+Open data
-Basic information
Entry | Database: PDB / ID: 6ze2 | |||||||||||||||||||||
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Title | FAD-dependent oxidoreductase from Chaetomium thermophilum | |||||||||||||||||||||
Components | FAD-dependent oxidoreductase | |||||||||||||||||||||
Keywords | OXIDOREDUCTASE / Chaetomium thermophilum / glucose-methanol-choline oxidoreductase | |||||||||||||||||||||
Function / homology | DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / FORMIC ACID Function and homology information | |||||||||||||||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å | |||||||||||||||||||||
Authors | Svecova, L. / Skalova, T. / Kolenko, P. / Koval, T. / Oestergaard, L.H. / Dohnalek, J. | |||||||||||||||||||||
Funding support | Czech Republic, 6items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ze2.cif.gz | 513.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ze2.ent.gz | 403.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ze2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/6ze2 ftp://data.pdbj.org/pub/pdb/validation_reports/ze/6ze2 | HTTPS FTP |
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-Related structure data
Related structure data | 6ze3C 6ze4C 6ze5C 6ze6C 6ze7C 7aa2C 4yntS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/804 / Data set type: diffraction image data |
-Links
-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.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Gene: CTHT_0048040 / Production host: Aspergillus oryzae (mold) |
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-Sugars , 2 types, 9 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 1669 molecules
#3: Chemical | #5: Chemical | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.1 % |
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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 cystamine, protein concentration 8 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→46.69 Å / Num. obs: 268173 / % possible obs: 95.4 % / Observed criterion σ(I): -3.7 / Redundancy: 3.2 % / Biso Wilson estimate: 12.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.31→1.33 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2 / Num. unique obs: 13444 / CC1/2: 0.795 / Rpim(I) all: 0.34 / Rrim(I) all: 0.599 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YNT Resolution: 1.31→46.69 Å / Cor.coef. Fo:Fc: 0.987 / SU B: 1.156 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.037 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: 17.369 Å2
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Refinement step | Cycle: LAST / Resolution: 1.31→46.69 Å
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Refine LS restraints |
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LS refinement shell |
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