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- PDB-6d41: Bacteriodes uniformis beta-glucuronidase 1 bound to D-glucaro-1,5... -

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Basic information

Entry
Database: PDB / ID: 6d41
TitleBacteriodes uniformis beta-glucuronidase 1 bound to D-glucaro-1,5-lactone
ComponentsBeta-galactosidase/beta-glucuronidase
KeywordsHYDROLASE
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
Chem-GCB / Beta-galactosidase/beta-glucuronidase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWalton, W.G. / Pellock, S.J. / Redinbo, M.R.
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 17, 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 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Beta-galactosidase/beta-glucuronidase
A: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,38914
Polymers140,1972
Non-polymers1,19212
Water27,0411501
1
B: Beta-galactosidase/beta-glucuronidase
A: Beta-galactosidase/beta-glucuronidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)282,77828
Polymers280,3944
Non-polymers2,38424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area21480 Å2
ΔGint-100 kcal/mol
Surface area76040 Å2
MethodPISA
2
B: Beta-galactosidase/beta-glucuronidase
hetero molecules

B: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,20512
Polymers140,1972
Non-polymers1,00810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8340 Å2
ΔGint-48 kcal/mol
Surface area40560 Å2
MethodPISA
3
A: Beta-galactosidase/beta-glucuronidase
hetero molecules

A: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,57316
Polymers140,1972
Non-polymers1,37614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8360 Å2
ΔGint-49 kcal/mol
Surface area40250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.066, 130.156, 94.490
Angle α, β, γ (deg.)90.00, 100.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1317-

HOH

21B-1373-

HOH

31A-1368-

HOH

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Components

#1: Protein Beta-galactosidase/beta-glucuronidase


Mass: 70098.500 Da / Num. of mol.: 2
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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Sugar ChemComp-GCB / (2S,3S,4S,5R)-3,4,5-trihydroxy-6-oxo-oxane-2-carboxylic acid / D-GLUCARO-1,5-LACTONE


Type: D-saccharide / Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1501 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 16% PEG 1000, Tris pH 8.5, 2mM Saccharolactone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.9→29.934 Å / Num. obs: 114979 / % possible obs: 97.7 % / Redundancy: 6.9 % / Net I/σ(I): 16.6
Reflection shellResolution: 1.9→1.93 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D1N

6d1n


Resolution: 1.9→29.934 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.05
RfactorNum. reflection% reflection
Rfree0.1686 2003 1.74 %
Rwork0.1399 --
obs0.1404 114965 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9520 0 76 1501 11097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079877
X-RAY DIFFRACTIONf_angle_d0.85513388
X-RAY DIFFRACTIONf_dihedral_angle_d15.7815852
X-RAY DIFFRACTIONf_chiral_restr0.0571402
X-RAY DIFFRACTIONf_plane_restr0.0051719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.24411350.19287913X-RAY DIFFRACTION96
1.9475-2.00020.2221650.17547929X-RAY DIFFRACTION96
2.0002-2.0590.18581230.15978016X-RAY DIFFRACTION97
2.059-2.12550.2021500.15547945X-RAY DIFFRACTION97
2.1255-2.20140.18361410.1498023X-RAY DIFFRACTION97
2.2014-2.28950.15911340.1447975X-RAY DIFFRACTION97
2.2895-2.39370.18971470.1478054X-RAY DIFFRACTION97
2.3937-2.51980.23071400.15368082X-RAY DIFFRACTION98
2.5198-2.67760.19941410.14788064X-RAY DIFFRACTION98
2.6776-2.88420.16821480.14428090X-RAY DIFFRACTION98
2.8842-3.17410.16061380.14138144X-RAY DIFFRACTION98
3.1741-3.63270.13381440.12518201X-RAY DIFFRACTION99
3.6327-4.57430.13281440.11098199X-RAY DIFFRACTION99
4.5743-29.93740.14611530.13468327X-RAY DIFFRACTION99

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