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- PDB-6gxc: Bacterial oligosaccharyltransferase PglB in complex with an inhib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gxc | ||||||
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Title | Bacterial oligosaccharyltransferase PglB in complex with an inhibitory peptide and a reactive lipid-linked oligosaccharide analog | ||||||
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![]() | MEMBRANE PROTEIN / Glycosyltransferase / Lipid-linked oligosaccharide / Ternary complex | ||||||
Function / homology | ![]() undecaprenyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / glycosyltransferase activity / post-translational protein modification / magnesium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Napiorkowska, M. / Locher, K.P. / Boilevin, J. / Darbre, T. / Reymond, J.-L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of bacterial oligosaccharyltransferase PglB bound to a reactive LLO and an inhibitory peptide. Authors: Napiorkowska, M. / Boilevin, J. / Darbre, T. / Reymond, J.L. / Locher, K.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 | ![]() | 155.7 KB | Display | ![]() |
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PDB format | ![]() | 127.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 650 KB | Display | ![]() |
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Full document | ![]() | 684.9 KB | Display | |
Data in XML | ![]() | 30.3 KB | Display | |
Data in CIF | ![]() | 40.7 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 84565.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: RM2100 / D67 / ATCC BAA-1060 / Gene: pglB, Cla_1253 / Production host: ![]() ![]() References: UniProt: B9KDD4, undecaprenyl-diphosphooligosaccharide-protein glycotransferase |
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#2: Protein/peptide | Mass: 839.808 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
-Non-polymers , 5 types, 6 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/FFK.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/FFK.gif)
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-MES / | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-FFK / [( | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.97 Å3/Da / Density % sol: 75.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.4 Details: 0.1M glycine, pH 9.4, 0.15M magnesium acetate, and 30% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.401→41.094 Å / Num. obs: 24002 / % possible obs: 92.08 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rrim(I) all: 0.069 / Net I/σ(I): 23.28 |
Reflection shell | Resolution: 3.401→3.49 Å / Redundancy: 4.8 % / CC1/2: 0.676 / Rrim(I) all: 1.44 / % possible all: 33.7 |
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Processing
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Refinement | Resolution: 3.401→41.094 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.17
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.401→41.094 Å
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Refine LS restraints |
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LS refinement shell |
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