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- PDB-9hyj: AlfB fucosidase in complex with Fucose -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9hyj
TitleAlfB fucosidase in complex with Fucose
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / Fucosidase
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome
Similarity search - Function
Alpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesLactobacillaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMarina, A. / Gallego del Sol, F.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN) Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Unveiling the structural bases of alpha-L-fucosidase B activity through mutants boosting transfucosylation efficiency.
Authors: Becerra, J.E. / Gallego Del Sol, F. / Rubio-Del-Campo, A. / Rodriguez-Diaz, J. / Monedero, V. / Marina, A. / Yebra, M.J.
History
DepositionJan 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-L-fucosidase
B: Alpha-L-fucosidase
C: Alpha-L-fucosidase
D: Alpha-L-fucosidase
E: Alpha-L-fucosidase
F: Alpha-L-fucosidase


Theoretical massNumber of molelcules
Total (without water)281,2976
Polymers281,2976
Non-polymers00
Water19,7621097
1
A: Alpha-L-fucosidase
B: Alpha-L-fucosidase
C: Alpha-L-fucosidase
D: Alpha-L-fucosidase


Theoretical massNumber of molelcules
Total (without water)187,5314
Polymers187,5314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-61 kcal/mol
Surface area62260 Å2
2
E: Alpha-L-fucosidase
F: Alpha-L-fucosidase

E: Alpha-L-fucosidase
F: Alpha-L-fucosidase


Theoretical massNumber of molelcules
Total (without water)187,5314
Polymers187,5314
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area10640 Å2
ΔGint-68 kcal/mol
Surface area62040 Å2
Unit cell
Length a, b, c (Å)167.162, 308.288, 173.859
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Alpha-L-fucosidase


Mass: 46882.848 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillaceae (bacteria) / Gene: LCBD_2849 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A806EKD1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1097 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 3% PEG 8000, 25% MPD, 7% Taximate pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97928 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.25→49.27 Å / Num. obs: 211026 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.992 / Rpim(I) all: 0.07 / Net I/σ(I): 7.9
Reflection shellResolution: 2.25→2.37 Å / Num. unique obs: 30623 / CC1/2: 0.655 / Rpim(I) all: 0.382

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→49.03 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20903 10593 -RANDOM
Rwork0.17958 ---
obs0.18105 200357 99.92 %-
Displacement parametersBiso mean: 37.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0 Å2-0 Å2
2--0.77 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.25→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19631 0 0 1097 20728
LS refinement shellResolution: 2.25→2.308 Å /
Rfactor% reflection
Rfree0.301 -
Rwork0.295 -
obs-99.97 %

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