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Yorodumi- PDB-7ncv: Crystal structure of reduced glutaredoxin 2 from Chlamydomonas re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ncv | ||||||
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Title | Crystal structure of reduced glutaredoxin 2 from Chlamydomonas reinhardtii | ||||||
Components | Glutaredoxin, CPYC type | ||||||
Keywords | OXIDOREDUCTASE / Chlamydomonas reinhardtii glutaredoxin | ||||||
Function / homology | Function and homology information glutathione disulfide oxidoreductase activity / cellular response to oxidative stress / cytoplasm Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Roret, T. / Didierjean, C. | ||||||
Citation | Journal: Antioxidants (Basel) / Year: 2021 Title: Atypical Iron-Sulfur Cluster Binding, Redox Activity and Structural Properties of Chlamydomonas reinhardtii Glutaredoxin 2. Authors: Roret, T. / Zhang, B. / Moseler, A. / Dhalleine, T. / Gao, X.H. / Couturier, J. / Lemaire, S.D. / Didierjean, C. / Johnson, M.K. / Rouhier, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ncv.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ncv.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ncv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/7ncv ftp://data.pdbj.org/pub/pdb/validation_reports/nc/7ncv | HTTPS FTP |
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-Related structure data
Related structure data | 7ncwC 2flsS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11356.931 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Cys56 residue is oxidized into a sulfenic acid. / Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: GRX2, CHLRE_12g550400v5, CHLREDRAFT_195611 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8IYH1 | ||||
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#2: Chemical | ChemComp-ACT / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.63 % |
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Crystal grow | Temperature: 277 K / Method: microbatch Details: 30% (w/v) PEG 8000 0.1 M sodium cacodylate pH 6.5 0.2 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9785 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→39.53 Å / Num. obs: 20838 / % possible obs: 96.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.42 Å2 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.023 / Rrim(I) all: 0.049 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.5→1.58 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2951 / Rpim(I) all: 0.202 / Rrim(I) all: 0.414 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FLS Resolution: 1.5→39.53 Å / SU ML: 0.103 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.108 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.95 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→39.53 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -15.462756453 Å / Origin y: -13.1805433618 Å / Origin z: 7.42526830367 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 1 through 107) |