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- PDB-8z63: alpha-L-fucosidase from Pontiella sulfatireligans F21 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8z63
Titlealpha-L-fucosidase from Pontiella sulfatireligans F21
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / GH family 29 / Pontiella sulfatireligans F21 / Kiritmatiellaeota
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesPontiella sulfatireligans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsZhao, P. / Bai, L. / Wang, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Study on the function and diversity of key enzymes degrading fucoidan in Kiritimatiellaeota
Authors: Zhao, P. / Bai, L.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 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


Theoretical massNumber of molelcules
Total (without water)84,6762
Polymers84,6762
Non-polymers00
Water00
1
A: Alpha-L-fucosidase


Theoretical massNumber of molelcules
Total (without water)42,3381
Polymers42,3381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-L-fucosidase


Theoretical massNumber of molelcules
Total (without water)42,3381
Polymers42,3381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.061, 79.822, 89.724
Angle α, β, γ (deg.)90.00, 98.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-L-fucosidase


Mass: 42337.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pontiella sulfatireligans (bacteria) / Gene: SCARR_01449 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6C2UIZ6
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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.82→47.8 Å / Num. obs: 16715 / % possible obs: 94.78 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1097 / Net I/σ(I): 12.27
Reflection shellResolution: 2.822→2.922 Å / Num. unique obs: 16715 / CC1/2: 0.997

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→47.8 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 29.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2754 817 4.89 %
Rwork0.2165 --
obs0.2194 16715 94.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.82→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5407 0 0 0 5407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045448
X-RAY DIFFRACTIONf_angle_d0.9337370
X-RAY DIFFRACTIONf_dihedral_angle_d5.707716
X-RAY DIFFRACTIONf_chiral_restr0.046752
X-RAY DIFFRACTIONf_plane_restr0.011958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-30.36761190.28952388X-RAY DIFFRACTION86
3-3.230.35951400.282544X-RAY DIFFRACTION92
3.23-3.550.29991410.24882662X-RAY DIFFRACTION96
3.56-4.070.24761470.21332731X-RAY DIFFRACTION98
4.07-5.120.25791430.18472754X-RAY DIFFRACTION99
5.13-47.80.25061270.20042819X-RAY DIFFRACTION98

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