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- PDB-9pnj: Crystal structure of the GH29-like fucosidase FucWf4 -

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Basic information

Entry
Database: PDB / ID: 9pnj
TitleCrystal structure of the GH29-like fucosidase FucWf4
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / fucose / fucoidan / glycoside hydrolase / CAZyme.
Function / homologyGlycoside hydrolase, family 29 / Alpha-L-fucosidase / alpha-L-fucosidase activity / Glycoside hydrolase superfamily / carbohydrate metabolic process / Alpha-L-fucosidase
Function and homology information
Biological speciesWenyingzhuangia fucanilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHiggins, M.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structural insights into a fucosidase involved in fucoidan degradation.
Authors: Bailey, B. / Winchester, A. / McClain, D. / Clingaman, M. / Higgins, M.A.
History
DepositionJul 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-L-fucosidase
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,8089
Polymers120,4492
Non-polymers3597
Water6,936385
1
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4355
Polymers60,2241
Non-polymers2114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3734
Polymers60,2241
Non-polymers1483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.973, 99.332, 124.554
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Alpha-L-fucosidase


Mass: 60224.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wenyingzhuangia fucanilytica (bacteria)
Gene: AXE80_07370 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: A0A1B1Y5Q3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 8000, 0.2 M MgCl2, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97947 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.2→39.45 Å / Num. obs: 54172 / % possible obs: 98.7 % / Redundancy: 13.7 % / Biso Wilson estimate: 45.66 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.1
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 1 / Num. unique obs: 4341 / CC1/2: 0.934

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.45 Å / SU ML: 0.4591 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.1041
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2438 1935 3.68 %
Rwork0.1896 50579 -
obs0.1916 52514 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.87 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7639 0 22 385 8046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00767869
X-RAY DIFFRACTIONf_angle_d0.860210701
X-RAY DIFFRACTIONf_chiral_restr0.05251155
X-RAY DIFFRACTIONf_plane_restr0.00751382
X-RAY DIFFRACTIONf_dihedral_angle_d16.3062788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.58111010.52222615X-RAY DIFFRACTION70.31
2.25-2.310.39041190.38813232X-RAY DIFFRACTION86.54
2.31-2.380.35751410.29243698X-RAY DIFFRACTION99.17
2.38-2.460.35961410.2743670X-RAY DIFFRACTION99.22
2.46-2.550.3431350.28233528X-RAY DIFFRACTION93.37
2.55-2.650.37551430.24723697X-RAY DIFFRACTION99.53
2.65-2.770.3091430.21983724X-RAY DIFFRACTION99.18
2.77-2.920.25651430.21853740X-RAY DIFFRACTION99.59
2.92-3.10.26541430.21443737X-RAY DIFFRACTION99.56
3.1-3.340.23491440.19993745X-RAY DIFFRACTION99.56
3.34-3.670.2231420.18423682X-RAY DIFFRACTION96.54
3.67-4.20.21881420.15113758X-RAY DIFFRACTION98.76
4.2-5.30.18251490.13273846X-RAY DIFFRACTION99.95
5.3-39.450.20841490.1543907X-RAY DIFFRACTION97.5

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