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Yorodumi- PDB-7bn6: Crystal structure of G. sulphuraria ene-reductase GsOYE in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bn6 | ||||||
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Title | Crystal structure of G. sulphuraria ene-reductase GsOYE in complex with b-angelica lactone | ||||||
Components | NADPH2 dehydrogenase-like protein | ||||||
Keywords | OXIDOREDUCTASE / NADPH dehydrogenase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Galdieria sulphuraria (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Robescu, M.S. / Bergantino, E. / Hall, M. / Cendron, L. | ||||||
Citation | Journal: Acs Catalysis / Year: 2022 Title: Asymmetric Proton Transfer Catalysis by Stereocomplementary Old Yellow Enzymes for C=C Bond Isomerization Reaction Authors: Robescu, M.S. / Cendron, L. / Bacchin, A. / Wagner, K. / Reiter, T. / Janicki, I. / Merusic, K. / Illek, M. / Aleotti, M. / Bergantino, E. / Hall, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bn6.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bn6.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bn6_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7bn6_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7bn6_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 7bn6_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/7bn6 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/7bn6 | HTTPS FTP |
-Related structure data
Related structure data | 7blfC 7bn7C 7bo0C 6s0gS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45494.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: Gasu_54250 / Production host: Escherichia coli (E. coli) / References: UniProt: M2XAQ9 #2: Chemical | ChemComp-U5N / ( | #3: Chemical | #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: 2.1 Å3/Da / Density % sol: 41.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M MgCl2 hexahydrate or 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: ID30B / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Nov 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→48.48 Å / Num. obs: 288040 / % possible obs: 97.93 % / Redundancy: 2.5 % / Biso Wilson estimate: 17.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.5→1.554 Å / Rmerge(I) obs: 0.4332 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 27828 / CC1/2: 0.702 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S0G Resolution: 1.5→48.48 Å / SU ML: 0.2117 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4495 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 23.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→48.48 Å
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Refine LS restraints |
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LS refinement shell |
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