+Open data
-Basic information
Entry | Database: PDB / ID: 4xyw | ||||||
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Title | Glycosyltransferases WbnH | ||||||
Components | O-antigen biosynthesis glycosyltransferase WbnH | ||||||
Keywords | TRANSFERASE / Glycosyltransferases WbnH GT4 | ||||||
Function / homology | UDP-GalNAc:alpha-D-GalNAc-diphosphoundecaprenol alpha-1,3-N-acetylgalactosaminyltransferase / Glycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / O antigen biosynthetic process / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / O-antigen biosynthesis glycosyltransferase WbnH Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Li, F. | ||||||
Citation | Journal: To Be Published Title: Glycosyltransferases WbnH Authors: Li, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xyw.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xyw.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 4xyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xyw_validation.pdf.gz | 439.6 KB | Display | wwPDB validaton report |
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Full document | 4xyw_full_validation.pdf.gz | 443.4 KB | Display | |
Data in XML | 4xyw_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 4xyw_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/4xyw ftp://data.pdbj.org/pub/pdb/validation_reports/xy/4xyw | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 38219.988 Da / Num. of mol.: 1 / Mutation: S144N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: wbnH, wbwH, wcmA / Production host: Escherichia coli (E. coli) References: UniProt: P0DMP6, UDP-GalNAc:alpha-D-GalNAc-diphosphoundecaprenol alpha-1,3-N-acetylgalactosaminyltransferase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 0.2M Li2SO4, 0.1M CAPS, 1.2M Sodium phosphate monobasic, 0.8M Potassium phosphate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 23421 / % possible obs: 99 % / Redundancy: 11.1 % / Net I/σ(I): 23.52 |
-Processing
Software |
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Refinement | Resolution: 2.2→26.963 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→26.963 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 24.6946 Å / Origin y: 21.5194 Å / Origin z: 78.3253 Å
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Refinement TLS group | Selection details: all |