+Open data
-Basic information
Entry | Database: PDB / ID: 6eca | |||||||||
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Title | Lactobacillus rhamnosus Beta-glucuronidase | |||||||||
Components | Beta-glucuronidase | |||||||||
Keywords | HYDROLASE / Glycosyl hydrolase | |||||||||
Function / homology | Function and homology information beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Lactobacillus rhamnosus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.853 Å | |||||||||
Authors | Biernat, K.A. / Pellock, S.J. / Bhatt, A.P. / Bivins, M.M. / Walton, W.G. / Tran, B.N.T. / Wei, L. / Snider, M.C. / Cesmat, A.P. / Tripathy, A. ...Biernat, K.A. / Pellock, S.J. / Bhatt, A.P. / Bivins, M.M. / Walton, W.G. / Tran, B.N.T. / Wei, L. / Snider, M.C. / Cesmat, A.P. / Tripathy, A. / Erie, D.A. / Redinbo, M.R.R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Sci Rep / Year: 2019 Title: Structure, function, and inhibition of drug reactivating human gut microbial beta-glucuronidases. Authors: Biernat, K.A. / Pellock, S.J. / Bhatt, A.P. / Bivins, M.M. / Walton, W.G. / Tran, B.N.T. / Wei, L. / Snider, M.C. / Cesmat, A.P. / Tripathy, A. / Erie, D.A. / Redinbo, M.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eca.cif.gz | 248.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eca.ent.gz | 198.2 KB | Display | PDB format |
PDBx/mmJSON format | 6eca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eca_validation.pdf.gz | 458.4 KB | Display | wwPDB validaton report |
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Full document | 6eca_full_validation.pdf.gz | 476.7 KB | Display | |
Data in XML | 6eca_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 6eca_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/6eca ftp://data.pdbj.org/pub/pdb/validation_reports/ec/6eca | HTTPS FTP |
-Related structure data
Related structure data | 6ec6C 6ed1C 6ed2C 3lpgS 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: 71397.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus rhamnosus (bacteria) Gene: BGK71_00200, CCE29_06935, DBP98_01505, PY66_04435, PY91_01090 Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0D6U8U4, UniProt: A0A2A5L2J1*PLUS #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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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: 2.93 Å3/Da / Density % sol: 58.02 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 17% PEG3350, 0.4 M NaCl, and and 0.1 Tris HCl pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→29.5 Å / Num. obs: 374145 / % possible obs: 99.2 % / Redundancy: 9.3 % / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.85→2.97 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LPG Resolution: 2.853→29.497 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.26 / Phase error: 20.29
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.853→29.497 Å
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Refine LS restraints |
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LS refinement shell |
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