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Yorodumi- PDB-6zll: Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zll | ||||||
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Title | Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP-Galacturonic acid and NAD | ||||||
Components | Epimerase domain-containing protein | ||||||
Keywords | OXIDOREDUCTASE / epimerase / UDP-Galacturonic 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 / 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: 1.85 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 | 6zll.cif.gz | 268.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zll.ent.gz | 216.4 KB | Display | PDB format |
PDBx/mmJSON format | 6zll.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zll_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 6zll_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6zll_validation.xml.gz | 47.6 KB | Display | |
Data in CIF | 6zll_validation.cif.gz | 65.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/6zll ftp://data.pdbj.org/pub/pdb/validation_reports/zl/6zll | HTTPS FTP |
-Related structure data
Related structure data | 6zl6C 6zlaC 6zldC 6zljC 6zlkC 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-UGB / ( #3: Chemical | ChemComp-NAD / #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: 2.53 Å3/Da / Density % sol: 51.43 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 Details: 200 mM potassium acetate, 14-24% PEG3350, 2 mM NAD+, 2 mM UDP-Galacturonic acid |
-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: 1.85→46.09 Å / Num. obs: 107680 / % possible obs: 93 % / Redundancy: 6.9 % / CC1/2: 0.99 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.85→1.898 Å / Num. unique obs: 7482 / CC1/2: 0.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U4Q Resolution: 1.85→46.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.552 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.134 / 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: 109.18 Å2 / Biso mean: 37.109 Å2 / Biso min: 22.64 Å2
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Refinement step | Cycle: final / Resolution: 1.85→46.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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