[English] 日本語
Yorodumi- PDB-6yq6: Promiscuous Reductase LugOII Catalyzes Keto-reduction at C1 durin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yq6 | ||||||
---|---|---|---|---|---|---|---|
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: 2.08 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6yq6.cif.gz | 183.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6yq6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/6yq6 ftp://data.pdbj.org/pub/pdb/validation_reports/yq/6yq6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6ypzC 6yq0C 6yq3C 4ospS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains AAA BBB) / NCS ensembles : (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 | ChemComp-EDO / #3: Chemical | ChemComp-PEG / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.61 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.3 M NaCl, 0.1 M Na Cacodylate, pH 6.5, 1.5 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
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: 2.08→47.471 Å / Num. obs: 87905 / % possible obs: 99.8 % / Redundancy: 20.9 % / Biso Wilson estimate: 33.82 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.399 / Rrim(I) all: 0.409 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.08→2.13 Å / Rmerge(I) obs: 2.839 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 14133 / CC1/2: 0.431 / Rrim(I) all: 2.912 / % possible all: 99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4osp Resolution: 2.08→47.471 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.175 / WRfactor Rwork: 0.14 / SU B: 7.502 / SU ML: 0.099 / Average fsc free: 0.9287 / Average fsc work: 0.935 / Cross valid method: FREE R-VALUE / ESU R: 0.135 / ESU R Free: 0.13 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 28.094 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→47.471 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|