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- PDB-6bo6: Eubacterium eligens beta-glucuronidase bound to UNC4917 glucuroni... -

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Basic information

Entry
Database: PDB / ID: 6bo6
TitleEubacterium eligens beta-glucuronidase bound to UNC4917 glucuronic acid conjugate
ComponentsGlycoside Hydrolase Family 2 candidate b-glucuronidase
KeywordsHYDROLASE / glycosyl hydrolase / beta-glucuronidase / HORMONE
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process / signaling receptor binding / extracellular space
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 ...Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / 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 / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-E0V / Beta-glucuronidase
Similarity search - Component
Biological speciesEubacterium eligens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.801 Å
AuthorsPellock, S.J. / Walton, W.G. / Redinbo, M.R.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
National Science Foundation (NSF, United States) United States
CitationJournal: ACS Cent Sci / Year: 2018
Title: Gut Microbial beta-Glucuronidase Inhibition via Catalytic Cycle Interception.
Authors: Pellock, S.J. / Creekmore, B.C. / Walton, W.G. / Mehta, N. / Biernat, K.A. / Cesmat, A.P. / Ariyarathna, Y. / Dunn, Z.D. / Li, B. / Jin, J. / James, L.I. / Redinbo, M.R.
History
DepositionNov 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside Hydrolase Family 2 candidate b-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1112
Polymers69,6061
Non-polymers5061
Water34219
1
A: Glycoside Hydrolase Family 2 candidate b-glucuronidase
hetero molecules

A: Glycoside Hydrolase Family 2 candidate b-glucuronidase
hetero molecules

A: Glycoside Hydrolase Family 2 candidate b-glucuronidase
hetero molecules

A: Glycoside Hydrolase Family 2 candidate b-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,4468
Polymers278,4244
Non-polymers2,0224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_554y,x,-z-2/31
crystal symmetry operation10_444-y-1,-x-1,-z-2/31
Buried area12480 Å2
ΔGint-80 kcal/mol
Surface area66570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.443, 179.443, 133.778
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Glycoside Hydrolase Family 2 candidate b-glucuronidase


Mass: 69605.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium eligens (strain ATCC 27750 / VPI C15-48) (bacteria)
Strain: ATCC 27750 / VPI C15-48 / Gene: EUBELI_20590 / Production host: Escherichia coli (E. coli) / References: UniProt: C4Z6Z2
#2: Chemical ChemComp-E0V / 4-(4-beta-D-glucopyranuronosylpiperazin-1-yl)-2,7-bis(methylamino)pyrido[3',2':4,5]thieno[3,2-d]pyrimidine


Mass: 505.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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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: 4.47 Å3/Da / Density % sol: 72.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 400, 0.1 M bis-tris pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.8→29.37 Å / Num. obs: 31703 / % possible obs: 99.9 % / Redundancy: 17.5 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.02 / Rrim(I) all: 0.085 / Net I/σ(I): 29.2
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.672 / Num. unique obs: 4515 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 2.801→29.368 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.14
RfactorNum. reflection% reflection
Rfree0.2918 1959 6.29 %
Rwork0.2576 --
obs0.2598 31149 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.801→29.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3982 0 35 19 4036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054128
X-RAY DIFFRACTIONf_angle_d0.7445596
X-RAY DIFFRACTIONf_dihedral_angle_d7.2862395
X-RAY DIFFRACTIONf_chiral_restr0.047576
X-RAY DIFFRACTIONf_plane_restr0.004724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-2.87090.38221310.32041899X-RAY DIFFRACTION92
2.8709-2.94840.32571360.29421959X-RAY DIFFRACTION94
2.9484-3.03510.32821290.27092005X-RAY DIFFRACTION96
3.0351-3.1330.31511350.26652040X-RAY DIFFRACTION97
3.133-3.24480.32791400.28062057X-RAY DIFFRACTION99
3.2448-3.37450.33511390.2912046X-RAY DIFFRACTION98
3.3745-3.52790.32131360.2642097X-RAY DIFFRACTION99
3.5279-3.71350.29471400.25762095X-RAY DIFFRACTION100
3.7135-3.94570.3091420.22742109X-RAY DIFFRACTION100
3.9457-4.24950.24221410.22612108X-RAY DIFFRACTION100
4.2495-4.67560.24321420.22152137X-RAY DIFFRACTION100
4.6756-5.34860.27071450.23272151X-RAY DIFFRACTION100
5.3486-6.72530.28851470.26452185X-RAY DIFFRACTION100
6.7253-29.36990.30141560.29352302X-RAY DIFFRACTION100

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