+Open data
-Basic information
Entry | Database: PDB / ID: 7kws | ||||||
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Title | Cj1441 with NAD+ and UDP-glucose | ||||||
Components | UDP-glucose 6-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Dehydrogenase / Polysaccharide / CARBOHYDRATE | ||||||
Function / homology | Function and homology information UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / polysaccharide biosynthetic process / NAD binding Similarity search - Function | ||||||
Biological species | Campylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Riegert, A.S. / Raushel, F.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2021 Title: Functional and Structural Characterization of the UDP-Glucose Dehydrogenase Involved in Capsular Polysaccharide Biosynthesis from Campylobacter jejuni . Authors: Riegert, A.S. / Raushel, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kws.cif.gz | 177 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kws.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 7kws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/7kws ftp://data.pdbj.org/pub/pdb/validation_reports/kw/7kws | HTTPS FTP |
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-Related structure data
Related structure data | 1dljS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45148.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter) Strain: ATCC 700819 / NCTC 11168 / Gene: kfiD, Cj1441c / Plasmid: pET31b / Details (production host): C-his / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0P8H3, UDP-glucose 6-dehydrogenase #2: Chemical | #3: Chemical | #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: 2.14 Å3/Da / Density % sol: 42.65 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5.0 mM UDP-glucose, 5.0 mM NAD+, 1.0 mM DTT, 32% pentaerythritol ethoxylate, 50 mM ammonium sulfate, 50 mM BIS-TRIS, 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.12709 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12709 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→46.44 Å / Num. obs: 43332 / % possible obs: 96.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 38.68 Å2 / Rsym value: 0.041 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.09→2.14 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.43 / Num. unique obs: 2003 / Rsym value: 0.184 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DLJ Resolution: 2.09→46.44 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.55 Å2 / Biso mean: 48.4346 Å2 / Biso min: 24.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→46.44 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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