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- PDB-8get: R. hominis 2 beta-glucuronidase bound to norquetiapine-glucuronide -

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Basic information

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


beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / 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 ...Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / 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-D-glucopyranuronic acid / FLAVIN MONONUCLEOTIDE / : / Glycoside hydrolase family 2 protein
Similarity search - Component
Biological speciesRoseburia hominis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
Revision 1.2Jun 26, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-galactosidase
B: beta-galactosidase
C: beta-galactosidase
D: beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,27618
Polymers344,2094
Non-polymers3,06814
Water00
1
A: beta-galactosidase
C: beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,9599
Polymers172,1042
Non-polymers1,8557
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-galactosidase
hetero molecules

D: beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,3179
Polymers172,1042
Non-polymers1,2137
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1/2,z+1/21
Unit cell
Length a, b, c (Å)100.466, 146.290, 281.432
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: 86052.133 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H10O7
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
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-ZG5 / 11-(4-beta-D-glucopyranuronosylpiperazin-1-yl)dibenzo[b,f][1,4]thiazepine


Mass: 471.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N3O6S
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: 59 %
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: 2.9→48.05 Å / Num. obs: 82560 / % possible obs: 89 % / Redundancy: 1.9 % / Biso Wilson estimate: 65.6 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06691 / Rpim(I) all: 0.06691 / Rrim(I) all: 0.09463 / Net I/σ(I): 8.69
Reflection shellResolution: 2.9→3.004 Å / Rmerge(I) obs: 0.5845 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 8379 / CC1/2: 0.627 / CC star: 0.878 / Rpim(I) all: 0.5845 / Rrim(I) all: 0.8266

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Processing

Software
NameVersionClassification
phenix.refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.05 Å / SU ML: 0.475 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.8081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.269 1999 2.42 %
Rwork0.224 80509 -
obs0.2251 82508 89.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.82 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20463 0 207 0 20670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003221232
X-RAY DIFFRACTIONf_angle_d0.609628908
X-RAY DIFFRACTIONf_chiral_restr0.0453030
X-RAY DIFFRACTIONf_plane_restr0.00343760
X-RAY DIFFRACTIONf_dihedral_angle_d18.04017449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.39871440.3645794X-RAY DIFFRACTION91.03
2.97-3.050.42331450.34025863X-RAY DIFFRACTION91.21
3.05-3.140.34421440.31695788X-RAY DIFFRACTION91.01
3.14-3.240.37931440.29965798X-RAY DIFFRACTION90.75
3.24-3.360.35121420.29315747X-RAY DIFFRACTION89.87
3.36-3.490.3841440.25655779X-RAY DIFFRACTION90.57
3.49-3.650.28381440.23585783X-RAY DIFFRACTION90.21
3.65-3.850.25911430.22045738X-RAY DIFFRACTION89.34
3.85-4.090.26651420.21025753X-RAY DIFFRACTION89.36
4.09-4.40.24661410.19045672X-RAY DIFFRACTION87.92
4.4-4.840.21381420.16895695X-RAY DIFFRACTION88.07
4.84-5.550.21951410.18495712X-RAY DIFFRACTION87.48
5.55-6.980.24211410.2095647X-RAY DIFFRACTION86.03
6.98-48.050.20511420.20215740X-RAY DIFFRACTION84.08

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