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Yorodumi- PDB-6jz6: b-glucuronidase from Ruminococcus gnavus in complex with C6-subst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jz6 | ||||||
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Title | b-glucuronidase from Ruminococcus gnavus in complex with C6-substituted uronic isofagomine | ||||||
Components | Beta-glucuronidase | ||||||
Keywords | HYDROLASE / b-glucuronidase | ||||||
Function / homology | Function and homology information : / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process / signaling receptor binding / extracellular space Similarity search - Function | ||||||
Biological species | Ruminococcus gnavus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.605 Å | ||||||
Authors | Dashnyam, P. / Lin, H.Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Substituent Position of Iminocyclitols Determines the Potency and Selectivity for Gut Microbial Xenobiotic-Reactivating Enzymes. Authors: Dashnyam, P. / Lin, H.Y. / Chen, C.Y. / Gao, S. / Yeh, L.F. / Hsieh, W.C. / Tu, Z. / Lin, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jz6.cif.gz | 493.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jz6.ent.gz | 401.9 KB | Display | PDB format |
PDBx/mmJSON format | 6jz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jz6_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6jz6_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6jz6_validation.xml.gz | 51.7 KB | Display | |
Data in CIF | 6jz6_validation.cif.gz | 78.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/6jz6 ftp://data.pdbj.org/pub/pdb/validation_reports/jz/6jz6 | HTTPS FTP |
-Related structure data
Related structure data | 6jz1C 6jz2C 6jz3C 6jz4C 6jz5C 6jz7C 6jz8C 5z18S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 70038.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Gene: uidA / Production host: Escherichia coli (E. coli) / References: UniProt: Q6W7J7 #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: 2.51 Å3/Da / Density % sol: 50.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 70% MPD, 0.1 M HEPES, pH 7.5, 0.2 M CaCl2 |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 17, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→30 Å / Num. obs: 174580 / % possible obs: 97.2 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.033 / Rrim(I) all: 0.076 / Χ2: 0.874 / Net I/σ(I): 10.3 / Num. measured all: 908745 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Z18 Resolution: 1.605→29.001 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.19 Å2 / Biso mean: 18.4676 Å2 / Biso min: 3.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.605→29.001 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 218.9248 Å / Origin y: -859.9004 Å / Origin z: 361.7432 Å
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Refinement TLS group |
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