+Open data
-Basic information
Entry | Database: PDB / ID: 6eji | ||||||
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Title | Structure of a glycosyltransferase | ||||||
Components | WlaC protein | ||||||
Keywords | TRANSFERASE / Glycosyltransferase | ||||||
Function / homology | Function and homology information UDP-sulfoquinovose:DAG sulfoquinovosyltransferase activity / sulfolipid biosynthetic process / glycolipid biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Campylobacter jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Ramirez, A.S. / Boilevin, J. / Mehdipour, A.R. / Hummer, G. / Darbre, T. / Reymond, J.L. / Locher, K.P. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase. Authors: Ramirez, A.S. / Boilevin, J. / Mehdipour, A.R. / Hummer, G. / Darbre, T. / Reymond, J.L. / 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 | 6eji.cif.gz | 160.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eji.ent.gz | 131.1 KB | Display | PDB format |
PDBx/mmJSON format | 6eji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/6eji ftp://data.pdbj.org/pub/pdb/validation_reports/ej/6eji | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43255.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: wlaC / Production host: Escherichia coli (E. coli) / References: UniProt: O86151 |
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-Non-polymers , 6 types, 216 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / #6: Chemical | #7: 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: 3.37 Å3/Da / Density % sol: 63.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, potassium iodide, mops |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→29.95 Å / Num. obs: 179312 / % possible obs: 89.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.39 |
Reflection shell | Resolution: 2.3→2.382 Å / Rmerge(I) obs: 1.234 / Mean I/σ(I) obs: 2.59 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→29.942 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→29.942 Å
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Refine LS restraints |
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LS refinement shell |
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