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Yorodumi- PDB-7aau: Crystal structure of nitrosoglutathione reductase from Chlamydomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aau | |||||||||
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Title | Crystal structure of nitrosoglutathione reductase 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: 2.301 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 | 7aau.cif.gz | 461.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aau.ent.gz | 378.9 KB | Display | PDB format |
PDBx/mmJSON format | 7aau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aau_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7aau_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7aau_validation.xml.gz | 95.9 KB | Display | |
Data in CIF | 7aau_validation.cif.gz | 136.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/7aau ftp://data.pdbj.org/pub/pdb/validation_reports/aa/7aau | HTTPS FTP |
-Related structure data
Related structure data | 7aasC 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
-Protein , 1 types, 6 molecules ABCDEF
#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 |
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-Non-polymers , 6 types, 1491 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Details
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 % / Description: stick crystals |
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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: ELETTRA / Beamline: 5.2R / Wavelength: 0.9137 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 4, 2015 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9137 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.3→117.4 Å / Num. obs: 102418 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 22.16 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.087 / Rrim(I) all: 0.18 / Net I/σ(I): 8.3 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DLA Resolution: 2.301→48.565 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 23.33 / 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: 91.48 Å2 / Biso mean: 31.6457 Å2 / Biso min: 12.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.301→48.565 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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