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Yorodumi- PDB-7ouj: Crystal structure of the flavoprotein monooxygenase RubL from rub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ouj | ||||||||||||
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Title | Crystal structure of the flavoprotein monooxygenase RubL from rubromycin biosynthesis | ||||||||||||
Components | RubL | ||||||||||||
Keywords | FLAVOPROTEIN / monooxygenase / griseorhodin A biosynthesis / rubromycin biosynthesis | ||||||||||||
Function / homology | FAD-binding domain / FAD binding domain / FAD binding / FAD/NAD(P)-binding domain superfamily / (2S)-hexane-1,2,6-triol / FLAVIN-ADENINE DINUCLEOTIDE / 4-HYDROXYPROLINE / Putative polyketide hydroxylase Function and homology information | ||||||||||||
Biological species | Streptomyces collinus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.573 Å | ||||||||||||
Authors | Saleem-Batcha, R. / Toplak, M. / Teufel, R. | ||||||||||||
Funding support | Germany, Austria, 3items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Catalytic Control of Spiroketal Formation in Rubromycin Polyketide Biosynthesis. Authors: Toplak, M. / Saleem-Batcha, R. / Piel, J. / Teufel, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ouj.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ouj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ouj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ouj_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7ouj_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7ouj_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 7ouj_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/7ouj ftp://data.pdbj.org/pub/pdb/validation_reports/ou/7ouj | HTTPS FTP |
-Related structure data
Related structure data | 7oucC 7oudC 3ihgS C: citing same article (ref.) S: Starting model for refinement |
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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, 1 molecules AAA
#1: Protein | Mass: 57918.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HYP is ligand from crystallisation buffer / Source: (gene. exp.) Streptomyces collinus (bacteria) / Gene: rubL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KY42 |
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-Non-polymers , 6 types, 201 molecules
#2: Chemical | ChemComp-FAD / | ||||||
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#3: Chemical | ChemComp-CL / | ||||||
#4: Chemical | #5: Chemical | ChemComp-HYP / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
-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: 2.34 Å3/Da / Density % sol: 47.43 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 mM DL-Arginine hydrochloride, 20 mM DL-Threonine, 20 mM DL-Histidine monohydrochloride monohydrate, 20 mM DL-5-Hydroxylysine hydrochloride, 20 mM trans-4-hydroxy-L-proline, 100 mM BES/TEA ...Details: 20 mM DL-Arginine hydrochloride, 20 mM DL-Threonine, 20 mM DL-Histidine monohydrochloride monohydrate, 20 mM DL-5-Hydroxylysine hydrochloride, 20 mM trans-4-hydroxy-L-proline, 100 mM BES/TEA pH 7.5 buffer system, 12.5% PEG 4000 and 20% 1,2,6-Hexanetriol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 9, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→46.08 Å / Num. obs: 70014 / % possible obs: 94 % / Redundancy: 2.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.57→1.66 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 10481 / CC1/2: 0.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IHG Resolution: 1.573→37.778 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.18 / SU B: 2.014 / SU ML: 0.066 / Average fsc free: 0.8812 / Average fsc work: 0.8859 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.087 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: 27.196 Å2
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Refinement step | Cycle: LAST / Resolution: 1.573→37.778 Å
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Refine LS restraints |
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LS refinement shell |
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