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Yorodumi- PDB-7uz2: Structure of beta-glycosidase from Sulfolobus solfataricus in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uz2 | ||||||
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Title | Structure of beta-glycosidase from Sulfolobus solfataricus in complex with C5a-fluoro-valienide. | ||||||
Components | Beta-galactosidase | ||||||
Keywords | HYDROLASE / Covalent Inhibition / Glycoside Hydrolase | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Saccharolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Danby, P.M. / Jeong, A. / Sim, L. / Sweeney, R.P. / Wardman, J.F. / Geissner, A. / Worrall, L.J. / Strynadka, N.C.J. / Withers, S.G. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Vinyl Halide-Modified Unsaturated Cyclitols are Mechanism-Based Glycosidase Inhibitors. Authors: Danby, P.M. / Jeong, A. / Sim, L. / Sweeney, R.P. / Wardman, J.F. / Karimi, R. / Geissner, A. / Worrall, L.J. / Reid, J.P. / Strynadka, N.C.J. / Withers, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uz2.cif.gz | 391.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uz2.ent.gz | 311.9 KB | Display | PDB format |
PDBx/mmJSON format | 7uz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uz2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7uz2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7uz2_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 7uz2_validation.cif.gz | 54.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/7uz2 ftp://data.pdbj.org/pub/pdb/validation_reports/uz/7uz2 | HTTPS FTP |
-Related structure data
Related structure data | 7uz1C 1uwrS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 56826.465 Da / Num. of mol.: 2 / Mutation: A235H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus solfataricus (archaea) Gene: HFC64_10340, SSOP1_3114, SULA_0798, SULB_0800, SULC_0798, SULZ_04135 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3K5E4 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 3.44 Å3/Da / Density % sol: 64.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10 - 13 % PEG 4000, 0.1 M Sodium Acetate, 0.2M Ammonium Acetate, 5% ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→47.8 Å / Num. obs: 136568 / % possible obs: 99.9 % / Redundancy: 10.2 % / CC1/2: 1 / Rmerge(I) obs: 0.027 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.83→1.88 Å / Rmerge(I) obs: 1.115 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 6735 / CC1/2: 0.28 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1uwr Resolution: 1.83→45.419 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.211 / SU B: 4.186 / SU ML: 0.115 / Average fsc free: 0.8168 / Average fsc work: 0.8297 / Cross valid method: FREE R-VALUE / ESU R: 0.113 / ESU R Free: 0.114 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: 41.337 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→45.419 Å
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Refine LS restraints |
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LS refinement shell |
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