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- PDB-6jz8: b-glucuronidase from Ruminococcus gnavus in complex with D-glucar... -

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Basic information

Entry
Database: PDB / ID: 6jz8
Titleb-glucuronidase from Ruminococcus gnavus in complex with D-glucaro 1,5-lactone
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / b-glucuronidase
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily ...Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-GCB / Beta-glucuronidase
Similarity search - Component
Biological species[Ruminococcus] gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.583 Å
AuthorsDashnyam, P. / Lin, H.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: 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
DepositionApr 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4624
Polymers140,0782
Non-polymers3842
Water19,8531102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-23 kcal/mol
Surface area41860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.560, 103.345, 112.281
Angle α, β, γ (deg.)90.000, 130.990, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-934-

HOH

21A-1092-

HOH

31B-1075-

HOH

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Components

#1: Protein Beta-glucuronidase


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: Sugar ChemComp-GCB / (2S,3S,4S,5R)-3,4,5-trihydroxy-6-oxo-oxane-2-carboxylic acid / D-GLUCARO-1,5-LACTONE


Type: D-saccharide / Mass: 192.124 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 70% MPD, 0.1 M HEPES, pH 7.5, 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→30 Å / Num. obs: 183679 / % possible obs: 97.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Χ2: 0.889 / Net I/σ(I): 15.7 / Num. measured all: 1120545
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.645.40.552179850.8420.2610.6120.75195.4
1.64-1.75.90.428180540.910.1930.470.82395.9
1.7-1.7860.295182160.9570.1310.3230.90696.3
1.78-1.876.20.203182270.9790.0890.2220.96396.6
1.87-1.996.30.133182360.9890.0580.1451.06297
1.99-2.146.30.087184390.9950.0380.0951.00397.4
2.14-2.366.30.06184730.9970.0260.0650.89897.8
2.36-2.76.30.045185920.9980.020.050.78498.1
2.7-3.46.20.038186790.9980.0170.0420.74698.4
3.4-306.10.041187780.9970.0180.0450.9398

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Processing

Software
NameVersionClassification
PHENIX1.9 1692refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z19

5z19


Resolution: 1.583→29.95 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1744 1995 -
Rwork0.1625 --
obs-183679 96.26 %
Displacement parametersBiso max: 73.61 Å2 / Biso mean: 17.4162 Å2 / Biso min: 4.67 Å2
Refinement stepCycle: LAST / Resolution: 1.583→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9486 0 26 1102 10614
LS refinement shellResolution: 1.583→1.64 Å
RfactorNum. reflection% reflection
Rfree0.1744 --
Rwork0.1625 --
obs-3330 87.65 %

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