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- PDB-6u0p: Crystal structure of PieE, the flavin-dependent monooxygenase inv... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6u0p | ||||||
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Title | Crystal structure of PieE, the flavin-dependent monooxygenase involved in the biosynthesis of piericidin A1 | ||||||
![]() | 2,4-dichlorophenol 6-monooxygenase | ||||||
![]() | FLAVOPROTEIN / flavin-dependent monooxygenase | ||||||
Function / homology | ![]() oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shi, R. / Manenda, M. / Picard, M.-E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analyses of the Group A flavin-dependent monooxygenase PieE reveal a sliding FAD cofactor conformation bridging OUT and IN conformations. Authors: Manenda, M.S. / Picard, M.E. / Zhang, L. / Cyr, N. / Zhu, X. / Barma, J. / Pascal, J.M. / Couture, M. / Zhang, C. / Shi, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 729.8 KB | Display | ![]() |
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PDB format | ![]() | 595.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 698.9 KB | Display | ![]() |
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Full document | ![]() | 722.8 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 52.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6u0sC ![]() 4z2uS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 64754.434 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CAG99_26330 / Plasmid: pET28a / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 2393 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-PGE / #4: Chemical | ChemComp-1PE / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.03 % / Mosaicity: 0.37 ° |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7.5 / Details: 30% PEG 400, 0.2M MgCl2, and 0.1 HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jan 8, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.02→49.34 Å / Num. obs: 270573 / % possible obs: 99.8 % / Redundancy: 4.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.054 / Rrim(I) all: 0.122 / Net I/σ(I): 8.8 / Num. measured all: 1275602 / Scaling rejects: 559 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Z2U Resolution: 2.02→49.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.039 / SU ML: 0.107 / SU R Cruickshank DPI: 0.1613 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.142 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 123.52 Å2 / Biso mean: 34.364 Å2 / Biso min: 14.03 Å2
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Refinement step | Cycle: final / Resolution: 2.02→49.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.072 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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