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- PDB-9hz1: Crystal structure of AlfB -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9hz1
TitleCrystal structure of AlfB
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 / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
4-nitrophenyl 6-deoxy-alpha-L-galactopyranoside / Alpha-L-fucosidase
Similarity search - Component
Biological speciesLactobacillaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 12, 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)283,00912
Polymers281,2976
Non-polymers1,7126
Water20,4471135
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)188,6728
Polymers187,5314
Non-polymers1,1414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-59 kcal/mol
Surface area62560 Å2
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)188,6728
Polymers187,5314
Non-polymers1,1414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area10030 Å2
ΔGint-57 kcal/mol
Surface area62420 Å2
Unit cell
Length a, b, c (Å)167.832, 309.991, 175.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: Sugar
ChemComp-JFZ / 4-nitrophenyl 6-deoxy-alpha-L-galactopyranoside / 4-nitrophenyl-alpha-L-fucose / 4-nitrophenyl 6-deoxy-alpha-L-galactoside / 4-nitrophenyl 6-deoxy-L-galactoside / 4-nitrophenyl 6-deoxy-galactoside


Type: L-saccharide / Mass: 285.250 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H15NO7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1135 / 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: 69.64 %
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: 0.97924 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.4→49.2 Å / Num. obs: 177281 / % possible obs: 100 % / Redundancy: 7.5 % / Rpim(I) all: 0.0062 / Net I/σ(I): 11
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 8725 / Rpim(I) all: 0.377 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.67 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.043 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18953 8663 4.9 %RANDOM
Rwork0.16426 ---
obs0.16549 168584 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.514 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å20 Å2
2--0.9 Å2-0 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.4→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19622 0 120 1135 20877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01220333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.80127746
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37852439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.3235132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.516103102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.22995
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216096
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6273.1179786
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.3455.57412212
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.653.50310547
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.43431.2330156
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 696 -
Rwork0.272 12291 -
obs--99.99 %

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