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- PDB-6ze7: Chaetomium thermophilum FAD-dependent oxidoreductase in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ze7 | |||||||||||||||||||||
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Title | Chaetomium thermophilum FAD-dependent oxidoreductase in complex with 4-nitrophenol | |||||||||||||||||||||
![]() | FAD-dependent oxidoreductase | |||||||||||||||||||||
![]() | OXIDOREDUCTASE / Chaetomium thermophilum / glucose-methanol-choline oxidoreductase / 4-nitrophenol / co-crystallization | |||||||||||||||||||||
Function / homology | ACETATE ION / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / FORMIC ACID / P-NITROPHENOL / TRIETHYLENE GLYCOL![]() | |||||||||||||||||||||
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 | ![]() | 301.9 KB | Display | ![]() |
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PDB format | ![]() | 229.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 60.2 KB | Display | |
Data in CIF | ![]() | 94.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ze2SC ![]() 6ze3C ![]() 6ze4C ![]() 6ze5C ![]() 6ze6C ![]() 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, 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 , 9 types, 1514 molecules ![](data/chem/img/FDA.gif)
![](data/chem/img/NPO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NPO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #5: Chemical | #6: Chemical | ChemComp-FMT / #7: Chemical | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-MG / #11: Chemical | ChemComp-NA / | #12: 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: 2.32 Å3/Da / Density % sol: 47.1 % |
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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 4-nitrophenol, 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: Oct 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.23 Å / Num. obs: 186872 / % possible obs: 99.5 % / Observed criterion σ(I): -3.7 / Redundancy: 5.2 % / Biso Wilson estimate: 11.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.042 / Rrim(I) all: 0.096 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 9171 / CC1/2: 0.668 / Rpim(I) all: 0.429 / Rrim(I) all: 1.008 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ZE2 Resolution: 1.5→47.23 Å / Cor.coef. Fo:Fc: 0.976 / SU B: 1.18 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.066 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: 15.971 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→47.23 Å
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Refine LS restraints |
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LS refinement shell |
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