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Open data
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Basic information
Entry | Database: PDB / ID: 5o24 | ||||||
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Title | Lytic transglycosylase in action | ||||||
![]() | 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. / Hoauz, A. / Boneca, I.G. | ||||||
![]() | ![]() 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 | ![]() | 149.7 KB | Display | ![]() |
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PDB format | ![]() | 111.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.9 KB | Display | ![]() |
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Full document | ![]() | 442.7 KB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 48.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o1jC ![]() 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 65103.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0Y5YPU4, UniProt: Q9JXP1*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.12 % / Description: Rod Shape |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 100 mM CHES pH 9.5, 100 mM tri sodium citrate, 30% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 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: 1.429→45.74 Å / Num. obs: 110571 / % possible obs: 97.46 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.06356 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.429→1.48 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 0.41 / Num. unique obs: 10064 / Rpim(I) all: 0.8801 / % possible all: 90.47 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YIM ![]() 4yim Resolution: 1.429→45.74 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.429→45.74 Å
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Refine LS restraints |
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LS refinement shell |
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