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Yorodumi- PDB-6zld: Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zld | ||||||
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Title | Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP-Glucuronic acid and NAD | ||||||
Components | Epimerase domain-containing protein | ||||||
Keywords | OXIDOREDUCTASE / epimerase / UDP-Glucuronic acid / NAD / UDP-sugar binding protein | ||||||
Function / homology | NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / catalytic activity / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / Epimerase domain-containing protein Function and homology information | ||||||
Biological species | Bacillus cereus HuA2-4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Iacovino, L.G. / Savino, S. / Mattevi, A. | ||||||
Funding support | Italy, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Crystallographic snapshots of UDP-glucuronic acid 4-epimerase ligand binding, rotation, and reduction. Authors: Iacovino, L.G. / Savino, S. / Borg, A.J.E. / Binda, C. / Nidetzky, B. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zld.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zld.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 6zld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/6zld ftp://data.pdbj.org/pub/pdb/validation_reports/zl/6zld | HTTPS FTP |
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-Related structure data
Related structure data | 6zl6C 6zlaC 6zljC 6zlkC 6zllC 5u4qS S: Starting model for refinement C: citing same article (ref.) |
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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: 36526.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus HuA2-4 (bacteria) / Gene: IG7_05634 / Production host: Escherichia coli (E. coli) / References: UniProt: J8BY31 #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 Å3/Da / Density % sol: 38.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 200 mM potassium acetate and 14-24% PEG3350, 2 mM UDP-glucuronic acid, 2 mM NAD+ |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.22 Å / Num. obs: 49095 / % possible obs: 95 % / Redundancy: 1.6 % / CC1/2: 0.99 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.8→1.84 Å / Num. unique obs: 3399 / CC1/2: 0.78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U4Q Resolution: 1.8→45.22 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.085 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 74.39 Å2 / Biso mean: 22.478 Å2 / Biso min: 10.41 Å2
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Refinement step | Cycle: final / Resolution: 1.8→45.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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