+Open data
-Basic information
Entry | Database: PDB / ID: 7omi | ||||||
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Title | Bs164 in complex with mannocyclophellitol epoxide | ||||||
Components | Glyco_hydro_42M domain-containing protein | ||||||
Keywords | HYDROLASE / Inhibitor complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides salyersiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Armstrong, Z. / Mcgregor, N. / Davies, G. | ||||||
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 | 7omi.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7omi.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7omi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7omi_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7omi_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 7omi_validation.xml.gz | 149.8 KB | Display | |
Data in CIF | 7omi_validation.cif.gz | 215.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/7omi ftp://data.pdbj.org/pub/pdb/validation_reports/om/7omi | HTTPS FTP |
-Related structure data
Related structure data | 7odjC 7omsC 7op6C 7op7C 6t7gS 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 12 molecules AAABBBCCCDDDEEEFFF
#1: Protein | Mass: 76676.672 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides salyersiae (bacteria) / Gene: HMPREF1071_03408 / Production host: Escherichia coli (E. coli) / References: UniProt: I9SUA3 #5: Sugar | ChemComp-VKN / ( |
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-Non-polymers , 4 types, 2182 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-TLA / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Ammonium tartrate pH 6.5 , 14 % PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976284 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976284 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→65.87 Å / Num. obs: 438305 / % possible obs: 97.2 % / Redundancy: 3.1 % / CC1/2: 0.994 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.76→1.79 Å / Num. unique obs: 21409 / CC1/2: 0.302 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6T7G Resolution: 1.76→65.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.135 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: 34.914 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→65.87 Å
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Refine LS restraints |
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LS refinement shell |
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