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Yorodumi- PDB-8v4h: X-ray structure of the NADP-dependent reductase from Campylobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8v4h | |||||||||
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Title | X-ray structure of the NADP-dependent reductase from Campylobacter jejuni responsible for the synthesis of CDP-glucitol in the presence of CDP-glucitol | |||||||||
Components | Putative nucleotide sugar dehydratase | |||||||||
Keywords | OXIDOREDUCTASE / capsular polysaccharide / short chain dehydrogenase | |||||||||
Function / homology | NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / PHOSPHATE ION / Chem-YCX / Putative nucleotide sugar dehydratase Function and homology information | |||||||||
Biological species | Campylobacter jejuni (Campylobacter) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Thoden, J.B. / Schumann, M.E. / Holden, H.M. / Raushel, F.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2024 Title: Biosynthesis of Cytidine Diphosphate-6-d-Glucitol for the Capsular Polysaccharides of Campylobacter jejuni. Authors: Ghosh, M.K. / Narindoshvili, T. / Thoden, J.B. / Schumann, M.E. / Holden, H.M. / 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 | 8v4h.cif.gz | 157.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v4h.ent.gz | 121.2 KB | Display | PDB format |
PDBx/mmJSON format | 8v4h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8v4h_validation.pdf.gz | 978.9 KB | Display | wwPDB validaton report |
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Full document | 8v4h_full_validation.pdf.gz | 986 KB | Display | |
Data in XML | 8v4h_validation.xml.gz | 28 KB | Display | |
Data in CIF | 8v4h_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/8v4h ftp://data.pdbj.org/pub/pdb/validation_reports/v4/8v4h | HTTPS FTP |
-Related structure data
Related structure data | 8v4gC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41094.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: HS:5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: A0A0U3AP28 |
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-Non-polymers , 5 types, 199 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.26 Å3/Da / Density % sol: 45.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Protein incubated with 5 mM CDP-glucitol and 5 mN NADPH. Precipitant: 10-14 % w/v poly(ethylene glycol) 8000, 200 mM LiCl, and 100 mM HEPPS (pH 8.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å |
Detector | Type: Bruker PHOTON II / Detector: PIXEL / Date: Jun 16, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 37429 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Rsym value: 0.073 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4430 / Rsym value: 0.38 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.06 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.869 / SU B: 8.926 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.257 / 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: 33.918 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→39.06 Å
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