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Yorodumi- PDB-6u0p: Crystal structure of PieE, the flavin-dependent monooxygenase inv... -
+Open data
-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 | ||||||
Components | 2,4-dichlorophenol 6-monooxygenase | ||||||
Keywords | FLAVOPROTEIN / flavin-dependent monooxygenase | ||||||
Function / homology | Function and homology information 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 | Streptomyces sp. SCSIO 03032 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Shi, R. / Manenda, M. / Picard, M.-E. | ||||||
Funding support | Canada, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u0p.cif.gz | 729.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u0p.ent.gz | 595.5 KB | Display | PDB format |
PDBx/mmJSON format | 6u0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u0p_validation.pdf.gz | 698.9 KB | Display | wwPDB validaton report |
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Full document | 6u0p_full_validation.pdf.gz | 722.8 KB | Display | |
Data in XML | 6u0p_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 6u0p_validation.cif.gz | 52.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/6u0p ftp://data.pdbj.org/pub/pdb/validation_reports/u0/6u0p | HTTPS FTP |
-Related structure data
Related structure data | 6u0sC 4z2uS 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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1 |
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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.) Streptomyces sp. SCSIO 03032 (bacteria) Gene: CAG99_26330 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W0C4C9 |
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-Non-polymers , 6 types, 2393 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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