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- PDB-8qc3: Crystal structure of oxidoreductive sulfoquinovosidase from Arthr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qc3 | ||||||
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Title | Crystal structure of oxidoreductive sulfoquinovosidase from Arthrobacter sp. U41 (ArSqgA)in complex with co-factor NAD+ | ||||||
![]() | Oxidoreductase | ||||||
![]() | HYDROLASE / oxidoreductive / sulfoquinovose / glycoside hydrolase | ||||||
Function / homology | Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharma, M. / Davies, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Widespread Family of NAD + -Dependent Sulfoquinovosidases at the Gateway to Sulfoquinovose Catabolism. Authors: Kaur, A. / Pickles, I.B. / Sharma, M. / Madeido Soler, N. / Scott, N.E. / Pidot, S.J. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.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 | ![]() | 151.9 KB | Display | ![]() |
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PDB format | ![]() | 116.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 990.6 KB | Display | ![]() |
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Full document | ![]() | 996.9 KB | Display | |
Data in XML | ![]() | 26.9 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qc2C ![]() 8qc5C ![]() 8qc6C ![]() 8qc8C 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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Unit cell |
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Components
#1: Protein | Mass: 42939.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 0.2 M potassium nitrate pH 6.8, 20% (w/v) PEG3350, 2 mM NAD+ |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 21, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→45.36 Å / Num. obs: 20601 / % possible obs: 98.7 % / Redundancy: 6.3 % / CC1/2: 0.961 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.072 / Rrim(I) all: 0.18 / Χ2: 0.88 / Net I/σ(I): 7 / Num. measured all: 130389 |
Reflection shell | Resolution: 2.65→2.78 Å / % possible obs: 98.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.785 / Num. measured all: 17890 / Num. unique obs: 2715 / CC1/2: 0.709 / Rpim(I) all: 0.336 / Rrim(I) all: 0.856 / Χ2: 0.93 / Net I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 39.535 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→45.3 Å
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Refine LS restraints |
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