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Yorodumi- PDB-6yq3: Promiscuous Reductase LugOII Catalyzes Keto-reduction at C1 durin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yq3 | ||||||
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Title | Promiscuous Reductase LugOII Catalyzes Keto-reduction at C1 during Lugdunomycin Biosynthesis | ||||||
Components | Monooxygenase | ||||||
Keywords | ANTIBIOTIC / lugdunomycin / keto-reduction / short chain alcohol reductase / Rossmann fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces sp. QL37 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Xiao, X. / Elsayed, S.S. / Wu, C. / van der Heul, H. / Prota, A. / Huang, J. / Guo, R. / Abrahams, J.P. / van Wezel, G.P. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yq3.cif.gz | 192.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yq3.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yq3_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6yq3_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6yq3_validation.xml.gz | 27 KB | Display | |
Data in CIF | 6yq3_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/6yq3 ftp://data.pdbj.org/pub/pdb/validation_reports/yq/6yq3 | HTTPS FTP |
-Related structure data
Related structure data | 6ypzC 6yq0C 6yq6C 4ospS 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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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains AAA BBB) |
-Components
#1: Protein | Mass: 26797.248 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. QL37 (bacteria) / Gene: C5F59_12925 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2S6PN47 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | 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: 2.13 Å3/Da / Density % sol: 42.27 % |
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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: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→24.7 Å / Num. obs: 60525 / % possible obs: 98.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 16.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.064 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.57→1.61 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 6124 / CC1/2: 0.818 / Rrim(I) all: 0.566 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4osp Resolution: 1.57→24.696 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.996 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.077 / ESU R Free: 0.075 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.537 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→24.696 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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