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Yorodumi- PDB-7odj: Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocycl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7odj | |||||||||
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Title | Exo-mannosidase from Cellvibrio mixtus bound to N-alkyl mannocyclophellitol aziridine | |||||||||
Components | Man5A | |||||||||
Keywords | 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 Function and homology information | |||||||||
Biological species | Cellvibrio mixtus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | McGregor, N.G.S. / Davies, G.J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Org.Biomol.Chem. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7odj.cif.gz | 329 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7odj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7odj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/7odj ftp://data.pdbj.org/pub/pdb/validation_reports/od/7odj | HTTPS FTP |
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-Related structure data
Related structure data | 7omiC 7omsC 7op6C 7op7C 1uuqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Cellvibrio mixtus (bacteria) / Gene: man5A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6QT42 | ||||||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å | ||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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