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- PDB-6ncz: Crystal structure of hybrid beta-glucuronidase/beta-galacturonida... -

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Basic information

Entry
Database: PDB / ID: 6ncz
TitleCrystal structure of hybrid beta-glucuronidase/beta-galacturonidase from Fusicatenibacter saccharivorans bound to phenyl-thio-beta-D-glucuronide
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / glycoside hydrolase family 2 / beta-glucuronidase / beta-galacturonidase
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / 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 ...Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / 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 domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
phenyl 1-thio-beta-D-glucopyranosiduronic acid / Beta-glucuronidase
Similarity search - Component
Biological speciesFusicatenibacter saccharivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWalton, W.G. / Pellock, S.J. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Biochemistry / Year: 2019
Title: Selecting a Single Stereocenter: The Molecular Nuances That Differentiate beta-Hexuronidases in the Human Gut Microbiome.
Authors: Pellock, S.J. / Walton, W.G. / Redinbo, M.R.
History
DepositionDec 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 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 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-glucuronidase
B: Beta-glucuronidase
C: Beta-glucuronidase
D: Beta-glucuronidase
E: Beta-glucuronidase
F: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)429,85418
Polymers427,5836
Non-polymers2,27012
Water31,8511768
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25600 Å2
ΔGint-58 kcal/mol
Surface area119450 Å2
2
A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2856
Polymers142,5282
Non-polymers7574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-21 kcal/mol
Surface area41970 Å2
MethodPISA
3
C: Beta-glucuronidase
E: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2856
Polymers142,5282
Non-polymers7574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-19 kcal/mol
Surface area42280 Å2
MethodPISA
4
D: Beta-glucuronidase
F: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2856
Polymers142,5282
Non-polymers7574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-20 kcal/mol
Surface area42430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.134, 116.916, 117.604
Angle α, β, γ (deg.)60.32, 62.53, 87.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-glucuronidase


Mass: 71263.914 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusicatenibacter saccharivorans (bacteria)
Gene: uidA_2, ERS852406_01826 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A174EHD1, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1768 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium tartrate dibasic, 20% (w/v) PEG 3350 with 1 mM phenyl-thio-beta-D-glucuronide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.2→29.7 Å / Num. obs: 215731 / % possible obs: 97.4 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.071 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.093 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 21435 / CC1/2: 0.498 / Rpim(I) all: 0.664 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LPF

3lpf


Resolution: 2.2→29.67 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 2010 0.93 %
Rwork0.1806 --
obs0.181 215654 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28928 0 150 1768 30846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00829756
X-RAY DIFFRACTIONf_angle_d0.94340256
X-RAY DIFFRACTIONf_dihedral_angle_d7.47517810
X-RAY DIFFRACTIONf_chiral_restr0.0564280
X-RAY DIFFRACTIONf_plane_restr0.0055200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.32051680.306215157X-RAY DIFFRACTION97
2.255-2.31590.31491170.287715168X-RAY DIFFRACTION97
2.3159-2.38410.30271360.265815093X-RAY DIFFRACTION96
2.3841-2.4610.30651550.253715103X-RAY DIFFRACTION97
2.461-2.54890.27041330.235115236X-RAY DIFFRACTION97
2.5489-2.65090.30461320.21415256X-RAY DIFFRACTION97
2.6509-2.77150.23841670.207815249X-RAY DIFFRACTION98
2.7715-2.91740.25291430.205615243X-RAY DIFFRACTION97
2.9174-3.10010.28481440.193115342X-RAY DIFFRACTION98
3.1001-3.33910.21591450.182115317X-RAY DIFFRACTION98
3.3391-3.67460.19591430.16215322X-RAY DIFFRACTION98
3.6746-4.2050.17321430.134915376X-RAY DIFFRACTION98
4.205-5.2930.16781430.126215368X-RAY DIFFRACTION98
5.293-29.67260.14731410.155815414X-RAY DIFFRACTION98

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