+Open data
-Basic information
Entry | Database: PDB / ID: 6o08 | ||||||
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Title | Gluconobacter Ene-Reductase (GluER) | ||||||
Components | N-ethylmaleimide reductase | ||||||
Keywords | OXIDOREDUCTASE / G OXYDANS / OLD YELLOW ENZYME / LACTAM CYCLASE / WT GLUER | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Gluconobacter oxydans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å | ||||||
Authors | Garfinkle, S.E. / Jeffrey, P. / Hyster, T.K. | ||||||
Citation | Journal: Science / Year: 2019 Title: Photoexcitation of flavoenzymes enables a stereoselective radical cyclization. Authors: Biegasiewicz, K.F. / Cooper, S.J. / Gao, X. / Oblinsky, D.G. / Kim, J.H. / Garfinkle, S.E. / Joyce, L.A. / Sandoval, B.A. / Scholes, G.D. / Hyster, T.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o08.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o08.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 6o08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o08_validation.pdf.gz | 812.9 KB | Display | wwPDB validaton report |
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Full document | 6o08_full_validation.pdf.gz | 818.5 KB | Display | |
Data in XML | 6o08_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 6o08_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/6o08 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/6o08 | HTTPS FTP |
-Related structure data
Related structure data | 6mywSC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40358.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Gene: nox, AD934_01855, AD950_09540 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): pET22b / References: UniProt: A1E8I9 |
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-Non-polymers , 6 types, 263 molecules
#2: Chemical | ChemComp-FMN / | ||||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-NA / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 100 MM SODIUM ACETATE MONOHYDRATE PH 4.6, 150 MM AMMONIUM SULFATE, 25% (W/V) PEG 4000 PH range: 4.2-5/0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 1.798→27.99 Å / Num. obs: 32965 / % possible obs: 99.27 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.066 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.798→1.83 Å / Rmerge(I) obs: 1.235 / Num. unique all: 1702 / CC1/2: 0.924 / Rpim(I) all: 0.557 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MYW Resolution: 1.798→27.99 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 4.514 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.129 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.562 Å2
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Refinement step | Cycle: 1 / Resolution: 1.798→27.99 Å
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Refine LS restraints |
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