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- PDB-6ncx: Crystal structure of GH2 beta-galacturonidase from Eisenbergiella... -

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Basic information

Entry
Database: PDB / ID: 6ncx
TitleCrystal structure of GH2 beta-galacturonidase from Eisenbergiella tayi bound to galacturonate
ComponentsBeta-galacturonidase
KeywordsHYDROLASE / glycoside hydrolase family 2 / beta-galacturonidase
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 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-D-galactopyranuronic acid / Beta-glucuronidase
Similarity search - Component
Biological speciesEisenbergiella tayi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 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 1.3Jul 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 1.4Mar 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

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Assembly

Deposited unit
D: Beta-galacturonidase
A: Beta-galacturonidase
B: Beta-galacturonidase
C: Beta-galacturonidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,98512
Polymers263,0664
Non-polymers9188
Water18,9881054
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13060 Å2
ΔGint-87 kcal/mol
Surface area76310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.342, 156.038, 124.285
Angle α, β, γ (deg.)90.00, 101.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-galacturonidase


Mass: 65766.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eisenbergiella tayi (bacteria) / Gene: uidA_6, BEI59_03660, BEI61_03198 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E3AEY6, beta-glucuronidase
#2: Sugar
ChemComp-ADA / alpha-D-galactopyranuronic acid / alpha-D-galacturonic acid / D-galacturonic acid / galacturonic acid / ALPHA D-GALACTURONIC ACID / D-Galacturonic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O7
IdentifierTypeProgram
DGalpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 1054 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris:HCl, pH 6.5, 25% (w/v) PEG 3350, 1 mM GalA

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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: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.25→29.88 Å / Num. obs: 114891 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.1485 / Net I/σ(I): 6.7
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 65156 / CC1/2: 0.674 / Rpim(I) all: 0.609 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 2.25→29.877 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.97
RfactorNum. reflection% reflection
Rfree0.275 1987 1.73 %
Rwork0.2212 --
obs0.2221 114628 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→29.877 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17961 0 56 1054 19071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818503
X-RAY DIFFRACTIONf_angle_d0.92625116
X-RAY DIFFRACTIONf_dihedral_angle_d18.09110902
X-RAY DIFFRACTIONf_chiral_restr0.0552616
X-RAY DIFFRACTIONf_plane_restr0.0053279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30630.37261260.33627660X-RAY DIFFRACTION95
2.3063-2.36860.32271310.30628025X-RAY DIFFRACTION99
2.3686-2.43820.37171710.29328032X-RAY DIFFRACTION100
2.4382-2.51690.31861460.27188069X-RAY DIFFRACTION100
2.5169-2.60680.36871310.25358039X-RAY DIFFRACTION100
2.6068-2.71110.32661390.24178060X-RAY DIFFRACTION100
2.7111-2.83440.32271390.24478065X-RAY DIFFRACTION100
2.8344-2.98370.33591520.23358089X-RAY DIFFRACTION100
2.9837-3.17050.28391410.22158048X-RAY DIFFRACTION100
3.1705-3.4150.27671430.21718091X-RAY DIFFRACTION100
3.415-3.7580.22161410.19318121X-RAY DIFFRACTION100
3.758-4.30040.22661400.1758103X-RAY DIFFRACTION100
4.3004-5.41280.20131420.16878143X-RAY DIFFRACTION100
5.4128-29.87950.2311450.20618096X-RAY DIFFRACTION99

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