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Yorodumi- PDB-8qc8: Crystal structure of NAD-dependent glycoside hydrolase from Flavo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qc8 | |||||||||
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Title | Crystal structure of NAD-dependent glycoside hydrolase from Flavobacterium sp. (strain K172) in complex with co-factor NAD+ | |||||||||
Components | Gfo/Idh/MocA family oxidoreductase | |||||||||
Keywords | HYDROLASE / oxidoreductive / sulfoquinovose / glycoside hydrolase | |||||||||
Function / homology | NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / : Function and homology information | |||||||||
Biological species | Paenarthrobacter ureafaciens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Pickles, I.B. / Sharma, M. / Davies, G.J. | |||||||||
Funding support | European Union, United Kingdom, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qc8.cif.gz | 292.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qc8.ent.gz | 232.8 KB | Display | PDB format |
PDBx/mmJSON format | 8qc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/8qc8 ftp://data.pdbj.org/pub/pdb/validation_reports/qc/8qc8 | HTTPS FTP |
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-Related structure data
Related structure data | 8qc2C 8qc3C 8qc5C 8qc6C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42881.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenarthrobacter ureafaciens (bacteria) Gene: FV140_09610 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7D7VZ79 #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NAD / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-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: 45.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM bis-tris propane pH 7, 0.02 mM sodium and potassium phosphate, 28% (w/v) PEG3350, 1 mM MnCl2, 5 mM NAD+ |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→59.45 Å / Num. obs: 63829 / % possible obs: 99.7 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.055 / Rrim(I) all: 0.2 / Χ2: 0.92 / Net I/σ(I): 8 / Num. measured all: 830971 |
Reflection shell | Resolution: 2.35→2.41 Å / % possible obs: 97.8 % / Redundancy: 10.2 % / Rmerge(I) obs: 1.779 / Num. measured all: 44513 / Num. unique obs: 4352 / CC1/2: 0.933 / Rpim(I) all: 0.573 / Rrim(I) all: 1.874 / Χ2: 0.86 / Net I/σ(I) obs: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→59.45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 14.836 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R: 0.468 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 53.444 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→59.45 Å
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