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- PDB-5z1b: Structure of Bifidobacterium dentium beta-glucuronidase complexed... -

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Basic information

Entry
Database: PDB / ID: 5z1b
TitleStructure of Bifidobacterium dentium beta-glucuronidase complexed with coumarin-3-O-glucuronide
ComponentsGlycosyl hydrolase family 2, TIM barrel domain protein
KeywordsHYDROLASE / beta-glucuronidase / GH2
Function / homology
Function and homology information


beta-glucuronidase activity / beta-glucuronidase / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / 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 ...Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / 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
beta-D-glucopyranuronic acid / 3-HYDROXY-2H-CHROMEN-2-ONE / Glycosyl hydrolase family 2, TIM barrel domain protein
Similarity search - Component
Biological speciesBifidobacterium dentium ATCC 27679 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsDashnyam, P. / Lin, H.Y. / Lin, C.H.
CitationJournal: To Be Published
Title: Dissection of the substrate preference and structure of gut microbial-glucuronidases identifies the major bacteria causing xenobiotic toxicity
Authors: Dashnyam, P. / Mudududdla, R. / Hsieh, T.J. / Lin, T.C. / Lin, H.Y. / Chen, P.Y. / Hsu, C.Y. / Lin, C.H.
History
DepositionDec 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase family 2, TIM barrel domain protein
B: Glycosyl hydrolase family 2, TIM barrel domain protein
C: Glycosyl hydrolase family 2, TIM barrel domain protein
D: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,95112
Polymers308,5264
Non-polymers1,4258
Water41,6692313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21590 Å2
ΔGint-119 kcal/mol
Surface area75090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.340, 104.165, 160.673
Angle α, β, γ (deg.)90.000, 90.400, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid
31chain C and segid
41chain D and segid

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 0 / Label seq-ID: 24

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and segidAA
2chain B and segidBB
3chain C and segidCC
4chain D and segidDD

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Components

#1: Protein
Glycosyl hydrolase family 2, TIM barrel domain protein


Mass: 77131.430 Da / Num. of mol.: 4 / Mutation: E479A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium dentium ATCC 27679 (bacteria)
Gene: uidA, HMPREF0168_2111 / Production host: Escherichia coli (E. coli) / References: UniProt: E0QAF3, beta-glucuronidase
#2: Sugar
ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid / Glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SE2 / 3-HYDROXY-2H-CHROMEN-2-ONE


Mass: 162.142 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C9H6O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2313 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 100mM Sodium cacodylate, pH 6.5, 18%(w/v) PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 527681 / % possible obs: 99.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.29 Å2 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.025 / Rrim(I) all: 0.049 / Χ2: 0.925 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.53.20.57515970.7450.360.6770.90897.8
1.5-1.563.50.428524460.8580.2610.5030.9399.3
1.56-1.633.60.311527040.9230.1870.3630.94699.5
1.63-1.723.60.219527360.9590.1310.2560.95999.7
1.72-1.833.70.148528680.9790.0890.1730.96199.7
1.83-1.973.70.092528610.9910.0550.1080.94799.8
1.97-2.173.70.052529680.9970.0310.060.86299.8
2.17-2.483.70.04529830.9970.0240.0471.00499.8
2.48-3.123.70.031530340.9970.0190.0371.18299.8
3.12-303.70.016534840.9990.010.0190.55399.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→29.164 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.01
RfactorNum. reflection% reflection
Rfree0.1602 2002 40 %
Rwork0.1301 --
obs0.1302 499890 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.71 Å2 / Biso mean: 21.5978 Å2 / Biso min: 6.28 Å2
Refinement stepCycle: final / Resolution: 1.45→29.164 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19696 0 96 2313 22105
Biso mean--26.9 31.72 -
Num. residues----2493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01220325
X-RAY DIFFRACTIONf_angle_d1.39527663
X-RAY DIFFRACTIONf_chiral_restr0.0672908
X-RAY DIFFRACTIONf_plane_restr0.0083665
X-RAY DIFFRACTIONf_dihedral_angle_d12.5467239
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11746X-RAY DIFFRACTION5.339TORSIONAL
12B11746X-RAY DIFFRACTION5.339TORSIONAL
13C11746X-RAY DIFFRACTION5.339TORSIONAL
14D11746X-RAY DIFFRACTION5.339TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4499-1.48620.2352860.1835216882177458
1.4862-1.52640.20581120.163279962810874
1.5264-1.57130.20441330.1513340103414390
1.5713-1.6220.20261460.1403372303737699
1.622-1.680.16971540.12913757337727100
1.68-1.74720.16991520.11933752237674100
1.7472-1.82670.15921470.11143764037787100
1.8267-1.9230.11831540.11333760737761100
1.923-2.04350.13421500.11343762737777100
2.0435-2.20120.14011490.11713767637825100
2.2012-2.42260.16321540.12953769937853100
2.4226-2.77290.18421560.14233779237948100
2.7729-3.49270.17161530.1407376713782499
3.4927-29.17010.1431560.12723815738313100

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