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Yorodumi- PDB-6zlk: Equilibrium Structure of UDP-Glucuronic acid 4-epimerase from Bac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zlk | ||||||
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Title | Equilibrium Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP-Glucuronic acid/UDP-Galacturonic acid and NAD | ||||||
Components | Epimerase domain-containing protein | ||||||
Keywords | OXIDOREDUCTASE / epimerase / UDP-Glucuronic acid / UDP-Galacturonic acid / equilibrium / 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 / Chem-UGB / Epimerase domain-containing protein Function and homology information | ||||||
Biological species | Bacillus cereus HuA2-4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Iacovino, L.G. / 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 | 6zlk.cif.gz | 288.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zlk.ent.gz | 231.3 KB | Display | PDB format |
PDBx/mmJSON format | 6zlk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/6zlk ftp://data.pdbj.org/pub/pdb/validation_reports/zl/6zlk | HTTPS FTP |
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-Related structure data
Related structure data | 6zl6C 6zlaC 6zldC 6zljC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36526.957 Da / Num. of mol.: 4 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 | ChemComp-NAD / #3: Chemical | ChemComp-UGA / #4: Chemical | ChemComp-UGB / ( #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: 2.25 Å3/Da / Density % sol: 45.31 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 / Details: 200 mM potassium acetate, 14-24% PEG3350 |
-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: 1.5→49.37 Å / Num. obs: 190286 / % possible obs: 97 % / Redundancy: 3.8 % / CC1/2: 0.99 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.5→1.53 Å / Num. unique obs: 14125 / CC1/2: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U4Q Resolution: 1.5→49.37 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.922 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.076 / 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: 128.99 Å2 / Biso mean: 23.947 Å2 / Biso min: 9.05 Å2
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Refinement step | Cycle: final / Resolution: 1.5→49.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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