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Yorodumi- PDB-7p9d: Crystal structure of Chlamydomonas reinhardtii NADPH Dependent Th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p9d | ||||||
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Title | Crystal structure of Chlamydomonas reinhardtii NADPH Dependent Thioredoxin Reductase 1 domain | ||||||
Components | Thioredoxin reductase | ||||||
Keywords | OXIDOREDUCTASE / flavoprotein / FAD binding domain | ||||||
Function / homology | Function and homology information regulation of starch biosynthetic process / regulation of chlorophyll biosynthetic process / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / positive regulation of catalytic activity / enzyme activator activity / removal of superoxide radicals / cell redox homeostasis / chloroplast / hydrogen peroxide catabolic process Similarity search - Function | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å | ||||||
Authors | Singh, R.K. / Marchetti, G.M. / Hippler, M. / Kuemmel, D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2021 Title: Structural analysis revealed a novel conformation of the NTRC reductase domain from Chlamydomonas reinhardtii. Authors: Marchetti, G.M. / Fusser, F. / Singh, R.K. / Brummel, M. / Koch, O. / Kummel, D. / Hippler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p9d.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p9d.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 7p9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p9d_validation.pdf.gz | 754.9 KB | Display | wwPDB validaton report |
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Full document | 7p9d_full_validation.pdf.gz | 755.8 KB | Display | |
Data in XML | 7p9d_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 7p9d_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/7p9d ftp://data.pdbj.org/pub/pdb/validation_reports/p9/7p9d | HTTPS FTP |
-Related structure data
Related structure data | 7p9eC 3d8xS 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
#1: Protein | Mass: 52462.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_01g054150v5 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A2K3E888, thioredoxin-disulfide reductase |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M mixture of DL-Glutamic acid monohydrate, DL-Alanine, Glycine, DL-Lysine monohydrochloride, DL-Serine; 0.1 M of Tris (base), BICINE with pH-8.5; 20% of v/v Ethylene glycol, 10 % of w/v PEG 8000 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 22317 / % possible obs: 99.7 % / Redundancy: 25.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.157 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.99→2.11 Å / Redundancy: 25.6 % / Rmerge(I) obs: 1.757 / Num. unique obs: 3471 / CC1/2: 0.857 / Rrim(I) all: 1.371 / % possible all: 98 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3d8x Resolution: 1.99→42.57 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.593 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.89 Å2 / Biso mean: 38.659 Å2 / Biso min: 23.33 Å2
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Refinement step | Cycle: final / Resolution: 1.99→42.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.993→2.045 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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