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- PDB-6d7f: Bacteroides uniformis beta-glucuronidase 1 bound to thiophenyl-be... -

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Basic information

Entry
Database: PDB / ID: 6d7f
TitleBacteroides uniformis beta-glucuronidase 1 bound to thiophenyl-beta-D-glucuronide
ComponentsBeta-galactosidase/beta-glucuronidase
KeywordsHYDROLASE / glycosyl hydrolase 2 / beta-glucuronidase
Function / homology
Function and homology information


beta-glucuronidase / beta-glucuronidase activity / carbohydrate metabolic process
Similarity search - Function
: / 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, 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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
phenyl 1-thio-beta-D-glucopyranosiduronic acid / Beta-galactosidase/beta-glucuronidase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWalton, W.G. / Pellock, S.J. / 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: J. Biol. Chem. / Year: 2018
Title: Three structurally and functionally distinct beta-glucuronidases from the human gut microbeBacteroides uniformis.
Authors: Pellock, S.J. / Walton, W.G. / Biernat, K.A. / Torres-Rivera, D. / Creekmore, B.C. / Xu, Y. / Liu, J. / Tripathy, A. / Stewart, L.J. / Redinbo, M.R.
History
DepositionApr 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase/beta-glucuronidase
B: Beta-galactosidase/beta-glucuronidase
C: Beta-galactosidase/beta-glucuronidase
D: Beta-galactosidase/beta-glucuronidase
E: Beta-galactosidase/beta-glucuronidase
F: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)424,23636
Polymers420,5916
Non-polymers3,64530
Water28,1211561
1
A: Beta-galactosidase/beta-glucuronidase
D: Beta-galactosidase/beta-glucuronidase
hetero molecules

F: Beta-galactosidase/beta-glucuronidase
hetero molecules

C: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,87825
Polymers280,3944
Non-polymers2,48421
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_544-y,x-y-1,z-1/31
Buried area18600 Å2
ΔGint-114 kcal/mol
Surface area76940 Å2
2
B: Beta-galactosidase/beta-glucuronidase
E: Beta-galactosidase/beta-glucuronidase
hetero molecules

B: Beta-galactosidase/beta-glucuronidase
E: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,71522
Polymers280,3944
Non-polymers2,32118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area18000 Å2
ΔGint-89 kcal/mol
Surface area77770 Å2
3
A: Beta-galactosidase/beta-glucuronidase
D: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,48513
Polymers140,1972
Non-polymers1,28811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-52 kcal/mol
Surface area40680 Å2
MethodPISA
4
B: Beta-galactosidase/beta-glucuronidase
hetero molecules

E: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,35811
Polymers140,1972
Non-polymers1,1619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area6780 Å2
ΔGint-41 kcal/mol
Surface area41110 Å2
MethodPISA
5
C: Beta-galactosidase/beta-glucuronidase
hetero molecules

F: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,39312
Polymers140,1972
Non-polymers1,19610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+y+1,-x,z-2/31
Buried area6920 Å2
ΔGint-55 kcal/mol
Surface area40720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)252.177, 252.177, 107.289
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-1562-

HOH

21E-916-

HOH

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Components

#1: Protein
Beta-galactosidase/beta-glucuronidase


Mass: 70098.500 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Gene: uidA_4, ERS417307_01040 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A174CQK8, beta-glucuronidase
#2: Sugar
ChemComp-FYJ / phenyl 1-thio-beta-D-glucopyranosiduronic acid / phenyl 1-thio-beta-D-glucosiduronic acid / phenyl 1-thio-D-glucosiduronic acid / phenyl 1-thio-glucosiduronic acid


Type: D-saccharide / Mass: 286.301 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H14O6S
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1561 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium Sulfate, 20% PEG 3350, 10mM Thiophenyl-beta-D-glucuronide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.4→29.3 Å / Num. obs: 152030 / % possible obs: 99.8 % / Redundancy: 20.3 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 23.4
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.296 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.33
RfactorNum. reflection% reflection
Rfree0.2467 2001 1.32 %
Rwork0.1739 --
obs0.1749 151995 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28560 0 233 1561 30354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00729543
X-RAY DIFFRACTIONf_angle_d0.90940037
X-RAY DIFFRACTIONf_dihedral_angle_d15.49617456
X-RAY DIFFRACTIONf_chiral_restr0.0534200
X-RAY DIFFRACTIONf_plane_restr0.0055130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.30441410.222710563X-RAY DIFFRACTION100
2.46-2.52650.30651410.218510698X-RAY DIFFRACTION100
2.5265-2.60080.33121420.214310613X-RAY DIFFRACTION100
2.6008-2.68470.3381440.211710654X-RAY DIFFRACTION100
2.6847-2.78060.29991420.21110616X-RAY DIFFRACTION100
2.7806-2.89180.29841390.205810675X-RAY DIFFRACTION100
2.8918-3.02330.28181390.203610643X-RAY DIFFRACTION100
3.0233-3.18250.22561460.192710738X-RAY DIFFRACTION100
3.1825-3.38160.23431440.187610716X-RAY DIFFRACTION100
3.3816-3.64230.26181450.174210699X-RAY DIFFRACTION100
3.6423-4.0080.26541420.160610757X-RAY DIFFRACTION100
4.008-4.5860.19751430.140810774X-RAY DIFFRACTION100
4.586-5.77070.19861460.139410826X-RAY DIFFRACTION100
5.7707-29.29770.21470.14911022X-RAY DIFFRACTION100

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