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- PDB-5oa4: Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72I mutan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5oa4 | ||||||
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Title | Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72I mutant in complex with 4-methoxycyclopeptin (1) | ||||||
![]() | Iron/alpha-ketoglutarate-dependent dioxygenase asqJ | ||||||
![]() | OXIDOREDUCTASE / Antibiotics / Quinolone Biosynthesis / Molecular Engineering / Desaturase / Catalytic Mechanism / Mutagenesis / pi-stacking | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Groll, M. / Braeuer, A. / Kaila, V.R.I. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.2 KB | Display | ![]() |
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PDB format | ![]() | 110.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 744.6 KB | Display | ![]() |
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Full document | ![]() | 744.6 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5oa7C ![]() 5oa8C ![]() 6eozC ![]() 5dapS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33992.883 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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-Non-polymers , 5 types, 339 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/58D.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/58D.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NI / |
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#3: Chemical | ChemComp-58D / ( |
#4: Chemical | ChemComp-TRS / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.06 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 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: 42587 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.55→1.65 Å / Rmerge(I) obs: 0.539 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DAP Resolution: 1.55→15 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 3.338 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.068 / 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: 26.508 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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