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Yorodumi- PDB-6fy9: The crystal structure of EncM complex with xenon under 15 bars Xe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fy9 | ||||||
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Title | The crystal structure of EncM complex with xenon under 15 bars Xe 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: 3.65 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 | 6fy9.cif.gz | 93.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fy9.ent.gz | 70.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/6fy9 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/6fy9 | HTTPS FTP |
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-Related structure data
Related structure data | 6foqC 6fowC 6fp3C 6fy8C 6fyaC 6fybC 6fycC 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: 50074.371 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.01 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1M HEPES-Na, 0.2M Calcium Acetate, 20% 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: 0.91881 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91881 Å / Relative weight: 1 |
Reflection | Resolution: 3.65→44.107 Å / Num. obs: 38691 / % possible obs: 99.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 3.65→3.85 Å / Rmerge(I) obs: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XLO Resolution: 3.65→44.107 Å / SU ML: 0.55 / Cross valid method: NONE / σ(F): 0.38 / Phase error: 34.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.65→44.107 Å
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Refine LS restraints |
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LS refinement shell |
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