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Open data
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Basic information
Entry | Database: PDB / ID: 7dqx | ||||||
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Title | Crystal structure of xanthine dehydrogenase family protein | ||||||
![]() | (6-hydroxypseudooxynicotine dehydrogenase complex subunit ...) x 4 | ||||||
![]() | OXIDOREDUCTASE / KDH | ||||||
Function / homology | ![]() 6-hydroxypseudooxynicotine dehydrogenase / 6-hydroxypseudooxynicotine dehydrogenase activity / nicotine catabolic process / FAD binding / 2 iron, 2 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lei, W. | ||||||
![]() | ![]() Title: crystal structure of xanthine dehydrogenase family protein Authors: Lei, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 900.8 KB | Display | ![]() |
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PDB format | ![]() | 737.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 98.2 KB | Display | |
Data in CIF | ![]() | 128.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-6-hydroxypseudooxynicotine dehydrogenase complex subunit ... , 4 types, 6 molecules ADBCFE
#1: Protein | Mass: 86474.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: kdhC, kdhL / Production host: ![]() ![]() References: UniProt: Q933N0, 6-hydroxypseudooxynicotine dehydrogenase #2: Protein | | Mass: 31469.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: kdhA, kdhM / Production host: ![]() ![]() References: UniProt: O87681, 6-hydroxypseudooxynicotine dehydrogenase #3: Protein | Mass: 17660.904 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: kdhB, kdhS / Production host: ![]() ![]() References: UniProt: O87682, 6-hydroxypseudooxynicotine dehydrogenase #4: Protein | | Mass: 31469.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: kdhA, kdhM / Production host: ![]() ![]() References: UniProt: O87681, 6-hydroxypseudooxynicotine dehydrogenase |
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-Non-polymers , 4 types, 10 molecules ![](data/chem/img/MCN.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/MO.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/FES.gif)
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-FES / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: Nonius Kappa CCD / Detector: CCD / Date: Dec 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.43→147.24 Å / Num. obs: 56814 / % possible obs: 96 % / Redundancy: 12.2 % / CC1/2: 0.87 / Net I/σ(I): 1.1 |
Reflection shell | Resolution: 3.43→3.55 Å / Num. unique obs: 5553 / CC1/2: 0.512 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.74 Å2 / Biso mean: 67.87 Å2 / Biso min: 31.2 Å2
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Refinement step | Cycle: final / Resolution: 3.44→147.24 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3.443→3.532 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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