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Yorodumi- PDB-8qc2: Crystal structure of NAD-dependent glycoside hydrolase from Flavo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qc2 | |||||||||
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Title | Crystal structure of NAD-dependent glycoside hydrolase from Flavobacterium sp. (strain K172) in complex with co-factor NAD+ and sulfoquinovose (SQ) | |||||||||
Components | Gfo/Idh/MocA family oxidoreductase | |||||||||
Keywords | HYDROLASE / oxidoreductive / sulfoquinovose / glycoside hydrolase | |||||||||
Function / homology | NICOTINAMIDE-ADENINE-DINUCLEOTIDE / sulfoquinovose / : Function and homology information | |||||||||
Biological species | Paenarthrobacter ureafaciens (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 8qc2.cif.gz | 306.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qc2.ent.gz | 247.1 KB | Display | PDB format |
PDBx/mmJSON format | 8qc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qc2_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 8qc2_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 8qc2_validation.xml.gz | 59.9 KB | Display | |
Data in CIF | 8qc2_validation.cif.gz | 84.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/8qc2 ftp://data.pdbj.org/pub/pdb/validation_reports/qc/8qc2 | HTTPS FTP |
-Related structure data
Related structure data | 8qc3C 8qc5C 8qc6C 8qc8C 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 on special symmetry positions |
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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-NAD / #3: Chemical | ChemComp-R7R / #4: Chemical | ChemComp-TRS / #5: 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: 2.42 Å3/Da / Density % sol: 49.28 % |
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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, 5 mM NAD+ and 1 mM manganese chloride. SQ powder soaked into the well directly for around 2 minutes |
-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: 2.3→51.19 Å / Num. obs: 73391 / % possible obs: 100 % / Redundancy: 13.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.288 / Rpim(I) all: 0.08 / Rrim(I) all: 0.299 / Χ2: 0.88 / Net I/σ(I): 6.2 / Num. measured all: 1014728 |
Reflection shell | Resolution: 2.3→2.35 Å / % possible obs: 100 % / Redundancy: 14.4 % / Rmerge(I) obs: 1.616 / Num. measured all: 64373 / Num. unique obs: 4478 / CC1/2: 0.876 / Rpim(I) all: 0.438 / Rrim(I) all: 1.675 / Χ2: 0.85 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.06 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.836 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.24 / 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: 29.867 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→49.06 Å
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