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Yorodumi- PDB-4uss: Populus trichocarpa glutathione transferase X1-1 (GHR1), complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uss | |||||||||
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Title | Populus trichocarpa glutathione transferase X1-1 (GHR1), complexed with glutathione | |||||||||
Components | GLUTATHIONYL HYDROQUINONE REDUCTASE | |||||||||
Keywords | TRANSFERASE / CLASS XI / POPLAR / PLASTIDS | |||||||||
Function / homology | Function and homology information Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutaredoxin / Glutaredoxin / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | POPULUS TRICHOCARPA (black cottonwood) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Lallement, P.A. / Meux, E. / Gualberto, J.M. / Dumaracay, S. / Favier, F. / Didierjean, C. / Saul, F. / Haouz, A. / Morel-Rouhier, M. / Gelhaye, E. ...Lallement, P.A. / Meux, E. / Gualberto, J.M. / Dumaracay, S. / Favier, F. / Didierjean, C. / Saul, F. / Haouz, A. / Morel-Rouhier, M. / Gelhaye, E. / Rouhier, N. / Hecker, A. | |||||||||
Citation | Journal: FEBS Lett. / Year: 2015 Title: Glutathionyl-Hydroquinone Reductases from Poplar are Plastidial Proteins that Deglutathionylate Both Reduced and Oxidized Glutathionylated Quinones. Authors: Lallement, P. / Meux, E. / Gualberto, J.M. / Dumarcay, S. / Favier, F. / Didierjean, C. / Saul, F. / Haouz, A. / Morel-Rouhier, M. / Gelhaye, E. / Rouhier, N. / Hecker, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uss.cif.gz | 126 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uss.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 4uss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uss_validation.pdf.gz | 698.8 KB | Display | wwPDB validaton report |
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Full document | 4uss_full_validation.pdf.gz | 699.5 KB | Display | |
Data in XML | 4uss_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 4uss_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/4uss ftp://data.pdbj.org/pub/pdb/validation_reports/us/4uss | HTTPS FTP |
-Related structure data
Related structure data | 3ppuS 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: 37180.754 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-359 Source method: isolated from a genetically manipulated source Details: THE EXPRESSED PROTEIN IS DEVOID OF THE FIRST 34 AMINO ACIDS. Source: (gene. exp.) POPULUS TRICHOCARPA (black cottonwood) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B9ICN7, glutathione transferase | ||||
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#2: Chemical | ChemComp-GSH / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | DISCREPANCIES IN SEQUENCE ARE DUE TO POLYMORPHISM. AUTHORS HAVE CLARIFIED THAT DISCREPANCIES IN ...DISCREPANC | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.64 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.82656 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2011 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.82656 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19.53 Å / Num. obs: 10702 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 35.73 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PPU Resolution: 2.5→19.525 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 24 / 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: 2.5→19.525 Å
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Refine LS restraints |
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LS refinement shell |
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