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- PDB-6ld6: Structure of Bifidobacterium dentium beta-glucuronidase -

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Basic information

Entry
Database: PDB / ID: 6ld6
TitleStructure of Bifidobacterium dentium beta-glucuronidase
ComponentsLacZ1 Beta-galactosidase
KeywordsHYDROLASE / Glycosidase
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process / signaling receptor binding / extracellular space
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-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesBifidobacterium dentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsLin, H.-Y. / Hsieh, T.-J. / Lin, C.-H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)108-2113-M-001-001 Taiwan
CitationJournal: Commun Biol / Year: 2021
Title: Entropy-driven binding of gut bacterial beta-glucuronidase inhibitors ameliorates irinotecan-induced toxicity.
Authors: Lin, H.Y. / Chen, C.Y. / Lin, T.C. / Yeh, L.F. / Hsieh, W.C. / Gao, S. / Burnouf, P.A. / Chen, B.M. / Hsieh, T.J. / Dashnyam, P. / Kuo, Y.H. / Tu, Z. / Roffler, S.R. / Lin, C.H.
History
DepositionNov 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LacZ1 Beta-galactosidase
B: LacZ1 Beta-galactosidase
C: LacZ1 Beta-galactosidase
D: LacZ1 Beta-galactosidase


Theoretical massNumber of molelcules
Total (without water)298,3554
Polymers298,3554
Non-polymers00
Water34,8591935
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20260 Å2
ΔGint-127 kcal/mol
Surface area75150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.583, 104.902, 160.620
Angle α, β, γ (deg.)90.000, 91.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
LacZ1 Beta-galactosidase


Mass: 74588.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium dentium (strain ATCC 27534 / DSM 20436 / JCM 1195 / Bd1) (bacteria)
Strain: ATCC 27534 / DSM 20436 / JCM 1195 / Bd1 / Gene: lacZ1, BDP_2112 / Production host: Escherichia coli (E. coli) / References: UniProt: D2Q7B1, beta-galactosidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1935 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium cacodylate, pH 6.5, 8% w/v PEG 20K

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.204→30 Å / Num. obs: 154379 / % possible obs: 98.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 22.25 Å2 / Rmerge(I) obs: 0.079 / Χ2: 0.992 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.21-2.2940.338139920.916190.3
2.29-2.384.20.292155110.934199.7
2.38-2.494.30.243154920.933199.8
2.49-2.624.30.198155370.942199.9
2.62-2.784.40.149155740.946199.9
2.78-34.40.108155980.962199.9
3-3.34.40.072155911.012199.9
3.3-3.784.40.052155891.07199.9
3.78-4.764.20.048156311.365199.8
4.76-304.20.034158640.825199.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k46

3k46


Resolution: 2.204→29.601 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.17
RfactorNum. reflection% reflection
Rfree0.2048 1950 1.33 %
Rwork0.1511 --
obs0.1518 146980 94.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.26 Å2 / Biso mean: 19.0425 Å2 / Biso min: 4 Å2
Refinement stepCycle: final / Resolution: 2.204→29.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19636 0 0 1935 21571
Biso mean---24.28 -
Num. residues----2480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02320160
X-RAY DIFFRACTIONf_angle_d1.78827428
X-RAY DIFFRACTIONf_chiral_restr0.0972880
X-RAY DIFFRACTIONf_plane_restr0.0123640
X-RAY DIFFRACTIONf_dihedral_angle_d11.88411732
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.204-2.25910.29781030.1769778072
2.2591-2.32010.24881280.1729975490
2.3201-2.38840.24361350.16711008393
2.3884-2.46540.23621380.1651027995
2.4654-2.55350.24781350.15921037795
2.5535-2.65570.1921400.15491042296
2.6557-2.77650.20711480.15331052997
2.7765-2.92270.19811410.15721067498
2.9227-3.10560.23591450.15951067598
3.1056-3.34510.20991450.15491076899
3.3451-3.68120.18681440.14731081399
3.6812-4.21260.15511460.1321085999
4.2126-5.30240.18541500.129910925100
5.3024-29.6010.20971520.158611092100

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