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- PDB-6se1: Structure of Salmonella ser. Paratyphi A lipopolysaccharide acety... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6se1 | ||||||
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Title | Structure of Salmonella ser. Paratyphi A lipopolysaccharide acetyltransferase periplasmic domain | ||||||
![]() | Putative lipopolysaccharide modification acyltransferase | ||||||
![]() | TRANSFERASE / SGNH / acetyltransferase / lipopolysaccharide | ||||||
Function / homology | SGNH domain / SGNH domain (fused to AT3 domains) / Acyltransferase 3 domain / Acyltransferase family / SGNH hydrolase superfamily / acyltransferase activity, transferring groups other than amino-acyl groups / membrane => GO:0016020 / DI(HYDROXYETHYL)ETHER / Acyltransferase![]() | ||||||
Biological species | Salmonella paratyphi A | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tindall, S.N. / Pearson, C. / Herman, R. / Jenkins, H.T. / Thomas, G.H. / Potts, J.R. / Van der Woude, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Acetylation of Surface Carbohydrates in Bacterial Pathogens Requires Coordinated Action of a Two-Domain Membrane-Bound Acyltransferase. Authors: Pearson, C.R. / Tindall, S.N. / Herman, R. / Jenkins, H.T. / Bateman, A. / Thomas, G.H. / Potts, J.R. / Van der Woude, M.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.9 KB | Display | ![]() |
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PDB format | ![]() | 167.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.4 KB | Display | ![]() |
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Full document | ![]() | 440.5 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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
#1: Protein | Mass: 29000.986 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Periplasmic domain of OafB (residues 377-640) from Salmonella ser. Paratyphi A recombinantly expressed in E. coli Origami 2 cells from the pETFPP_2 vector. Source: (gene. exp.) ![]() Strain: ATCC 9150 / SARB42 / Gene: SPA0467 / Plasmid: pETFPP_2 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM BisTris pH 5.5, 0.25 M Lithium sulfate, 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 93.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→47.39 Å / Num. obs: 126378 / % possible obs: 100 % / Redundancy: 7.7 % / CC1/2: 0.999 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.08→1.1 Å / Redundancy: 6.4 % / Num. unique obs: 6232 / CC1/2: 0.651 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: null Resolution: 1.08→47.39 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.941 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.024 Details: Hydrogens have been added in their 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: 13.657 Å2
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Refinement step | Cycle: LAST / Resolution: 1.08→47.39 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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