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

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Basic information

Entry
Database: PDB / ID: 9hyx
TitleAlfB fucosidase in complex with Fucose
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / Fucosidase
Function / homologyAlpha-L-fucosidase, metazoa-type / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Glycoside hydrolase superfamily / alpha-L-fucopyranose / Alpha-L-fucosidase
Function and homology information
Biological speciesLacticaseibacillus paracasei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,28212
Polymers281,2976
Non-polymers9856
Water20,9511163
1
A: Alpha-L-fucosidase
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0944
Polymers93,7662
Non-polymers3282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-20 kcal/mol
Surface area32890 Å2
2
C: Alpha-L-fucosidase
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0944
Polymers93,7662
Non-polymers3282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-19 kcal/mol
Surface area32750 Å2
3
E: Alpha-L-fucosidase
F: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0944
Polymers93,7662
Non-polymers3282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-21 kcal/mol
Surface area32770 Å2
Unit cell
Length a, b, c (Å)168.299, 309.675, 173.974
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.) Lacticaseibacillus paracasei (bacteria)
Gene: C0Q90_04930 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AB36XDR5
#2: Sugar
ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.03 Å3/Da / Density % sol: 69.47 %
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: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.3→49.3 Å / Num. obs: 200086 / % possible obs: 100 % / Redundancy: 7.6 % / Rpim(I) all: 0.063 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9847 / Rpim(I) all: 0.438 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49.29 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19651 9861 -RANDOM
Rwork0.17324 180312 --
obs0.17439 190173 99.95 %-
Displacement parametersBiso mean: 36.594 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å2-0 Å2-0 Å2
2--3.15 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19691 0 66 1163 20920
LS refinement shellResolution: 2.3→2.36 Å /
Rfactor% reflection
Rfree0.308 -
Rwork0.278 -
obs-99.99 %

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