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Yorodumi- PDB-5ogl: Structure of bacterial oligosaccharyltransferase PglB in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ogl | ||||||
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Title | Structure of bacterial oligosaccharyltransferase PglB in complex with an acceptor peptide and an lipid-linked oligosaccharide analog | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Oligosaccharyltransferase / Complex / Protein N-glycosylation / Bacteria | ||||||
Function / homology | Function and homology information undecaprenyl-diphosphooligosaccharide-protein glycotransferase / oligosaccharyl transferase activity / protein N-linked glycosylation via asparagine / glycosyltransferase activity / magnesium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Campylobacter lari (Campylobacter) Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Napiorkowska, M. / Boilevin, J. / Sovdat, T. / Darbre, T. / Reymond, J.-L. / Aebi, M. / Locher, K.P. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Molecular basis of lipid-linked oligosaccharide recognition and processing by bacterial oligosaccharyltransferase. Authors: Napiorkowska, M. / Boilevin, J. / Sovdat, T. / Darbre, T. / Reymond, J.L. / Aebi, M. / Locher, K.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ogl.cif.gz | 310.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ogl.ent.gz | 254.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ogl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/5ogl ftp://data.pdbj.org/pub/pdb/validation_reports/og/5ogl | HTTPS FTP |
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-Related structure data
Related structure data | 3rceS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 83037.312 Da / Num. of mol.: 1 Mutation: K2E, C17A, C30A, A108T, C360L, N535Q, Q536K, K549P, D550N, F553I, N556P, A600P, A602D, T606K, T607Q, V610I, M611T, I619S, F622Y, A624S, V627I, A630N, F663Y, F670Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter lari (strain RM2100 / D67 / ATCC BAA-1060) (Campylobacter) Strain: RM2100 / D67 / ATCC BAA-1060 / Gene: pglB, Cla_1253 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B9KDD4, undecaprenyl-diphosphooligosaccharide-protein glycotransferase |
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#2: Protein/peptide | Mass: 853.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Campylobacter jejuni (Campylobacter) |
-Non-polymers , 4 types, 24 molecules
#3: Chemical | #4: Chemical | ChemComp-9UB / [( | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5 Å3/Da / Density % sol: 75.4 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 9.4 Details: 0.1M glycine pH 9.4, 0.12M lithium sulfate, 29-31% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→47.767 Å / Num. obs: 46914 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.08725 / Rrim(I) all: 0.09107 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.358 / Mean I/σ(I) obs: 2.18 / Num. unique all: 4593 / CC1/2: 0.78 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RCE Resolution: 2.7→47.767 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 25.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→47.767 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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