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- PDB-6bjq: Eubacterium eligens beta-glucuronidase bound to glucuronic acid -

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Basic information

Entry
Database: PDB / ID: 6bjq
TitleEubacterium eligens beta-glucuronidase bound to glucuronic acid
ComponentsGlycoside Hydrolase Family 2 candidate b-glucuronidase
KeywordsHYDROLASE / Beta-glucuronidase / glycosyl hydrolase
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 / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranuronic acid / Beta-glucuronidase
Similarity search - Component
Biological speciesEubacterium eligens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPellock, S.J. / Walton, W.G. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) 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 6, 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)72,4152
Polymers72,2211
Non-polymers1941
Water1,15364
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)289,6598
Polymers288,8834
Non-polymers7774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area19520 Å2
ΔGint-115 kcal/mol
Surface area75130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.788, 179.788, 134.494
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-842-

HOH

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Components

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


Mass: 72220.680 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: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid / Glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 4.34 Å3/Da / Density % sol: 71.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / 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: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.7→29.965 Å / Num. obs: 35651 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.033 / Rrim(I) all: 0.124 / Net I/σ(I): 15.5
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 4649 / CC1/2: 0.954 / Rpim(I) all: 0.149 / Rrim(I) all: 0.564 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→29.965 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.85
RfactorNum. reflection% reflection
Rfree0.2413 1961 5.6 %
Rwork0.2179 --
obs0.2192 35008 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4804 0 13 64 4881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044937
X-RAY DIFFRACTIONf_angle_d0.7466693
X-RAY DIFFRACTIONf_dihedral_angle_d5.62908
X-RAY DIFFRACTIONf_chiral_restr0.048710
X-RAY DIFFRACTIONf_plane_restr0.004872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.76750.30911330.27052192X-RAY DIFFRACTION94
2.7675-2.84230.31671320.28892235X-RAY DIFFRACTION94
2.8423-2.92590.36471320.28832229X-RAY DIFFRACTION95
2.9259-3.02020.32191320.28252296X-RAY DIFFRACTION97
3.0202-3.12810.30021380.26082329X-RAY DIFFRACTION98
3.1281-3.25320.34141390.2532340X-RAY DIFFRACTION99
3.2532-3.4010.27521400.26792362X-RAY DIFFRACTION99
3.401-3.58010.24521400.23862367X-RAY DIFFRACTION100
3.5801-3.8040.2561420.22642397X-RAY DIFFRACTION100
3.804-4.0970.24061430.20242395X-RAY DIFFRACTION100
4.097-4.5080.22321440.18572409X-RAY DIFFRACTION100
4.508-5.15750.16851440.17322427X-RAY DIFFRACTION100
5.1575-6.4870.20521470.19692469X-RAY DIFFRACTION100
6.487-29.96650.21031550.1982600X-RAY DIFFRACTION100

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