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- PDB-6eca: Lactobacillus rhamnosus Beta-glucuronidase -

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Basic information

Entry
Database: PDB / ID: 6eca
TitleLactobacillus rhamnosus Beta-glucuronidase
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / Glycosyl hydrolase
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 / 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 ...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
Beta-glucuronidase / Beta-glucuronidase
Similarity search - Component
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.853 Å
AuthorsBiernat, 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
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA098468 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA207416 United States
CitationJournal: 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
DepositionAug 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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)143,1076
Polymers142,7952
Non-polymers3124
Water3,369187
1
A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)286,21412
Polymers285,5904
Non-polymers6238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area18320 Å2
ΔGint-115 kcal/mol
Surface area75210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.800, 154.800, 241.906
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Beta-glucuronidase


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 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→29.5 Å / Num. obs: 374145 / % possible obs: 99.2 % / Redundancy: 9.3 % / Net I/σ(I): 12.6
Reflection shellResolution: 2.85→2.97 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LPG

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
RfactorNum. reflection% reflection
Rfree0.2125 1996 4.97 %
Rwork0.149 --
obs0.1522 40158 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.853→29.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9478 0 19 187 9684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089782
X-RAY DIFFRACTIONf_angle_d0.92113269
X-RAY DIFFRACTIONf_dihedral_angle_d15.9555708
X-RAY DIFFRACTIONf_chiral_restr0.0511388
X-RAY DIFFRACTIONf_plane_restr0.0051742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8531-2.92430.32371270.22472428X-RAY DIFFRACTION90
2.9243-3.00330.28411390.20282669X-RAY DIFFRACTION100
3.0033-3.09160.26231430.18962711X-RAY DIFFRACTION100
3.0916-3.19130.27461410.1782701X-RAY DIFFRACTION100
3.1913-3.30520.23221410.16962709X-RAY DIFFRACTION100
3.3052-3.43740.23141420.162693X-RAY DIFFRACTION100
3.4374-3.59350.25241400.15842707X-RAY DIFFRACTION100
3.5935-3.78260.21971430.14882725X-RAY DIFFRACTION100
3.7826-4.01910.16851410.12552717X-RAY DIFFRACTION100
4.0191-4.32850.17311450.11722755X-RAY DIFFRACTION100
4.3285-4.76250.16311440.10212756X-RAY DIFFRACTION100
4.7625-5.44790.16661460.11322776X-RAY DIFFRACTION100
5.4479-6.84950.18071480.15322824X-RAY DIFFRACTION100
6.8495-29.49880.23311560.16832991X-RAY DIFFRACTION100

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