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Yorodumi- PDB-3gx8: Structural and biochemical characterization of yeast monothiol gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gx8 | ||||||
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Title | Structural and biochemical characterization of yeast monothiol glutaredoxin Grx5 | ||||||
Components | Monothiol glutaredoxin-5, mitochondrial | ||||||
Keywords | ELECTRON TRANSPORT / Trx fold / Mitochondrion / Redox-active center / Transit peptide / Transport | ||||||
Function / homology | Function and homology information Mitochondrial iron-sulfur cluster biogenesis / protein maturation by [4Fe-4S] cluster transfer / protein maturation by [2Fe-2S] cluster transfer / protein maturation by iron-sulfur cluster transfer / disulfide oxidoreductase activity / response to osmotic stress / protein-disulfide reductase activity / 2 iron, 2 sulfur cluster binding / cellular response to oxidative stress / electron transfer activity ...Mitochondrial iron-sulfur cluster biogenesis / protein maturation by [4Fe-4S] cluster transfer / protein maturation by [2Fe-2S] cluster transfer / protein maturation by iron-sulfur cluster transfer / disulfide oxidoreductase activity / response to osmotic stress / protein-disulfide reductase activity / 2 iron, 2 sulfur cluster binding / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.673 Å | ||||||
Authors | Wang, Y. / He, Y.X. / Yu, J. / Xiong, Y. / Chen, Y. / Zhou, C.Z. | ||||||
Citation | Journal: To be Published Title: Structural and biochemical characterization of yeast monothiol glutaredoxin Grx5 Authors: Wang, Y. / He, Y.X. / Yu, J. / Xiong, Y. / Chen, Y. / Zhou, C.Z. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Cloning, overproduction, purification, crystallization and preliminary X-ray diffraction analysis of yeast glutaredoxin Grx5 Authors: Wang, Y. / He, Y.X. / Yu, J. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gx8.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gx8.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gx8_validation.pdf.gz | 423.5 KB | Display | wwPDB validaton report |
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Full document | 3gx8_full_validation.pdf.gz | 423.9 KB | Display | |
Data in XML | 3gx8_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 3gx8_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/3gx8 ftp://data.pdbj.org/pub/pdb/validation_reports/gx/3gx8 | HTTPS FTP |
-Related structure data
Related structure data | 1ykaS 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
#1: Protein | Mass: 13359.029 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: S288C / Gene: GRX5 / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q02784 | ||
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#2: Chemical | #3: 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: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 8 Details: 1.6M NH4SO4, Tris-HCl, pH8.0, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 29, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→24.57 Å / Num. obs: 15256 / % possible obs: 98.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2020 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YKA Resolution: 1.673→24.214 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.871 / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.98 / Phase error: 20.42 / 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 / Bsol: 59.984 Å2 / ksol: 0.431 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.56 Å2 / Biso mean: 24.779 Å2 / Biso min: 10.71 Å2
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Refinement step | Cycle: LAST / Resolution: 1.673→24.214 Å
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Refine LS restraints |
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LS refinement shell |
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