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- PDB-8qc5: crystal structure of NAD-dependent glycoside hydrolase from Arthr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qc5 | ||||||
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Title | crystal structure of NAD-dependent glycoside hydrolase from Arthrobacter sp. U41 in complex with NAD+ cofactor and citrate | ||||||
![]() | Oxidoreductase | ||||||
![]() | HYDROLASE / NAD(H)-dependent / glycoside hydrolase / sulfoquinovose / sulfoglycolysis | ||||||
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 / CITRIC ACID / 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 | ![]() | 159.3 KB | Display | ![]() |
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PDB format | ![]() | 122.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8qc2C ![]() 8qc3C ![]() 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: Chemical | #4: 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: 2.43 Å3/Da / Density % sol: 49.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: protein was incubated with 2m M NAD+. crystals were grown in wells containing 1.8 M triammonium citrate pH7 |
-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: 1.95→49.33 Å / Num. obs: 60807 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.048 / Rrim(I) all: 0.18 / Χ2: 0.99 / Net I/σ(I): 11.9 / Num. measured all: 832666 |
Reflection shell | Resolution: 1.95→2 Å / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 1.251 / Num. measured all: 59824 / Num. unique obs: 4220 / CC1/2: 0.911 / Rpim(I) all: 0.343 / Rrim(I) all: 1.298 / Χ2: 0.97 / Net I/σ(I) obs: 2.5 |
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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: 29.385 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→49.3 Å
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Refine LS restraints |
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