+Open data
-Basic information
Entry | Database: PDB / ID: 6myw | ||||||
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Title | Gluconobacter Ene-Reductase (GluER) mutant - T36A | ||||||
Components | N-ethylmaleimide reductase | ||||||
Keywords | OXIDOREDUCTASE / G OXYDANS / OLD YELLOW ENZYME / LACTAM CYCLASE / T36A GLUER | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Gluconobacter oxydans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.157 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 | 6myw.cif.gz | 588.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6myw.ent.gz | 475.7 KB | Display | PDB format |
PDBx/mmJSON format | 6myw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6myw_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6myw_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6myw_validation.xml.gz | 71.7 KB | Display | |
Data in CIF | 6myw_validation.cif.gz | 109.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/my/6myw ftp://data.pdbj.org/pub/pdb/validation_reports/my/6myw | HTTPS FTP |
-Related structure data
Related structure data | 6o08C 3wjsS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 40328.277 Da / Num. of mol.: 4 / Mutation: T36A 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, 2004 molecules
#2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.88 % |
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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-2 / Wavelength: 0.9793 Å | |||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2018 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.157→156 Å / Num. obs: 458784 / % possible obs: 95.2 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.026 / Rrim(I) all: 0.066 / Χ2: 0.93 / Net I/σ(I): 13.3 | |||||||||||||||
Reflection shell | Resolution: 1.157→1.18 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 19128 / CC1/2: 0.852 / Rpim(I) all: 0.276 / Rrim(I) all: 0.675 / Χ2: 0.96 / % possible all: 81 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WJS Resolution: 1.157→29.28 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.447 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.006 / ESU R Free: 0.006 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESTRAINED ANISOTROPIC B-FACTORS ARE REFINED FOR PROTEIN AND FMN CO-FACTOR ATOMS, WITH ISOTROPIC B-FACTORS REFINED FOR SOLVENT MOLECULES.
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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: 12 Å2
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Refinement step | Cycle: 1 / Resolution: 1.157→29.28 Å
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Refine LS restraints |
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