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Yorodumi- PDB-6s31: Crystal structure of ene-reductase GsOYE from Galdieria sulphurar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s31 | |||||||||
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Title | Crystal structure of ene-reductase GsOYE from Galdieria sulphuraria in complex with 4-Hydroxybenzaldehyde | |||||||||
Components | NADPH2 dehydrogenase-like protein | |||||||||
Keywords | FLAVOPROTEIN / ene-reductase / Old Yellow Enzyme / Biocatalysis | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Galdieria sulphuraria (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | |||||||||
Authors | Robescu, M.R. / Niero, M. / Hall, M. / Bergantino, E. / Cendron, L. | |||||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2020 Title: Two new ene-reductases from photosynthetic extremophiles enlarge the panel of old yellow enzymes: CtOYE and GsOYE. Authors: Robescu, M.S. / Niero, M. / Hall, M. / 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 | 6s31.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s31.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 6s31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s31_validation.pdf.gz | 775.6 KB | Display | wwPDB validaton report |
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Full document | 6s31_full_validation.pdf.gz | 776.8 KB | Display | |
Data in XML | 6s31_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 6s31_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/6s31 ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s31 | HTTPS FTP |
-Related structure data
Related structure data | 6s0gC 6s23C 6s32C 2sogS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 45381.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: Gasu_54250 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M2XAQ9 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FMN / | #4: 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 | Density Matthews: 2.23 Å3/Da / Density % sol: 44.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M CaCl2 dihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 6000 |
-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: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→57.7 Å / Num. obs: 48778 / % possible obs: 99.72 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 4758 / % possible all: 99.12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2SOG Resolution: 1.63→57.679 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.85
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→57.679 Å
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Refine LS restraints |
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LS refinement shell |
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