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Yorodumi- PDB-3ruc: Specific recognition of N-acetylated substrates and domain flexib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ruc | ||||||
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Title | Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase | ||||||
Components | WbgU | ||||||
Keywords | ISOMERASE / Rossmann fold / UDP-hexose 4-epimerase | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine 4-epimerase / UDP-N-acetylglucosamine 4-epimerase activity / O antigen biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Plesiomonas shigelloides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Bhatt, V.S. / Guan, W. / Wang, P.G. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase Authors: Bhatt, V.S. / Guan, W. / Wang, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ruc.cif.gz | 553.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ruc.ent.gz | 455.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ruc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ruc_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 3ruc_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 3ruc_validation.xml.gz | 56.6 KB | Display | |
Data in CIF | 3ruc_validation.cif.gz | 77.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/3ruc ftp://data.pdbj.org/pub/pdb/validation_reports/ru/3ruc | HTTPS FTP |
-Related structure data
Related structure data | 3ru7C 3ru9C 3ruaC 3lu1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 39755.043 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plesiomonas shigelloides (bacteria) / Gene: wbgU / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7BJX9 #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-UD2 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 298.15 K / Method: microbatch under oil / pH: 6.5 Details: 25% PEG 3350, 0.2 M Ammonium Sulfate, 200 mM Bis Tris Propane pH 6.5 , microbatch under oil, temperature 298.15K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2011 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 92338 / Num. obs: 92338 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.1→2.14 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LU1 Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.877 / SU B: 13.108 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.208 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.694 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.149 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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