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- PDB-3nub: WbpE, an Aminotransferase from Pseudomonas aeruginosa Involved in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nub | ||||||
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Title | WbpE, an Aminotransferase from Pseudomonas aeruginosa Involved in O-antigen Assembly in Complex with Product as the External Aldimine | ||||||
![]() | Aminotransferase WbpE | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Larkin, A. / Olivier, N.B. / Imperiali, B. | ||||||
![]() | ![]() Title: Structural Analysis of WbpE from Pseudomonas aeruginosa PAO1: A Nucleotide Sugar Aminotransferase Involved in O-Antigen Assembly Authors: Larkin, A. / Olivier, N.B. / Imperiali, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.3 KB | Display | ![]() |
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PDB format | ![]() | 125.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3nu7SC ![]() 3nu8C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 38965.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / | ![]() #4: Chemical | ChemComp-SO4 / | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.19 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Crystallization conditions: 0.1 M Bis-Tris, pH 5.5, 0.2 M Ammonium sulfate, 25% PEG 3350 in the reservoir; Protein solution contains 25 mM HEPES, pH 8.0, 100 mM NaCl, 0.5% glycerol; Protein ...Details: Crystallization conditions: 0.1 M Bis-Tris, pH 5.5, 0.2 M Ammonium sulfate, 25% PEG 3350 in the reservoir; Protein solution contains 25 mM HEPES, pH 8.0, 100 mM NaCl, 0.5% glycerol; Protein incubated with 50 uM PLP and 20 mM UDP-GlcNAc(3NH2)A for 1 hr prior to setting up tray; Drop made by mixing 1.5 uL of protein and reservoir solutions., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 20, 2010 / Details: Toroidal Focusing Mirror |
Radiation | Monochromator: SI(111) Channel Cut Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→20 Å / Num. obs: 46379 / % possible obs: 98.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3NU7 Resolution: 1.9→19.9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.908 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R Free: 0.171 / 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: 19.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.904→1.953 Å / Total num. of bins used: 20
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