+Open data
-Basic information
Entry | Database: PDB / ID: 8ov9 | ||||||
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Title | Crystal structure of Ene-reductase 1 from black poplar mushroom | ||||||
Components | Ene-reductase 1 | ||||||
Keywords | OXIDOREDUCTASE / NAD/NADP-dependent dehydrogenase / ene/yne-reductase / fungal secondary metabolites | ||||||
Function / homology | Function and homology information 2-alkenal reductase [NAD(P)+] / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor Similarity search - Function | ||||||
Biological species | Cyclocybe aegerita (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | ||||||
Authors | Korf, L. / Essen, L.-O. / Karrer, D. / Ruehl, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Shifting the substrate scope of an ene/yne-reductase by loop engineering Authors: Karrer, D. / Wedler, E. / Mewe, C. / Gand, M. / Vogt, M.S. / Korf, L. / Essen, L.-O. / Ruehl, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ov9.cif.gz | 263.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ov9.ent.gz | 178.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ov9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ov9_validation.pdf.gz | 439.5 KB | Display | wwPDB validaton report |
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Full document | 8ov9_full_validation.pdf.gz | 441.8 KB | Display | |
Data in XML | 8ov9_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 8ov9_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/8ov9 ftp://data.pdbj.org/pub/pdb/validation_reports/ov/8ov9 | HTTPS FTP |
-Related structure data
Related structure data | 8ov8C 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 38181.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyclocybe aegerita (fungus) / Gene: ENR1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: A0A8A1QR26 | ||||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine pH 9.0, 1.6 M Ammonium sulfate 9 |
-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: 0.9763 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2020 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→41.58 Å / Num. obs: 867680 / % possible obs: 97.3 % / Redundancy: 12.8 % / Biso Wilson estimate: 13.39 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06758 / Rpim(I) all: 0.01922 / Rrim(I) all: 0.07033 / Net I/σ(I): 21.57 |
Reflection shell | Resolution: 1.41→1.43 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.4442 / Mean I/σ(I) obs: 2.99 / Num. unique obs: 6759 / CC1/2: 0.856 / CC star: 0.96 / Rpim(I) all: 0.2288 / Rrim(I) all: 0.5014 / % possible all: 50.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→41.58 Å / SU ML: 0.0969 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.308 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→41.58 Å
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Refine LS restraints |
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LS refinement shell |
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