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- PDB-6d6w: Bacteroides uniformis beta-glucuronidase 1 bound to glucuronate -

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Basic information

Entry
Database: PDB / ID: 6d6w
TitleBacteroides uniformis beta-glucuronidase 1 bound to glucuronate
ComponentsBeta-galactosidase/beta-glucuronidase
KeywordsHYDROLASE / glycosyl hydrolase / beta-glucuronidase
Function / homology
Function and homology information


beta-glucuronidase activity / beta-glucuronidase / carbohydrate metabolic process
Similarity search - Function
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
alpha-D-glucopyranuronic acid / Beta-glucuronidase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 23, 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 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Mar 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,41724
Polymers280,3944
Non-polymers2,02320
Water76,7804262
1
A: Beta-galactosidase/beta-glucuronidase
B: Beta-galactosidase/beta-glucuronidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)282,41724
Polymers280,3944
Non-polymers2,02320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area20310 Å2
ΔGint-100 kcal/mol
Surface area75940 Å2
2
C: Beta-galactosidase/beta-glucuronidase
hetero molecules

C: Beta-galactosidase/beta-glucuronidase
hetero molecules

D: Beta-galactosidase/beta-glucuronidase
hetero molecules

D: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,41724
Polymers280,3944
Non-polymers2,02320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_756-x+5/2,y+1/2,-z+11
Buried area20340 Å2
ΔGint-101 kcal/mol
Surface area76380 Å2
3
A: Beta-galactosidase/beta-glucuronidase
hetero molecules

B: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,20912
Polymers140,1972
Non-polymers1,01210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area8000 Å2
ΔGint-46 kcal/mol
Surface area40130 Å2
MethodPISA
4
C: Beta-galactosidase/beta-glucuronidase
hetero molecules

D: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,20912
Polymers140,1972
Non-polymers1,01210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area8000 Å2
ΔGint-45 kcal/mol
Surface area40360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.175, 133.920, 163.436
Angle α, β, γ (deg.)90.00, 100.31, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1502-

HOH

21A-1705-

HOH

31B-1475-

HOH

41B-1617-

HOH

51C-1481-

HOH

61C-1732-

HOH

71D-1768-

HOH

81D-1779-

HOH

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Components

#1: Protein
Beta-galactosidase/beta-glucuronidase


Mass: 70098.500 Da / Num. of mol.: 4
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-GCU / alpha-D-glucopyranuronic acid / alpha-D-glucuronic acid / D-glucuronic acid / glucuronic acid / Glucuronic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O7 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4262 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium Citrate: Citrate Acid, pH 5.5, 20% PEG 3000, 20mM Glucuronic Acid

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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: 1.8→29.98 Å / Num. all: 261960 / Num. obs: 261936 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.83 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.793 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.72
RfactorNum. reflection% reflection
Rfree0.2286 1999 0.76 %
Rwork0.1802 --
obs0.1806 261936 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19040 0 128 4262 23430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00619664
X-RAY DIFFRACTIONf_angle_d0.87426652
X-RAY DIFFRACTIONf_dihedral_angle_d15.94411636
X-RAY DIFFRACTIONf_chiral_restr0.0582800
X-RAY DIFFRACTIONf_plane_restr0.0053416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.25791420.211818514X-RAY DIFFRACTION100
1.845-1.89490.26431430.203418597X-RAY DIFFRACTION100
1.8949-1.95060.26991420.199918408X-RAY DIFFRACTION100
1.9506-2.01360.23711420.189618557X-RAY DIFFRACTION100
2.0136-2.08550.23061420.183918476X-RAY DIFFRACTION100
2.0855-2.1690.22861430.181918570X-RAY DIFFRACTION100
2.169-2.26770.221430.181718534X-RAY DIFFRACTION100
2.2677-2.38720.23921420.182218531X-RAY DIFFRACTION100
2.3872-2.53670.2331430.193318540X-RAY DIFFRACTION100
2.5367-2.73240.25291430.190418579X-RAY DIFFRACTION100
2.7324-3.00720.24391430.186318553X-RAY DIFFRACTION100
3.0072-3.44180.23091430.1718612X-RAY DIFFRACTION100
3.4418-4.33410.19531430.153718671X-RAY DIFFRACTION100
4.3341-29.79690.19881450.170418795X-RAY DIFFRACTION100

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