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- PDB-6ze6: FAD-dependent oxidoreductase from Chaetomium thermophilum in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ze6 | |||||||||||||||||||||
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Title | FAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment 4-nitrocatechol | |||||||||||||||||||||
![]() | FAD-dependent oxidoreductase | |||||||||||||||||||||
![]() | OXIDOREDUCTASE / Chaetomium thermophilum / glucose-methanol-choline oxidoreductase / 4-nitrocatechol / fragment screening | |||||||||||||||||||||
Function / homology | 4-NITROCATECHOL / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / FORMIC ACID![]() | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Svecova, L. / Skalova, T. / Kolenko, P. / Koval, T. / Oestergaard, L.H. / Dohnalek, J. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystallographic fragment screening-based study of a novel FAD-dependent oxidoreductase from Chaetomium thermophilum. Authors: Svecova, L. / Ostergaard, L.H. / Skalova, T. / Schnorr, K.M. / Koval', T. / Kolenko, P. / Stransky, J. / Sedlak, D. / Duskova, J. / Trundova, M. / Hasek, J. / Dohnalek, J. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 524.9 KB | Display | ![]() |
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PDB format | ![]() | 412.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 64.1 KB | Display | |
Data in CIF | ![]() | 102.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ze2SC ![]() 6ze3C ![]() 6ze4C ![]() 6ze5C ![]() 6ze7C ![]() 7aa2C S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 64267.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The provided sequence corresponds to the mass spectrometry analysis of sample used for crystallization. Source: (gene. exp.) ![]() Gene: CTHT_0048040 / Production host: ![]() ![]() |
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-Sugars , 2 types, 11 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 7 types, 1899 molecules ![](data/chem/img/FDA.gif)
![](data/chem/img/4NC.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/4NC.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #5: Chemical | ChemComp-4NC / #6: Chemical | ChemComp-FMT / #7: Chemical | #8: Chemical | ChemComp-CL / | #9: Chemical | ChemComp-NA / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 17 % (w/v) PEG MME 5000, 0.1 M sodium acetate, pH 5.5, 0.16 M magnesium formate, 20 mM MgCl2, protein concentration 8 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→29.063 Å / Num. obs: 314691 / % possible obs: 98.3 % / Observed criterion σ(I): -3.7 / Redundancy: 7.4 % / Biso Wilson estimate: 10 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.024 / Rrim(I) all: 0.065 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.26→1.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 14281 / CC1/2: 0.66 / Rpim(I) all: 0.439 / Rrim(I) all: 1.076 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ZE2 Resolution: 1.26→29.063 Å / Cor.coef. Fo:Fc: 0.985 / SU B: 0.997 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.034 Details: Hydrogens have been added for refinement in the riding positions. The last refinement cycle was performed against all reflections.
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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: 14.313 Å2
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Refinement step | Cycle: LAST / Resolution: 1.26→29.063 Å
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Refine LS restraints |
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LS refinement shell |
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