+Open data
-Basic information
Entry | Database: PDB / ID: 7wmd | ||||||
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Title | PQQ-dependent alcohol dehydrogenase detoxifying DON | ||||||
Components | PQQ-dependent alcohol dehydrogenase | ||||||
Keywords | TOXIN / Dehydrogenase / PQQ | ||||||
Biological species | Devosia albogilva (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chen, M. / Yang, H. / Lv, F. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Agric.Food Chem. / Year: 2022 Title: Structure-Function Analysis of a Quinone-Dependent Dehydrogenase Capable of Deoxynivalenol Detoxification. Authors: Yang, H. / Yan, R. / Li, Y. / Lu, Z. / Bie, X. / Zhao, H. / Lu, F. / Chen, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wmd.cif.gz | 123.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wmd.ent.gz | 91.6 KB | Display | PDB format |
PDBx/mmJSON format | 7wmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wmd_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 7wmd_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 7wmd_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 7wmd_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/7wmd ftp://data.pdbj.org/pub/pdb/validation_reports/wm/7wmd | HTTPS FTP |
-Related structure data
-Links
-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
#1: Protein | Mass: 61908.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Devosia albogilva (bacteria) / Production host: Escherichia coli (E. coli) | ||||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 0.2M Magnesium chloride hexahydrate, 0.1M BIS-Tris pH 5.5, 25% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2→40.43 Å / Num. obs: 37502 / % possible obs: 99 % / Redundancy: 6.63 % / CC1/2: 0.997 / Net I/σ(I): 15.33 |
Reflection shell | Resolution: 2→2.071 Å / Mean I/σ(I) obs: 5.41 / Num. unique obs: 5902 / CC1/2: 0.942 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CVB Resolution: 2→40.43 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.32 / Stereochemistry target values: ML
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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 max: 67.99 Å2 / Biso mean: 21.8135 Å2 / Biso min: 0.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→40.43 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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