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Yorodumi- PDB-7aas: Crystal structure of nitrosoglutathione reductase (GSNOR) from Ch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aas | |||||||||
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Title | Crystal structure of nitrosoglutathione reductase (GSNOR) from Chlamydomonas reinhardtii | |||||||||
Components | S-(hydroxymethyl)glutathione dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Alcohol dehydrogenase / Zinc-binding dehydrogenase | |||||||||
Function / homology | Function and homology information S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / : / nucleotide binding / zinc ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Fermani, S. / Zaffagnini, M. / Falini, G. / Lemaire, S.D. | |||||||||
Funding support | Italy, France, 2items
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Citation | Journal: Redox Biol / Year: 2020 Title: Structural and functional insights into nitrosoglutathione reductase from Chlamydomonas reinhardtii. Authors: Tagliani, A. / Rossi, J. / Marchand, C.H. / De Mia, M. / Tedesco, D. / Gurrieri, L. / Meloni, M. / Falini, G. / Trost, P. / Lemaire, S.D. / Fermani, S. / Zaffagnini, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aas.cif.gz | 474.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aas.ent.gz | 387.3 KB | Display | PDB format |
PDBx/mmJSON format | 7aas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/7aas ftp://data.pdbj.org/pub/pdb/validation_reports/aa/7aas | HTTPS FTP |
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-Related structure data
Related structure data | 7aauC 7av7C 4dlaS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 40455.410 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_12g543400v5 / Plasmid: pET3c / Production host: Escherichia coli (E. coli) References: UniProt: A0A2K3D6R4, S-(hydroxymethyl)glutathione dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PEG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris-HCl pH 8.5, 0.1 M MgCl2 or Mg(CH3CO2)2, and 12-15% w/v PEG 20K or 12% w/v PEG 8K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→56.973 Å / Num. obs: 208518 / % possible obs: 98.1 % / Redundancy: 5 % / Biso Wilson estimate: 13.624 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.035 / Rrim(I) all: 0.082 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 9027 / CC1/2: 0.686 / Rpim(I) all: 0.373 / Rrim(I) all: 0.656 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DLA Resolution: 1.8→56.973 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 21.73 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.68 Å2 / Biso mean: 24.127 Å2 / Biso min: 8.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→56.973 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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