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Open data
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Basic information
Entry | Database: PDB / ID: 7oms | ||||||
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Title | Bs164 in complex with mannocyclophellitol aziridine | ||||||
![]() | Glyco_hydro_42M domain-containing protein | ||||||
![]() | HYDROLASE / Inhibitor complex | ||||||
Function / homology | Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / beta-galactosidase activity / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily / carbohydrate metabolic process / Chem-VKH / Beta-galactosidase trimerisation domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McGregor, N. / Beenakker, T. / Kuo, C.L. / Wong, C.S. / Offren, W.A. / Armstrong, Z. / Codee, J.D.C. / Aerts, J.M.F.G. / Florea, B.I. / Overkleeft, H. / Davies, G.J. | ||||||
![]() | ![]() Title: Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases. Authors: McGregor, N.G.S. / Kuo, C.L. / Beenakker, T.J.M. / Wong, C.S. / Offen, W.A. / Armstrong, Z. / Florea, B.I. / Codee, J.D.C. / Overkleeft, H.S. / Aerts, J.M.F.G. / Davies, G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7odjC ![]() 7omiC ![]() 7op6C ![]() 7op7C ![]() 6t7gS 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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Noncrystallographic symmetry (NCS) | NCS domain:
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Components
#1: Protein | Mass: 76676.672 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-VKH / ( #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M ammonium tartrate pH 7.0, 13 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976246 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→99.597 Å / Num. obs: 277094 / % possible obs: 98.1 % / Redundancy: 3.5 % / CC1/2: 0.98 / Net I/σ(I): 3.2 |
Reflection shell | Resolution: 2.05→2.09 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 13602 / CC1/2: 0.655 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6T7G Resolution: 2.05→99.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.692 / SU ML: 0.213 / Cross valid method: FREE R-VALUE / ESU R: 0.23 / ESU R Free: 0.19 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.039 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→99.4 Å
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Refine LS restraints |
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