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Yorodumi- PDB-7av7: Crystal structure of S-nitrosylated nitrosoglutathione reductase(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7av7 | |||||||||
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Title | Crystal structure of S-nitrosylated nitrosoglutathione reductase(GSNOR)from Chlamydomonas reinhardtii, in complex with NAD+ | |||||||||
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: 2.9 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 | 7av7.cif.gz | 425.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7av7.ent.gz | 351.6 KB | Display | PDB format |
PDBx/mmJSON format | 7av7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7av7_validation.pdf.gz | 4.9 MB | Display | wwPDB validaton report |
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Full document | 7av7_full_validation.pdf.gz | 4.9 MB | Display | |
Data in XML | 7av7_validation.xml.gz | 82.2 KB | Display | |
Data in CIF | 7av7_validation.cif.gz | 108.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/7av7 ftp://data.pdbj.org/pub/pdb/validation_reports/av/7av7 | HTTPS FTP |
-Related structure data
Related structure data | 7aasC 7aauSC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 40484.410 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_12g543400v5 / Plasmid: pET-3c / Production host: Escherichia coli (E. coli) References: UniProt: A0A2K3D6R4, S-(hydroxymethyl)glutathione dehydrogenase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 12% w/v PEG 8K, 0.1 M Tris-HCl, 0.1 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9137 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 4, 2015 / Details: Cilindrical Mirror with 50 nm Pt-coating | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9137 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→48.623 Å / Num. obs: 195324 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.7 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.081 / Rrim(I) all: 0.16 / Rsym value: 0.118 / Net I/av σ(I): 3.2 / Net I/σ(I): 8.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7AAU Resolution: 2.9→48.5282 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 25.79 / 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: 111.9 Å2 / Biso mean: 37.0267 Å2 / Biso min: 7.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→48.5282 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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