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Yorodumi- PDB-6eoz: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72K mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6eoz | ||||||
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Title | Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72K mutant in complex with cyclopeptin (1b) | ||||||
Components | Iron/alpha-ketoglutarate-dependent dioxygenase asqJ | ||||||
Keywords | OXIDOREDUCTASE / Antibiotics / Quinolone Biosynthesis / Molecular Engineering / Desaturase / Catalytic Mechanism / Mutagenesis / pi-stacking | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Emericella nidulans (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Groll, M. / Braeuer, A. / Kaila, V.R.I. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ. Authors: Mader, S.L. / Brauer, A. / Groll, M. / Kaila, V.R.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eoz.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eoz.ent.gz | 107.6 KB | Display | PDB format |
PDBx/mmJSON format | 6eoz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/6eoz ftp://data.pdbj.org/pub/pdb/validation_reports/eo/6eoz | HTTPS FTP |
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-Related structure data
Related structure data | 5oa4C 5oa7C 5oa8C 5dapS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34008.906 Da / Num. of mol.: 1 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) Gene: asqJ, AN9227 / Plasmid: pET28b(+) / Details (production host): Cleavable SUMO-fusion tag / Production host: Escherichia coli (E. coli) References: UniProt: Q5AR53, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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#2: Chemical | ChemComp-NI / |
#3: Chemical | ChemComp-AKG / |
#4: Chemical | ChemComp-58K / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM TRIS/HCl, 1 M LiBr, 27% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 42404 / % possible obs: 98.7 % / Redundancy: 4.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.047 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.55→1.65 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.4 / CC1/2: 0.898 / Rpim(I) all: 0.555 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DAP Resolution: 1.55→15 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.797 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.065 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: 23.82 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→15 Å
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Refine LS restraints |
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