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- PDB-6tvk: Alpha-L-fucosidase isoenzyme 2 from Paenibacillus thiaminolyticus -

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Basic information

Entry
Database: PDB / ID: 6tvk
TitleAlpha-L-fucosidase isoenzyme 2 from Paenibacillus thiaminolyticus
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / ALPHA-L-FUCOSIDASE / GH151 / ACTIVE SITE COMPLEMENTATION / TETRAMER
Function / homology
Function and homology information


beta-galactosidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Hypothetical glycosyl hydrolase 6 / Hypothetical glycosyl hydrolase 6 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily
Similarity search - Domain/homology
HEXATANTALUM DODECABROMIDE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesPaenibacillus thiaminolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKovalova, T. / Koval, T. / Lipovova, P. / Dohnalek, J.
Funding support Czech Republic, 5items
OrganizationGrant numberCountry
Czech Academy of Sciences86652036 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000447 Czech Republic
European Regional Development FundCZ.02.1.01/0.0/0.0/16_013/0001776 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2015043 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0109 Czech Republic
CitationJournal: Febs J. / Year: 2022
Title: The first structure-function study of GH151 alpha-l-fucosidase uncovers new oligomerization pattern, active site complementation, and selective substrate specificity
Authors: Koval'ova, T. / Koval, T. / Stransky, J. / Kolenko, P. / Duskova, J. / Svecova, L. / Vodickova, P. / Spiwok, V. / Benesova, E. / Lipovova, P. / Dohnalek, J.
History
DepositionJan 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Data collection / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3267
Polymers77,8431
Non-polymers2,4826
Water6,431357
1
AAA: Alpha-L-fucosidase
hetero molecules

AAA: Alpha-L-fucosidase
hetero molecules

AAA: Alpha-L-fucosidase
hetero molecules

AAA: Alpha-L-fucosidase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, The tetramer was confirmed in solution using gel filtration., light scattering, The tetramer was confirmed in solution using dynamic light scattering., SAXS, The tetramer ...Evidence: gel filtration, The tetramer was confirmed in solution using gel filtration., light scattering, The tetramer was confirmed in solution using dynamic light scattering., SAXS, The tetramer was confirmed in solution using SAXS.
  • 321 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)321,30228
Polymers311,3734
Non-polymers9,92924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area26620 Å2
ΔGint-194 kcal/mol
Surface area86460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.118, 125.118, 231.905
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Alpha-L-fucosidase


Mass: 77843.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue Cys488 is oxidized
Source: (gene. exp.) Paenibacillus thiaminolyticus (bacteria)
Gene: aLfuk2, NCTC11027_00201 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K0JCW6

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Non-polymers , 5 types, 363 molecules

#2: Chemical ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br12Ta6
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.36 Å3/Da / Density % sol: 63.41 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Condition: 0.1 M NaCl, 1.5 M ammonium acetate, 0.1 M BIS-TRIS pH 6.5 The condition was diluted to 80% 5 mM maltose as an additive

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→49.08 Å / Num. obs: 63022 / % possible obs: 99.7 % / Redundancy: 40.1 % / Biso Wilson estimate: 43.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.031 / Rrim(I) all: 0.144 / Net I/σ(I): 25.5
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 42.3 % / Rmerge(I) obs: 3.57 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4375 / CC1/2: 0.822 / Rpim(I) all: 0.77 / Rrim(I) all: 3.653 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→49.08 Å / Cor.coef. Fo:Fc: 0.966 / SU B: 4.623 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens have been added in their riding positions. The final refinement cycle was performed against all measured intensities.
RfactorNum. reflection% reflection
Rfree0.2252 -4.9 %
Rwork0.1887 --
all0.189 --
obs-59829 99.617 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.086 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20.915 Å20 Å2
2--1.83 Å2-0 Å2
3----5.937 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5231 0 42 357 5630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135433
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174911
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.6737489
X-RAY DIFFRACTIONr_angle_other_deg1.321.57211389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2725665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62722.31303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16615901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5211536
X-RAY DIFFRACTIONr_chiral_restr0.0760.2669
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021168
X-RAY DIFFRACTIONr_nbd_refined0.1940.2963
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.24591
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22556
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22360
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0590.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.225
X-RAY DIFFRACTIONr_nbd_other0.2160.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1160.211
X-RAY DIFFRACTIONr_mcbond_it3.5795.4012645
X-RAY DIFFRACTIONr_mcbond_other3.5785.3992644
X-RAY DIFFRACTIONr_mcangle_it4.4298.1033306
X-RAY DIFFRACTIONr_mcangle_other4.4288.1053307
X-RAY DIFFRACTIONr_scbond_it4.715.8242786
X-RAY DIFFRACTIONr_scbond_other4.6675.8182783
X-RAY DIFFRACTIONr_scangle_it6.3548.6784087
X-RAY DIFFRACTIONr_scangle_other6.3238.6684082
X-RAY DIFFRACTIONr_lrange_it7.2862.065901
X-RAY DIFFRACTIONr_lrange_other7.27962.0695902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.3462250.3384584X-RAY DIFFRACTION99.9564
2.155-2.21400.3084463X-RAY DIFFRACTION99.9105
2.214-2.27800.284371X-RAY DIFFRACTION99.9771
2.278-2.34800.2584216X-RAY DIFFRACTION99.9289
2.348-2.42500.2434101X-RAY DIFFRACTION99.9513
2.425-2.5100.2223997X-RAY DIFFRACTION99.975
2.51-2.60400.1953841X-RAY DIFFRACTION99.974
2.604-2.71100.1913709X-RAY DIFFRACTION100
2.711-2.83100.2013553X-RAY DIFFRACTION100
2.831-2.96900.23390X-RAY DIFFRACTION99.2389
2.969-3.1300.1783266X-RAY DIFFRACTION99.9694
3.13-3.31900.1933076X-RAY DIFFRACTION99.9675
3.319-3.54800.1732919X-RAY DIFFRACTION99.9658
3.548-3.83200.1712723X-RAY DIFFRACTION99.9633
3.832-4.19800.1482534X-RAY DIFFRACTION99.9606
4.198-4.69200.1332294X-RAY DIFFRACTION100
4.692-5.41600.1462061X-RAY DIFFRACTION99.9515
5.416-6.6300.1791725X-RAY DIFFRACTION97.5679
6.63-9.35800.1681406X-RAY DIFFRACTION100
9.358-49.0800.301714X-RAY DIFFRACTION82.3529

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