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- PDB-6yq0: Promiscuous Reductase LugOII Catalyzes Keto-reduction at C1 durin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yq0 | ||||||
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Title | Promiscuous Reductase LugOII Catalyzes Keto-reduction at C1 during Lugdunomycin Biosynthesis | ||||||
![]() | Monooxygenase | ||||||
![]() | ANTIBIOTIC / lugdunomycin / keto-reduction / short chain alcohol reductase / Rossmann fold | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xiao, X. / Elsayed, S.S. / Wu, C. / van der Heul, H. / Prota, A. / Huang, J. / Guo, R. / Abrahams, J.P. / van Wezel, G.P. | ||||||
![]() | ![]() Title: Functional and Structural Insights into a Novel Promiscuous Ketoreductase of the Lugdunomycin Biosynthetic Pathway. Authors: Xiao, X. / Elsayed, S.S. / Wu, C. / van der Heul, H.U. / Metsa-Ketela, M. / Du, C. / Prota, A.E. / Chen, C.C. / Liu, W. / Guo, R.T. / Abrahams, J.P. / van Wezel, G.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 41.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ypzC ![]() 6yq3C ![]() 6yq6C ![]() 4ospS 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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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains AAA BBB) |
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Components
#1: Protein | Mass: 26797.248 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A2S6PN47 #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 0.1 M Na Malonate, 0.1 M BIS-TRIS prop, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→49.495 Å / Num. obs: 431114 / % possible obs: 95.4 % / Redundancy: 3.1 % / Biso Wilson estimate: 11.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.08→1.108 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 68021 / CC1/2: 0.801 / Rrim(I) all: 0.532 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4osp Resolution: 1.08→49.495 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.152 / WRfactor Rwork: 0.138 / SU B: 0.874 / SU ML: 0.02 / Average fsc free: 0.9442 / Average fsc work: 0.9468 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.03 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.502 Å2
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Refinement step | Cycle: LAST / Resolution: 1.08→49.495 Å
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Refine LS restraints |
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LS refinement shell |
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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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