / Num. of mol.: 1 / Mutation: H20F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: eif2g, SSO0412 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q980A5 |
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-Non-polymers , 5 types, 313 molecules
#2: Chemical | ChemComp-GCP / | ||||
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#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | ChemComp-FMT / #5: Chemical | #6: 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: 5.96 Å3/Da / Density % sol: 79.35 % |
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 4M sodium formiate, 0.1M sodium cacodylate, 1% MMEPEG 5K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 301K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 4, 2012 / Details: mirrors |
Radiation | Monochromator: Si-III crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.79 Å / Num. all: 48052 / Num. obs: 48037 / % possible obs: 99.97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 6.85 % / Rmerge(I) obs: 0.5764 / Mean I/σ(I) obs: 2.41 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SJY 3sjy Resolution: 2.305→46.788 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 21.06 / 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: 2.305→46.788 Å
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Refine LS restraints |
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LS refinement shell |
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