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- PDB-6d89: Bacteroides uniformis beta-glucuronidase 1 with N-terminal loop d... -

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Basic information

Entry
Database: PDB / ID: 6d89
TitleBacteroides uniformis beta-glucuronidase 1 with N-terminal loop deletion
ComponentsBeta-galactosidase/beta-glucuronidase
KeywordsHYDROLASE / glycosyl hydrolase 2 / beta-glucuronidase
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
CITRIC ACID / Beta-galactosidase/beta-glucuronidase
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 26, 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 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Beta-galactosidase/beta-glucuronidase
D: Beta-galactosidase/beta-glucuronidase
A: Beta-galactosidase/beta-glucuronidase
B: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,34112
Polymers276,4304
Non-polymers9108
Water32,0671780
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14360 Å2
ΔGint-93 kcal/mol
Surface area77330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.650, 199.191, 84.625
Angle α, β, γ (deg.)90.00, 102.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-galactosidase/beta-glucuronidase


Mass: 69107.555 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: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1780 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium Citrate: Citric Acid, pH 5.5, 20 % (w/v) PEG 3000

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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: 2→29.345 Å / Num. obs: 163378 / % possible obs: 98.4 % / Redundancy: 6.1 % / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.03 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.345 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3
RfactorNum. reflection% reflection
Rfree0.2295 1995 1.22 %
Rwork0.1761 --
obs0.1768 162878 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→29.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18705 0 56 1780 20541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00719283
X-RAY DIFFRACTIONf_angle_d0.84926144
X-RAY DIFFRACTIONf_dihedral_angle_d16.06111447
X-RAY DIFFRACTIONf_chiral_restr0.0542753
X-RAY DIFFRACTIONf_plane_restr0.0053367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.30291400.249111297X-RAY DIFFRACTION97
2.05-2.10540.28141420.245511357X-RAY DIFFRACTION97
2.1054-2.16740.31421400.239811382X-RAY DIFFRACTION97
2.1674-2.23730.321420.234711370X-RAY DIFFRACTION97
2.2373-2.31720.28611420.218611410X-RAY DIFFRACTION97
2.3172-2.410.27271420.212211432X-RAY DIFFRACTION98
2.41-2.51960.30431410.211311502X-RAY DIFFRACTION98
2.5196-2.65230.26861440.200811508X-RAY DIFFRACTION98
2.6523-2.81840.26981410.192711493X-RAY DIFFRACTION98
2.8184-3.03580.23381440.184111536X-RAY DIFFRACTION99
3.0358-3.34090.23291430.168611617X-RAY DIFFRACTION99
3.3409-3.82340.20421440.14711571X-RAY DIFFRACTION99
3.8234-4.81370.15861440.126511662X-RAY DIFFRACTION99
4.8137-29.34790.17031460.150811746X-RAY DIFFRACTION99

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