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- PDB-9hy7: AlfB fucosidase in complex with Fucose -

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Basic information

Entry
Database: PDB / ID: 9hy7
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
alpha-L-fucopyranose / Alpha-L-fucosidase
Similarity search - Component
Biological speciesLactobacillaceae bacterium (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 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 2.0Jun 18, 2025Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_nonpoly_scheme.auth_seq_num

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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)282,16112
Polymers281,1766
Non-polymers9856
Water25,1311395
1
A: Alpha-L-fucosidase
B: Alpha-L-fucosidase
C: Alpha-L-fucosidase
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,1088
Polymers187,4514
Non-polymers6574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-54 kcal/mol
Surface area62020 Å2
MethodPISA
2
E: Alpha-L-fucosidase
F: Alpha-L-fucosidase
hetero molecules

E: Alpha-L-fucosidase
F: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,1088
Polymers187,4514
Non-polymers6574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area11480 Å2
ΔGint-52 kcal/mol
Surface area61760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.179, 309.559, 175.139
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: 46862.727 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillaceae bacterium (bacteria) / Gene: LCBD_2849 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A806EKD1
#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.: 1395 / 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: 4.05 Å3/Da / Density % sol: 69.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 3% PEG 8000, 25% MPD, 7% Taximate pH5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→87.72 Å / Num. obs: 194496 / % possible obs: 97 % / Redundancy: 4.5 % / CC1/2: 0.984 / Rpim(I) all: 0.082 / Net I/σ(I): 7.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.3 % / Num. unique obs: 28669 / CC1/2: 0.719 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→87.72 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20474 9649 -RANDOM
Rwork0.17746 ---
obs0.17881 185098 96.77 %-
Displacement parametersBiso mean: 24.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0 Å20 Å2
2--1.23 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.3→87.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19778 0 66 1395 21239
LS refinement shellResolution: 2.3→2.42 Å /
Rfactor% reflection
Rfree0.258 -
Rwork0.233 -
obs-98.67 %

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