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Yorodumi- PDB-4rd1: Structure of aIF2-gamma H97A variant from Sulfolobus solfataricus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rd1 | ||||||
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Title | Structure of aIF2-gamma H97A variant from Sulfolobus solfataricus bound to GTP | ||||||
Components | Translation initiation factor 2 subunit gamma | ||||||
Keywords | TRANSLATION / Rossmann-fold | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Dubiez, E. / Aleksandrov, A. / Lazennec-Schurdevin, C. / Mechulam, Y. / Schmitt, E. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rd1.cif.gz | 194.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rd1.ent.gz | 151.8 KB | Display | PDB format |
PDBx/mmJSON format | 4rd1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rd1_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4rd1_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4rd1_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 4rd1_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/4rd1 ftp://data.pdbj.org/pub/pdb/validation_reports/rd/4rd1 | HTTPS FTP |
-Related structure data
Related structure data | 4rcyC 4rczSC 4rd0C 4rd2C 4rd3C 4rd4C 4rd6C C: citing same article (ref.) 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: 45782.160 Da / Num. of mol.: 1 / Fragment: aIF2-gamma subunit / Mutation: H97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: eif2g, SSO0412, sulfolobus solfataricus / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 rosetta / References: UniProt: Q980A5 |
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-Non-polymers , 6 types, 325 molecules
#2: Chemical | ChemComp-GTP / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Chemical | #7: 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: 2.21 Å3/Da / Density % sol: 44.43 % |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å |
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: 1.5→46.4 Å / Num. all: 65993 / Num. obs: 65993 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.42 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 8.66 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 7.15 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.25 / Rsym value: 0.533 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4RCZ Resolution: 1.5→44.112 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 19.75 / 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: 1.5→44.112 Å
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Refine LS restraints |
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LS refinement shell |
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