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Yorodumi- PDB-7o0t: Crystal structure of Chloroflexus aggregans ene-reductase CaOYE h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o0t | ||||||
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Title | Crystal structure of Chloroflexus aggregans ene-reductase CaOYE holoenzyme | ||||||
Components | NADH:flavin oxidoreductase/NADH oxidase | ||||||
Keywords | OXIDOREDUCTASE / ene-reductase / FMN-binding protein / Old Yellow Enzyme | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chloroflexus aggregans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Robescu, M.S. / Niero, M. / Loprete, G. / Bergantino, E. / Cendron, L. | ||||||
Citation | Journal: Microorganisms / Year: 2021 Title: A New Thermophilic Ene-Reductase from the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aggregans . Authors: Robescu, M.S. / Niero, M. / Loprete, G. / Cendron, L. / Bergantino, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o0t.cif.gz | 277.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o0t.ent.gz | 224.6 KB | Display | PDB format |
PDBx/mmJSON format | 7o0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7o0t_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7o0t_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7o0t_validation.xml.gz | 52.1 KB | Display | |
Data in CIF | 7o0t_validation.cif.gz | 71.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/7o0t ftp://data.pdbj.org/pub/pdb/validation_reports/o0/7o0t | HTTPS FTP |
-Related structure data
Related structure data | 5nuxS S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 37793.125 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chloroflexus aggregans (strain MD-66 / DSM 9485) (bacteria) Strain: MD-66 / DSM 9485 / Gene: Cagg_2779 / Production host: Escherichia coli (E. coli) / References: UniProt: B8G5D6 #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-MLI / #4: 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: 3.14 Å3/Da / Density % sol: 60.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM HEPES pH 7.0, 1.1 M sodium malonate dibasic monohydrate, 0.5% v/v Jeffamine |
-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: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→38.01 Å / Num. obs: 73908 / % possible obs: 99.3 % / Redundancy: 4.6 % / CC1/2: 0.969 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.4→2.61 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4571 / CC1/2: 0.74 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5nux Resolution: 2.4→38.01 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 124.95 Å2 / Biso mean: 34.188 Å2 / Biso min: 9.86 Å2
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Refinement step | Cycle: final / Resolution: 2.4→38.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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