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- PDB-5uj6: Crystal Structure of Bacteroides Uniformis beta-glucuronidase -

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Basic information

Entry
Database: PDB / ID: 5uj6
TitleCrystal Structure of Bacteroides Uniformis beta-glucuronidase
ComponentsGlycosyl hydrolases family 2, sugar binding domain protein
KeywordsHYDROLASE / Glucuronic-acid Carbohydrate
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 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain ...Malectin domain / Malectin domain / : / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / 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
Glycosyl hydrolases family 2, sugar binding domain protein
Similarity search - Component
Biological speciesBacteroides uniformis str. 3978 T3 ii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsWalton, W.G. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA098468 United States
CitationJournal: Structure / Year: 2017
Title: An Atlas of beta-Glucuronidases in the Human Intestinal Microbiome.
Authors: Pollet, R.M. / D'Agostino, E.H. / Walton, W.G. / Xu, Y. / Little, M.S. / Biernat, K.A. / Pellock, S.J. / Patterson, L.M. / Creekmore, B.C. / Isenberg, H.N. / Bahethi, R.R. / Bhatt, A.P. / ...Authors: Pollet, R.M. / D'Agostino, E.H. / Walton, W.G. / Xu, Y. / Little, M.S. / Biernat, K.A. / Pellock, S.J. / Patterson, L.M. / Creekmore, B.C. / Isenberg, H.N. / Bahethi, R.R. / Bhatt, A.P. / Liu, J. / Gharaibeh, R.Z. / Redinbo, M.R.
History
DepositionJan 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)201,74112
Polymers201,0632
Non-polymers67910
Water31,9771775
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-21 kcal/mol
Surface area57830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.728, 142.943, 181.686
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: 100531.320 Da / Num. of mol.: 2 / Fragment: UNP residues 31-886
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1775 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M Potassium Chloride

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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 EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→29.624 Å / Num. obs: 152573 / % possible obs: 99.4 % / Redundancy: 10.9 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 11 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 5 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→29.624 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.1
RfactorNum. reflection% reflection
Rfree0.1802 2000 1.31 %
Rwork0.1435 --
obs0.144 152481 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13575 0 40 1775 15390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114065
X-RAY DIFFRACTIONf_angle_d1.27619101
X-RAY DIFFRACTIONf_dihedral_angle_d13.1125171
X-RAY DIFFRACTIONf_chiral_restr0.0532016
X-RAY DIFFRACTIONf_plane_restr0.0072496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.25661390.19510513X-RAY DIFFRACTION99
1.9475-2.00020.21781420.181810588X-RAY DIFFRACTION99
2.0002-2.0590.25621400.175310594X-RAY DIFFRACTION99
2.059-2.12540.23061410.168210606X-RAY DIFFRACTION99
2.1254-2.20140.21420.163210657X-RAY DIFFRACTION99
2.2014-2.28950.18981410.154710638X-RAY DIFFRACTION99
2.2895-2.39360.20781420.15510667X-RAY DIFFRACTION99
2.3936-2.51980.19191420.152710720X-RAY DIFFRACTION99
2.5198-2.67760.19171430.153810730X-RAY DIFFRACTION100
2.6776-2.88410.19911440.154710798X-RAY DIFFRACTION100
2.8841-3.17410.18981430.149210802X-RAY DIFFRACTION100
3.1741-3.63270.18471440.13510867X-RAY DIFFRACTION100
3.6327-4.57410.13681470.114610974X-RAY DIFFRACTION100
4.5741-29.62720.13751500.125911327X-RAY DIFFRACTION100

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