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- PDB-8ges: R. hominis 2 beta-glucuronidase bound to UNC10201652-glucuronide -

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Basic information

Entry
Database: PDB / ID: 8ges
TitleR. hominis 2 beta-glucuronidase bound to UNC10201652-glucuronide
Componentsbeta-galactosidase
KeywordsHYDROLASE / beta-glucuronidase / inhibitor / glucuronide
Function / homology
Function and homology information


beta-galactosidase activity / carbohydrate metabolic process / nucleotide binding
Similarity search - Function
Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / 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 ...Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / 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-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-I9G / Glycoside hydrolase family 2 protein
Similarity search - Component
Biological speciesRoseburia hominis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 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.journal_volume / _citation.page_first / _citation.page_last / _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-galactosidase
D: beta-galactosidase
C: beta-galactosidase
B: beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,88018
Polymers343,5164
Non-polymers4,36414
Water1,22568
1
A: beta-galactosidase
B: beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,39812
Polymers171,7582
Non-polymers2,64110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: beta-galactosidase
C: beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,4826
Polymers171,7582
Non-polymers1,7244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.414, 145.950, 281.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein
beta-galactosidase


Mass: 85878.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseburia hominis (bacteria) / Gene: DWX93_05255 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A395V8I7
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-I9G / 8-(4-beta-D-glucopyranuronosylpiperazin-1-yl)-5-(morpholin-4-yl)-1,2,3,4-tetrahydro[1,2,3]triazino[4',5':4,5]thieno[2,3 -c]isoquinoline / UNC10201652-glucuronic acid conjugate


Mass: 587.648 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H33N7O7S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.17 M Ammonium Acetate, 0.085M Sodium Citrate:HCl, pH 5.6 and 25.5 % (w/v) PEG 4000, 15 % (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 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→49.96 Å / Num. obs: 113475 / % possible obs: 99.3 % / Redundancy: 2 % / Biso Wilson estimate: 56.08 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.07723 / Rpim(I) all: 0.07723 / Rrim(I) all: 0.1092 / Net I/σ(I): 7.37
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.7643 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 11246 / CC1/2: 0.559 / CC star: 0.847 / Rpim(I) all: 0.7643 / Rrim(I) all: 1.081 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.96 Å / SU ML: 0.4397 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2825 2000 1.76 %
Rwork0.2314 111414 -
obs0.2323 113414 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.83 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20494 0 299 68 20861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003421377
X-RAY DIFFRACTIONf_angle_d0.758929116
X-RAY DIFFRACTIONf_chiral_restr0.05183030
X-RAY DIFFRACTIONf_plane_restr0.00353766
X-RAY DIFFRACTIONf_dihedral_angle_d19.94687556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.43521410.37347866X-RAY DIFFRACTION99.48
2.77-2.840.39371420.35267871X-RAY DIFFRACTION99.63
2.84-2.930.42191410.33947887X-RAY DIFFRACTION99.73
2.93-3.020.42131430.32697918X-RAY DIFFRACTION99.85
3.02-3.130.371420.31727902X-RAY DIFFRACTION99.38
3.13-3.250.33991420.27537929X-RAY DIFFRACTION99.63
3.25-3.40.29591410.25427889X-RAY DIFFRACTION99.17
3.4-3.580.30871430.24037945X-RAY DIFFRACTION99.72
3.58-3.810.27611420.22847941X-RAY DIFFRACTION99.74
3.81-4.10.25091440.19797959X-RAY DIFFRACTION99.35
4.1-4.510.22451420.18897964X-RAY DIFFRACTION99.12
4.51-5.160.24261420.18377960X-RAY DIFFRACTION98.64
5.16-6.50.26671460.20798076X-RAY DIFFRACTION99.28
6.5-49.960.22691490.1988307X-RAY DIFFRACTION98.2

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