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- PDB-6ze5: FAD-dependent oxidoreductase from Chaetomium thermophilum in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ze5 | |||||||||||||||||||||
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Title | FAD-dependent oxidoreductase from Chaetomium thermophilum in complex with fragment 2-(1H-indol-3-yl)-N-[(1-methyl-1H-pyrrol-2-yl)methyl]ethanamine | |||||||||||||||||||||
![]() | FAD-dependent oxidoreductase | |||||||||||||||||||||
![]() | OXIDOREDUCTASE / Chaetomium thermophilum / glucose-methanol-choline oxidoreductase / 2-(1H-indol-3-yl)-N-[(1-methyl-1H-pyrrol-2-yl)methyl]ethanamine / fragment screening | |||||||||||||||||||||
Function / homology | Chem-4AQ / 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 | ![]() | 340.3 KB | Display | ![]() |
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PDB format | ![]() | 218 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 55.5 KB | Display | |
Data in CIF | ![]() | 85.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ze2SC ![]() 6ze3C ![]() 6ze4C ![]() 6ze6C ![]() 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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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, 8 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 , 5 types, 1283 molecules ![](data/chem/img/FDA.gif)
![](data/chem/img/4AQ.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/4AQ.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #5: Chemical | #6: Chemical | ChemComp-FMT / #7: Chemical | #8: 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: 2.39 Å3/Da / Density % sol: 48.6 % |
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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 6M / Detector: PIXEL / Date: Jun 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→43.4 Å / Num. obs: 105562 / % possible obs: 99.4 % / Observed criterion σ(I): -3.7 / Redundancy: 3.4 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.051 / Rrim(I) all: 0.094 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.82→1.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 0.673 / Num. unique obs: 5247 / CC1/2: 0.673 / Rpim(I) all: 0.469 / Rrim(I) all: 0.888 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ZE2 Resolution: 1.82→43.4 Å / SU ML: 0.1883 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 18.1567 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 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 | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→43.4 Å
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Refine LS restraints |
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LS refinement shell |
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