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- PDB-8b63: Crystal Structure of P. aeruginosa WaaG in complex with UDP-GalNAc -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b63 | ||||||
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Title | Crystal Structure of P. aeruginosa WaaG in complex with UDP-GalNAc | ||||||
![]() | UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG | ||||||
![]() | TRANSFERASE / glycosyltransferase / WaaG | ||||||
Function / homology | ![]() UDP-sulfoquinovose:DAG sulfoquinovosyltransferase activity / sulfolipid biosynthetic process / glycolipid biosynthetic process / lipopolysaccharide biosynthetic process / glycosyltransferase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Scaletti, E. / Gustafsson Westergren, R. / Stenmark, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional insights into the Pseudomonas aeruginosa glycosyltransferase WaaG and the implications for lipopolysaccharide biosynthesis. Authors: Scaletti, E.R. / Pettersson, P. / Patrick, J. / Shilling, P.J. / Westergren, R.G. / Daley, D.O. / Maler, L. / Widmalm, G. / Stenmark, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.7 KB | Display | ![]() |
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PDB format | ![]() | 124.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8b5qC ![]() 8b5sC ![]() 8b62C ![]() 2iv7S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41995.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-UD2 / | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-UDP / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M MIB pH 4.0, 25% w/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→55.042 Å / Num. obs: 43178 / % possible obs: 99.9 % / Redundancy: 4.9 % / CC1/2: 0.991 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.2→2.27 Å / Num. unique obs: 3679 / CC1/2: 0.554 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2IV7 Resolution: 2.2→55.04 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.317 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.221 / 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: 38.501 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→55.04 Å
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Refine LS restraints |
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