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- PDB-6ldb: Structure of Bifidobacterium dentium beta-glucuronidase complexed... -

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Basic information

Entry
Database: PDB / ID: 6ldb
TitleStructure of Bifidobacterium dentium beta-glucuronidase complexed with uronic isofagomine
ComponentsLacZ1 Beta-galactosidase
KeywordsHYDROLASE / inhibitor / glycosidase / isofagomine
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / 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 / 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 ...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 / 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 / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-SJ5 / Beta-glucuronidase
Similarity search - Component
Biological speciesBifidobacterium dentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)298,9998
Polymers298,3554
Non-polymers6454
Water48,4422689
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20040 Å2
ΔGint-123 kcal/mol
Surface area74570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.690, 104.640, 160.504
Angle α, β, γ (deg.)90.000, 91.290, 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: Chemical
ChemComp-SJ5 / (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid


Mass: 161.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2689 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 52.84 %
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: Aug 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 343510 / % possible obs: 93.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.029 / Rrim(I) all: 0.054 / Χ2: 1.01 / Net I/σ(I): 20.9 / Num. measured all: 1151120
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.713.30.353329530.8880.2210.4181.00390.4
1.71-1.783.20.266327130.9340.1660.315189.7
1.78-1.863.20.193325540.9590.1210.228189.2
1.86-1.963.20.138327800.9790.0870.1641.00589.8
1.96-2.083.20.095335750.9890.060.1120.98991.8
2.08-2.243.20.073349450.9930.0460.0861.00495.7
2.24-2.463.50.059357860.9950.0370.0691.00797.8
2.46-2.823.60.05359450.9960.030.0581.00698.1
2.82-3.553.50.038359960.9970.0240.0451.05898.1
3.55-303.40.025362630.9980.0160.031.01597.7

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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: 1.651→24.852 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.95
RfactorNum. reflection% reflection
Rfree0.1832 1939 -
Rwork0.1556 --
obs0.1558 334102 91.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.62 Å2 / Biso mean: 21.3139 Å2 / Biso min: 6.39 Å2
Refinement stepCycle: final / Resolution: 1.651→24.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19636 0 44 2689 22369
Biso mean--20 31.57 -
Num. residues----2480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01320232
X-RAY DIFFRACTIONf_angle_d1.28827532
X-RAY DIFFRACTIONf_chiral_restr0.0892896
X-RAY DIFFRACTIONf_plane_restr0.0093652
X-RAY DIFFRACTIONf_dihedral_angle_d11.0811780
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.651-1.6920.25461170.21182088681
1.692-1.73780.21461200.19522133182
1.7378-1.78890.21871290.18382171184
1.7889-1.84660.22731240.17822195185
1.8466-1.91260.18911330.17712231486
1.9126-1.98910.21411300.1712282588
1.9891-2.07960.19731400.1672362091
2.0796-2.18920.19241430.16342443194
2.1892-2.32630.21271450.15762518497
2.3263-2.50570.17141480.15812537598
2.5057-2.75760.2051510.16052551098
2.7576-3.1560.1851530.15842557598
3.156-3.97360.17081530.13612557998
3.9736-24.8520.14681530.13762587198

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