+Open data
-Basic information
Entry | Database: PDB / ID: 7lo1 | ||||||
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Title | FAD-dependent monooxygenase AfoD from A. nidulans | ||||||
Components | FAD-dependent monooxygenase afoD | ||||||
Keywords | FLAVOPROTEIN / AfoD / Flavin-dependent monooxygenase / FDMO / FAD | ||||||
Function / homology | Function and homology information asperfuranone biosynthetic process / secondary metabolite biosynthetic process / Oxidoreductases / FAD binding / monooxygenase activity / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Emericella nidulans (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Rodriguez Benitez, A. / Smith, J.L. / Narayan, A.R.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction. Authors: Chiang, C.H. / Wymore, T. / Rodriguez Benitez, A. / Hussain, A. / Smith, J.L. / Brooks 3rd, C.L. / Narayan, A.R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lo1.cif.gz | 403.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lo1.ent.gz | 268.3 KB | Display | PDB format |
PDBx/mmJSON format | 7lo1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/7lo1 ftp://data.pdbj.org/pub/pdb/validation_reports/lo/7lo1 | HTTPS FTP |
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-Related structure data
Related structure data | 6nesS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49088.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold) Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: afoD, AN1033 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5BEJ7, Oxidoreductases #2: Chemical | #3: Chemical | #4: 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: 2.4 Å3/Da / Density % sol: 48.75 % / Description: Crystals were sensitive to radiation |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: (0.2 M (NH4)2SO4, 0.1 M MES:NaOH pH 6.5, 30% w/v PEG 5K MME). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.017→44.75 Å / Num. obs: 763820 / % possible obs: 99.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 50.8 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1195 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.017→2.09 Å / Redundancy: 13 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 71983 / CC1/2: 0.712 / CC star: 0.912 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NES Resolution: 2.09→44.75 Å / SU ML: 0.3008 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2141 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→44.75 Å
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Refine LS restraints |
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LS refinement shell |
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