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Open data
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Basic information
Entry | Database: PDB / ID: 5o1j | |||||||||
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Title | Lytic transglycosylase in action | |||||||||
![]() | Putative soluble lytic murein transglycosylase | |||||||||
![]() | HYDROLASE / lytic transglycosylases / acid/base catalysis / peptidoglycan / bacteria | |||||||||
Function / homology | ![]() catalytic activity / hydrolase activity, hydrolyzing O-glycosyl compounds / periplasmic space / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Williams, A.H. / Rateau, L. / Hoauz, A. / Boneca, I.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: A step-by-stepin crystalloguide to bond cleavage and 1,6-anhydro-sugar product synthesis by a peptidoglycan-degrading lytic transglycosylase. Authors: Williams, A.H. / Wheeler, R. / Rateau, L. / Malosse, C. / Chamot-Rooke, J. / Haouz, A. / Taha, M.K. / Boneca, I.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.2 KB | Display | ![]() |
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PDB format | ![]() | 106.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5o24C ![]() 5o29C ![]() 5o2nC ![]() 6fpnC ![]() 4yim S: Starting model for refinement C: citing same article ( |
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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: 64111.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: NMB1949 / Details (production host): PGEX4TI / Production host: ![]() ![]() | ||
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-1,6- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-1,6-anhydro-N-acetyl-beta-D-glucopyranosamine Source method: isolated from a genetically manipulated source | ||
#3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.27 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Zinc acetate, or 0.1 M Sodium cacodylate pH 6.5, 0.1M 18%PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→71.66 Å / Num. obs: 54011 / % possible obs: 99.42 % / Redundancy: 4.4 % / Net I/σ(I): 7.81 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YIM ![]() 4yim Resolution: 1.9→71.66 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.375 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.151
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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: 34.721 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→71.66 Å
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Refine LS restraints |
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