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- PDB-7kgy: Beta-glucuronidase from Faecalibacterium prausnitzii bound to the... -

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Basic information

Entry
Database: PDB / ID: 7kgy
TitleBeta-glucuronidase from Faecalibacterium prausnitzii bound to the inhibitor UNC10201652-glucuronide
ComponentsBeta-glucuronidase
KeywordsHYDROLASE/INHIBITOR / Beta-glucuronidase / carbohydrate / glucuronic acid / inhibitor / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homologyChem-I9G
Function and homology information
Biological speciesFaecalibacterium prausnitzii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)GM137286 United States
CitationJournal: Nat Commun / Year: 2022
Title: Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract.
Authors: Zhang, J. / Walker, M.E. / Sanidad, K.Z. / Zhang, H. / Liang, Y. / Zhao, E. / Chacon-Vargas, K. / Yeliseyev, V. / Parsonnet, J. / Haggerty, T.D. / Wang, G. / Simpson, J.B. / Jariwala, P.B. / ...Authors: Zhang, J. / Walker, M.E. / Sanidad, K.Z. / Zhang, H. / Liang, Y. / Zhao, E. / Chacon-Vargas, K. / Yeliseyev, V. / Parsonnet, J. / Haggerty, T.D. / Wang, G. / Simpson, J.B. / Jariwala, P.B. / Beaty, V.V. / Yang, J. / Yang, H. / Panigrahy, A. / Minter, L.M. / Kim, D. / Gibbons, J.G. / Liu, L. / Li, Z. / Xiao, H. / Borlandelli, V. / Overkleeft, H.S. / Cloer, E.W. / Major, M.B. / Goldfarb, D. / Cai, Z. / Redinbo, M.R. / Zhang, G.
History
DepositionOct 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucuronidase
B: Beta-glucuronidase
C: Beta-glucuronidase
D: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,04911
Polymers276,4224
Non-polymers2,6277
Water29,3641630
1
A: Beta-glucuronidase
hetero molecules

B: Beta-glucuronidase
hetero molecules

D: Beta-glucuronidase
hetero molecules

C: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,04911
Polymers276,4224
Non-polymers2,6277
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-x+3/2,-y+1,z-1/21
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Buried area16880 Å2
ΔGint-95 kcal/mol
Surface area72140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.520, 128.405, 177.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Beta-glucuronidase /


Mass: 69105.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibacterium prausnitzii (bacteria)
Gene: uidA, ERS852426_02720 / Production host: Escherichia coli (E. coli) / References: beta-glucuronidase
#2: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1630 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15 mg/mL protein, 1800 uM 4-Nitrophenyl beta-D-glucuronide, 600 uM UNC10201652, 0.2 M potassium thiocyanate, 20%(w/v) PEG 3350

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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: Jul 26, 2019
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→44.32 Å / Num. obs: 132721 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.1033 / Net I/σ(I): 12.66
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.4471 / Mean I/σ(I) obs: 3.78 / Num. unique obs: 13115 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ED2

6ed2


Resolution: 2.2→44.32 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 19.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1929 1999 1.51 %
Rwork0.1468 --
obs0.1475 132686 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19009 0 182 1630 20821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819732
X-RAY DIFFRACTIONf_angle_d0.89726783
X-RAY DIFFRACTIONf_dihedral_angle_d10.7982662
X-RAY DIFFRACTIONf_chiral_restr0.0562800
X-RAY DIFFRACTIONf_plane_restr0.0053463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.21431410.16249197X-RAY DIFFRACTION100
2.26-2.320.24361410.16899235X-RAY DIFFRACTION100
2.32-2.380.26091420.16949269X-RAY DIFFRACTION100
2.38-2.460.23881420.15889276X-RAY DIFFRACTION100
2.46-2.550.25671410.16229246X-RAY DIFFRACTION100
2.55-2.650.20591430.15619271X-RAY DIFFRACTION100
2.65-2.770.21361420.15439319X-RAY DIFFRACTION100
2.77-2.920.2071420.15659268X-RAY DIFFRACTION100
2.92-3.10.21931420.15439286X-RAY DIFFRACTION100
3.1-3.340.18261430.14839333X-RAY DIFFRACTION100
3.34-3.680.17661430.13999357X-RAY DIFFRACTION100
3.68-4.210.16681430.1279404X-RAY DIFFRACTION100
4.21-5.30.14631450.12199463X-RAY DIFFRACTION100
5.3-44.320.17461490.15659763X-RAY DIFFRACTION100

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