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- PDB-6d50: Bacteroides uniforms beta-glucuronidase 2 bound to D-glucaro-1,5-... -

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Basic information

Entry
Database: PDB / ID: 6d50
TitleBacteroides uniforms beta-glucuronidase 2 bound to D-glucaro-1,5-lactone
ComponentsGlycosyl hydrolases family 2, sugar binding domain protein
KeywordsHYDROLASE / glycoside hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Malectin domain / Malectin domain / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / 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 ...Malectin domain / Malectin domain / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / 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 / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-GCB / Glycosyl hydrolases family 2, sugar binding domain protein
Similarity search - Component
Biological speciesBacteroides uniformis str. 3978 T3 ii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 19, 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 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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
A: Glycosyl hydrolases family 2, sugar binding domain protein
B: Glycosyl hydrolases family 2, sugar binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,3848
Polymers202,8742
Non-polymers5106
Water9,566531
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-16 kcal/mol
Surface area57860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.489, 141.880, 180.803
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyl hydrolases family 2, sugar binding domain protein


Mass: 101436.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis str. 3978 T3 ii (bacteria)
Gene: M094_3283 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A078SUX9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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.: 531 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium Chloride, 20% PEG 3350, 10mM Saccharolactone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→29.48 Å / Num. obs: 446802 / % possible obs: 99.9 % / Redundancy: 6.7 % / Net I/σ(I): 15.9
Reflection shellResolution: 2.5→2.56 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UJ6

5uj6


Resolution: 2.5→29.476 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.28
RfactorNum. reflection% reflection
Rfree0.2309 2000 2.98 %
Rwork0.166 --
obs0.168 67030 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13564 0 30 531 14125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814026
X-RAY DIFFRACTIONf_angle_d0.96819061
X-RAY DIFFRACTIONf_dihedral_angle_d14.0358277
X-RAY DIFFRACTIONf_chiral_restr0.0552021
X-RAY DIFFRACTIONf_plane_restr0.0062492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.3641400.20584578X-RAY DIFFRACTION100
2.5625-2.63170.28131420.18774594X-RAY DIFFRACTION100
2.6317-2.70910.30271410.19944580X-RAY DIFFRACTION100
2.7091-2.79650.31751410.20384583X-RAY DIFFRACTION100
2.7965-2.89640.2931410.19494600X-RAY DIFFRACTION100
2.8964-3.01220.25721420.20074607X-RAY DIFFRACTION100
3.0122-3.14920.28241420.19774615X-RAY DIFFRACTION100
3.1492-3.3150.28271420.19674613X-RAY DIFFRACTION100
3.315-3.52240.2451420.18654618X-RAY DIFFRACTION100
3.5224-3.79380.22841430.17014636X-RAY DIFFRACTION100
3.7938-4.17470.19061430.14714667X-RAY DIFFRACTION100
4.1747-4.77650.19031440.12514687X-RAY DIFFRACTION100
4.7765-6.00950.17491460.13614732X-RAY DIFFRACTION100
6.0095-29.47840.19761510.14894920X-RAY DIFFRACTION100

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