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- PDB-7olp: Dioxygenase AsqJ mutant (V72I) in complex with 2 and alpha-ketogl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7olp | ||||||
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Title | Dioxygenase AsqJ mutant (V72I) in complex with 2 and alpha-ketoglutarate | ||||||
![]() | Iron/alpha-ketoglutarate-dependent dioxygenase asqJ | ||||||
![]() | OXIDOREDUCTASE / Quinolone Biosynthesis / Molecular Engineering / Epoxidation / Catalytic Mechanism | ||||||
Function / homology | (-)-cyclopenine synthase / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / metal ion binding / 4-Methoxydehydrocyclopeptin / 2-OXOGLUTARIC ACID / NICKEL (II) ION / Iron/alpha-ketoglutarate-dependent dioxygenase asqJ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Auman, D. / Mader, S.L. / Ecker, F. / Dorst, K. / Braeuer, A. / Widmalm, G. / Groll, M. / Kaila, V.R.I. | ||||||
![]() | ![]() Title: Peroxy Intermediate Drives Carbon Bond Activation in the Dioxygenase AsqJ. Authors: Auman, D. / Ecker, F. / Mader, S.L. / Dorst, K.M. / Brauer, A. / Widmalm, G. / Groll, M. / Kaila, V.R.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.8 KB | Display | ![]() |
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PDB format | ![]() | 105.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7olkC ![]() 7ollC ![]() 7olmC ![]() 7oloC ![]() 7olqC ![]() 7olrC ![]() 7oltC ![]() 5dapS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 34063.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139 / Gene: asqJ, AN9227 / Production host: ![]() ![]() 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-58J / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM HEPES/NaOH, 1.25 M LiBr, 27% PEG 6000 / PH range: 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 42718 / % possible obs: 98.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.55→1.65 Å / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 7254 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DAP Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / SU B: 3.063 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.83 Å2 / Biso mean: 24.965 Å2 / Biso min: 16.44 Å2
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Refinement step | Cycle: final / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -20.985 Å / Origin y: -18.139 Å / Origin z: -13.317 Å
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Refinement TLS group |
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