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- PDB-6d4o: Eubacterium eligens beta-glucuronidase bound to an amoxapine-gluc... -

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Basic information

Entry
Database: PDB / ID: 6d4o
TitleEubacterium eligens beta-glucuronidase bound to an amoxapine-glucuronide conjugate
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 / 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 domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-FUV / Beta-glucuronidase
Similarity search - Component
Biological species[Eubacterium] eligens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPellock, S.J. / Walton, W.G. / Redinbo, M.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: ACS Cent Sci / Year: 2018
Title: Gut Microbial beta-Glucuronidase Inhibition via Catalytic Cycle Interception.
Authors: Pellock, S.J. / Creekmore, B.C. / Walton, W.G. / Mehta, N. / Biernat, K.A. / Cesmat, A.P. / Ariyarathna, Y. / Dunn, Z.D. / Li, B. / Jin, J. / James, L.I. / Redinbo, M.R.
History
DepositionApr 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / 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 / _citation_author.name
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3874
Polymers69,8351
Non-polymers5523
Water86548
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)281,55016
Polymers279,3404
Non-polymers2,21012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area16570 Å2
ΔGint-98 kcal/mol
Surface area73900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.954, 179.954, 134.941
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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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.) [Eubacterium] eligens (bacteria) / Gene: uidA, ERS852490_00568, ERS852492_02599 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A174ZZA3, beta-glucuronidase
#2: Chemical ChemComp-FUV / (5aR,9aR)-2-chloro-11-(4-beta-D-glucopyranuronosylpiperazin-1-yl)-5a,6,9,9a-tetrahydrodibenzo[b,f][1,4]oxazepine


Mass: 493.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28ClN3O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 4.52 Å3/Da / Density % sol: 72.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.05 M Bis-tris pH 6.5 45% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.9→29.45 Å / Num. obs: 29069 / % possible obs: 99.9 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.147 / Rrim(I) all: 0.155 / Net I/σ(I): 17
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 4621 / Rrim(I) all: 0.523 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.45 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.76
RfactorNum. reflection% reflection
Rfree0.244 2000 6.89 %
Rwork0.1992 --
obs0.2023 29040 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4739 0 36 48 4823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074897
X-RAY DIFFRACTIONf_angle_d1.2936644
X-RAY DIFFRACTIONf_dihedral_angle_d6.2962871
X-RAY DIFFRACTIONf_chiral_restr0.054700
X-RAY DIFFRACTIONf_plane_restr0.006864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-2.97260.3171410.27711910X-RAY DIFFRACTION100
2.9726-3.05290.29291400.22871882X-RAY DIFFRACTION100
3.0529-3.14260.27061400.23281896X-RAY DIFFRACTION100
3.1426-3.24390.27931390.22441890X-RAY DIFFRACTION100
3.2439-3.35970.27681410.23961904X-RAY DIFFRACTION100
3.3597-3.4940.28131400.22871897X-RAY DIFFRACTION100
3.494-3.65270.26711420.21421916X-RAY DIFFRACTION100
3.6527-3.84490.26081410.21321905X-RAY DIFFRACTION100
3.8449-4.08520.23441440.18161936X-RAY DIFFRACTION100
4.0852-4.39970.21941410.1761914X-RAY DIFFRACTION100
4.3997-4.84070.21991440.15971935X-RAY DIFFRACTION100
4.8407-5.53710.19161450.17031961X-RAY DIFFRACTION100
5.5371-6.9610.23181460.19261988X-RAY DIFFRACTION100
6.961-29.45340.23741560.19692106X-RAY DIFFRACTION100

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