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- PDB-5u21: X-ray structure of the WlaRF aminotransferase from Campylobacter ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5u21 | ||||||
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Title | X-ray structure of the WlaRF aminotransferase from Campylobacter jejuni, K184A mutant in complex with TDP-Qui3N | ||||||
![]() | Putative aminotransferase | ||||||
![]() | TRANSFERASE / aminotransferase / pyridoxal 5'-phosphate / lipooligosaccharide | ||||||
Function / homology | ![]() polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thoden, J.B. / Holden, H.M. / Dow, G.T. / Gilbert, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural investigation on WlaRG from Campylobacter jejuni: A sugar aminotransferase. Authors: Dow, G.T. / Gilbert, M. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 344.8 KB | Display | ![]() |
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PDB format | ![]() | 274.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 70.1 KB | Display | |
Data in CIF | ![]() | 103.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nysC ![]() 3nytC ![]() 3nyuC ![]() 5u1zSC ![]() 5u20C ![]() 5u23C ![]() 5u24C 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 43986.430 Da / Num. of mol.: 4 / Mutation: K184A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1607 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/TQP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TQP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-TQP / ( #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM MOPS (pH 7) 12-15% PEG-3350 1 mM PLP 10 mM TDP-Qui3N |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Aug 21, 2016 / Details: montel | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.6→50 Å / Num. obs: 194888 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/av σ(I): 10.2 / Net I/σ(I): 10.2 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 1.9 / % possible all: 92.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5u1z Resolution: 1.6→29.98 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.937 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.015 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.422 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→29.98 Å
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Refine LS restraints |
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