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- PDB-8geo: E. eligens beta-glucuronidase bound to 3-OH-desloratidine-glucuronide -

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Basic information

Entry
Database: PDB / ID: 8geo
TitleE. eligens beta-glucuronidase bound to 3-OH-desloratidine-glucuronide
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / beta-glucuronidase / inhibitor / glucuronide
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-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Beta-glucuronidase
Similarity search - Component
Biological speciesLachnospira eligens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsSimpson, J.B. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135218 United States
CitationJournal: Cell Host Microbe / Year: 2024
Title: Gut microbial beta-glucuronidases influence endobiotic homeostasis and are modulated by diverse therapeutics.
Authors: Simpson, J.B. / Walker, M.E. / Sekela, J.J. / Ivey, S.M. / Jariwala, P.B. / Storch, C.M. / Kowalewski, M.E. / Graboski, A.L. / Lietzan, A.D. / Walton, W.G. / Davis, K.A. / Cloer, E.W. / ...Authors: Simpson, J.B. / Walker, M.E. / Sekela, J.J. / Ivey, S.M. / Jariwala, P.B. / Storch, C.M. / Kowalewski, M.E. / Graboski, A.L. / Lietzan, A.D. / Walton, W.G. / Davis, K.A. / Cloer, E.W. / Borlandelli, V. / Hsiao, Y.C. / Roberts, L.R. / Perlman, D.H. / Liang, X. / Overkleeft, H.S. / Bhatt, A.P. / Lu, K. / Redinbo, M.R.
History
DepositionMar 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5224
Polymers69,8351
Non-polymers6873
Water543
1
A: Beta-glucuronidase
hetero molecules

A: Beta-glucuronidase
hetero molecules

A: Beta-glucuronidase
hetero molecules

A: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,08916
Polymers279,3404
Non-polymers2,74912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_554y,x,-z-2/31
crystal symmetry operation10_664-y+1,-x+1,-z-2/31
Buried area18320 Å2
ΔGint-110 kcal/mol
Surface area74420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.066, 180.066, 133.826
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

#1: Protein Beta-glucuronidase /


Mass: 69835.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospira eligens (bacteria) / Gene: uidA, ERS852490_00568, ERS852492_02599 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A174ZZA3, beta-glucuronidase
#2: Chemical ChemComp-ZBL / 8-chloro-11-(1-beta-D-glucopyranuronosylpiperidin-4-ylidene)-3-hydroxy-6,11-dihydro-5H-benzo[5,6]cyclohepta[1,2-b]pyridine


Mass: 502.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27ClN2O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.48 Å3/Da / Density % sol: 72.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.07 M Sodium cacodylate trihydrate, pH 6.5, 0.98 M sodium acetate trihydrate, and 30 % (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.89→48.45 Å / Num. obs: 29159 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 68.06 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03039 / Rpim(I) all: 0.03039 / Rrim(I) all: 0.04297 / Net I/σ(I): 13.9
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2733 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 5726 / CC1/2: 0.843 / CC star: 0.957 / Rpim(I) all: 0.2733 / Rrim(I) all: 0.4297 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→48.45 Å / SU ML: 0.4039 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7558
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2593 2000 6.86 %
Rwork0.219 27158 -
obs0.2218 29158 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.1 Å2
Refinement stepCycle: LAST / Resolution: 2.89→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4640 0 47 3 4690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214804
X-RAY DIFFRACTIONf_angle_d0.54026525
X-RAY DIFFRACTIONf_chiral_restr0.0417698
X-RAY DIFFRACTIONf_plane_restr0.0029846
X-RAY DIFFRACTIONf_dihedral_angle_d12.43891757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.960.39841390.32651895X-RAY DIFFRACTION100
2.96-3.040.3031410.28321906X-RAY DIFFRACTION100
3.04-3.130.28861390.26261894X-RAY DIFFRACTION100
3.13-3.230.33091410.27091913X-RAY DIFFRACTION99.95
3.23-3.350.3031420.25531916X-RAY DIFFRACTION99.95
3.35-3.480.30361390.23321904X-RAY DIFFRACTION100
3.48-3.640.26821420.23331911X-RAY DIFFRACTION100
3.64-3.830.28721410.22611921X-RAY DIFFRACTION100
3.83-4.070.22471420.20741933X-RAY DIFFRACTION100
4.07-4.390.20141430.18981934X-RAY DIFFRACTION100
4.39-4.830.22391420.18321938X-RAY DIFFRACTION100
4.83-5.530.24741450.1951968X-RAY DIFFRACTION100
5.53-6.960.27291480.22712004X-RAY DIFFRACTION100
6.96-48.450.24811560.20582121X-RAY DIFFRACTION99.96

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