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- PDB-6ncw: Crystal structure of a GH2 beta-galacturonidase from Eisenbergiel... -

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Basic information

Entry
Database: PDB / ID: 6ncw
TitleCrystal structure of a GH2 beta-galacturonidase from Eisenbergiella tayi bound to glycerol
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
Biological speciesEisenbergiella tayi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
A: Beta-galacturonidase
B: Beta-galacturonidase
C: Beta-galacturonidase
D: Beta-galacturonidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,12918
Polymers263,0664
Non-polymers1,06314
Water26,7701486
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-95 kcal/mol
Surface area74850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.930, 87.677, 124.375
Angle α, β, γ (deg.)93.29, 101.55, 90.37
Int Tables number1
Space group name H-MP1

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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: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1486 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1 M NaH2PO4/K2HPO4, pH 8.2

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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: 2.3→29.542 Å / Num. obs: 118452 / % possible obs: 97.9 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.0933 / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5087 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 11739 / CC1/2: 0.813 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 2.1→29.542 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 2012 1.3 %
Rwork0.1648 --
obs0.1654 155087 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→29.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18078 0 64 1486 19628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818637
X-RAY DIFFRACTIONf_angle_d0.92725279
X-RAY DIFFRACTIONf_dihedral_angle_d17.46410977
X-RAY DIFFRACTIONf_chiral_restr0.0572615
X-RAY DIFFRACTIONf_plane_restr0.0063301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.32211340.277210801X-RAY DIFFRACTION96
2.1525-2.21070.29231410.256910820X-RAY DIFFRACTION97
2.2107-2.27570.28341490.233110847X-RAY DIFFRACTION96
2.2757-2.34910.28111440.213710855X-RAY DIFFRACTION97
2.3491-2.43310.25571460.205710866X-RAY DIFFRACTION97
2.4331-2.53040.27561370.197410895X-RAY DIFFRACTION97
2.5304-2.64550.25861480.187510948X-RAY DIFFRACTION97
2.6455-2.78490.22071440.179110920X-RAY DIFFRACTION98
2.7849-2.95920.24451440.178310996X-RAY DIFFRACTION98
2.9592-3.18750.2351390.171911004X-RAY DIFFRACTION98
3.1875-3.50780.18751490.157511006X-RAY DIFFRACTION98
3.5078-4.01430.17291480.132211044X-RAY DIFFRACTION99
4.0143-5.05350.14781390.110511023X-RAY DIFFRACTION98
5.0535-29.54530.15051500.141111050X-RAY DIFFRACTION99

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