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- PDB-7odj: Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocycl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7odj | |||||||||
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Title | Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocyclophellitol aziridine | |||||||||
![]() | Man5A | |||||||||
![]() | HYDROLASE / Mannosidase / covalent inhibitor / cyclophellitol / cellvibrio | |||||||||
Function / homology | Mannan endo-1,4-beta-mannosidase-like / mannan endo-1,4-beta-mannosidase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / ACETATE ION / Chem-VEE / Man5A![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | McGregor, N.G.S. / Davies, G.J. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 329 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 719.6 KB | Display | ![]() |
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Full document | ![]() | 721.4 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7omiC ![]() 7omsC ![]() 7op6C ![]() 7op7C ![]() 1uuqS 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: 50230.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-VEE / ( | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.05 % / Description: Rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.2 M ammonium sulfate, 24% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 24, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97629 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.3→68.403 Å / Num. obs: 116329 / % possible obs: 98.8 % / Redundancy: 21.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.035 / Rrim(I) all: 0.121 / Net I/σ(I): 21.3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1UUQ Resolution: 1.3→68.403 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.357 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.04 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: 15.895 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→68.403 Å
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Refine LS restraints |
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LS refinement shell |
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