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Yorodumi- PDB-6fyc: The crystal structure of EncM L144M mutant complex with dioxygen ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fyc | ||||||
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Title | The crystal structure of EncM L144M mutant complex with dioxygen under 15 bars O2 pressure | ||||||
Components | Putative FAD-dependent oxygenase EncM | ||||||
Keywords | FLAVOPROTEIN / monooxygenase / flavin-N5-oxide / FAD / EncM / oxygenating species / oxygen binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces maritimus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Saleem-Batcha, R. / Teufel, R. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Enzymatic control of dioxygen binding and functionalization of the flavin cofactor. Authors: Saleem-Batcha, R. / Stull, F. / Sanders, J.N. / Moore, B.S. / Palfey, B.A. / Houk, K.N. / Teufel, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fyc.cif.gz | 190.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fyc.ent.gz | 150.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/6fyc ftp://data.pdbj.org/pub/pdb/validation_reports/fy/6fyc | HTTPS FTP |
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-Related structure data
Related structure data | 6foqC 6fowC 6fp3C 6fy8C 6fy9C 6fyaC 6fybC 6fydC 6fyeC 6fyfC 6fygC 4xloS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 50092.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces maritimus (bacteria) / Gene: encM / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KHK2 #2: Chemical | #3: Chemical | #4: 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: 295 K / Method: vapor diffusion, sitting drop Details: 0.1M HEPES-Na, 0.2M Calcium Acetate, 20% - 30% PEG 3350, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99997 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.68 Å / Num. obs: 61351 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2→2.11 Å / Rmerge(I) obs: 0.54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XLO Resolution: 2→43.679 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 30.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.679 Å
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Refine LS restraints |
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LS refinement shell |
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