+Open data
-Basic information
Entry | Database: PDB / ID: 3w8w | ||||||
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Title | The crystal structure of EncM | ||||||
Components | Putative FAD-dependent oxygenase EncM | ||||||
Keywords | OXIDOREDUCTASE / monooxygenase / flavin binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces maritimus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Teufel, R. / Miyanaga, A. / Stull, F. / Michaudel, Q. / Louie, G. / Noel, J.P. / Baran, P.S. / Palfey, B. / Moore, B.S. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement. Authors: Teufel, R. / Miyanaga, A. / Michaudel, Q. / Stull, F. / Louie, G. / Noel, J.P. / Baran, P.S. / Palfey, B. / Moore, B.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w8w.cif.gz | 362.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w8w.ent.gz | 293 KB | Display | PDB format |
PDBx/mmJSON format | 3w8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/3w8w ftp://data.pdbj.org/pub/pdb/validation_reports/w8/3w8w | HTTPS FTP |
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-Related structure data
Related structure data | 3w8xC 3w8zC 4xloC 2bvgS 3w8y 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: 50413.703 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 (E. coli) References: UniProt: Q9KHK2, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of one atom of oxygen (internal monooxygenases or ...References: UniProt: Q9KHK2, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of one atom of oxygen (internal monooxygenases or internal mixed-function oxidases) #2: Chemical | #3: 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: 2.37 Å3/Da / Density % sol: 48.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2mM DTT, 0.1M HEPES-Na, 0.2M calcium acetate, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2009 |
Radiation | Monochromator: double crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 67750 / Num. obs: 67411 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.95→1.98 Å / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BVG Resolution: 1.95→47.72 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.782 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→47.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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