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Open data
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Basic information
Entry | Database: PDB / ID: 7wmk | ||||||
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Title | PQQ-dependent alcohol dehydrogenase complexed with PQQ | ||||||
![]() | PQQ-dependent alcohol dehydrogenase | ||||||
![]() | TOXIN / dehydrogenase / PQQ | ||||||
Function / homology | ACETATE ION / PYRROLOQUINOLINE QUINONE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, M. / Yang, H. / Lv, F. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 309.3 KB | Display | ![]() |
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PDB format | ![]() | 251.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 844.4 KB | Display | ![]() |
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Full document | ![]() | 846.9 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 36.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wmdSC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61908.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 7 types, 325 molecules ![](data/chem/img/PQQ.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PQQ / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-EPE / | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.47 % |
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Crystal grow | Temperature: 293 K / Method: evaporation Details: 250mM Sodium acetate, 100mM BIS-Tris (pH 7.5), 150mM NaCl, 15% PEG 3350 |
-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: Jul 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→47.25 Å / Num. obs: 95115 / % possible obs: 98.7 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 14.16 |
Reflection shell | Resolution: 1.47→1.54 Å / Num. unique obs: 15196 / CC1/2: 0.894 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7WMD Resolution: 1.47→44.151 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 12.16 / 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: 113.9 Å2 / Biso mean: 21.9791 Å2 / Biso min: 0.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.47→44.151 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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