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- PDB-6gn6: Alpha-L-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus -

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Basic information

Entry
Database: PDB / ID: 6gn6
TitleAlpha-L-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / Alpha-L-fucosidase / GH29 / active site complementation / hexamer
Function / homology
Function and homology information


alpha-L-fucosidase / alpha-L-fucosidase activity / fucose metabolic process
Similarity search - Function
Alpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alpha-L-fucosidase
Similarity search - Component
Biological speciesPaenibacillus thiaminolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKovalova, T. / Koval, T. / Lipovova, P. / Dohnalek, J.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
European CommissionCZ.02.1.01/0.0/0.0/16_013/0001776 Czech Republic
European CommissionCZ.1.05/1.1.00/02.0109 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2015043 Czech Republic
CitationJournal: Glycobiology / Year: 2019
Title: Active site complementation and hexameric arrangement in the GH family 29; a structure-function study of alpha-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus.
Authors: Kovalova, T. / Koval, T. / Benesova, E. / Vodickova, P. / Spiwok, V. / Lipovova, P. / Dohnalek, J.
History
DepositionMay 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)314,31139
Polymers307,4976
Non-polymers6,81533
Water25,0771392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, The hexameric assembly in solution was confirmed by dynamic light scattering.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30000 Å2
ΔGint34 kcal/mol
Surface area92050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.772, 148.758, 194.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Alpha-L-fucosidase


Mass: 51249.449 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus thiaminolyticus (bacteria)
Gene: aLfuk1 / Plasmid: pET16b-alphaLF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E3PQQ9, alpha-L-fucosidase

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Sugars , 2 types, 14 molecules

#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 1411 molecules

#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1392 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (w/v) PEG 3350, 0.2 M Ammonium acetate, 0.1 M BIS-TRIS buffer, Additive: 50 mM Maltose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9201 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.2→48.93 Å / Num. obs: 157780 / % possible obs: 99.4 % / Observed criterion σ(I): -3.7 / Redundancy: 5 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSNovember 3, 2014data reduction
XDSNovember 3, 2014data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WVS

2wvs


Resolution: 2.2→48.93 Å / Cor.coef. Fo:Fc: 0.962 / SU B: 6.104 / SU ML: 0.134 / Cross valid method: FREE R-VALUE / ESU R: 0.214
Stereochemistry target values: THE STEREOCHEMISTRY LIBRARY OF CCP4 VERSION 7.0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LAST REFINEMENT CYCLE WAS PERFORMED AGAINST ALL REFLECTIONS OF THE DATA SET.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 7763 4.9 %RANDOM SELECTION
Rwork0.167 ---
obs0.169 157724 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2--0.29 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20508 0 455 1392 22355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01421651
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718701
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.67929388
X-RAY DIFFRACTIONr_angle_other_deg1.1811.6743935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78652553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56222.281263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.301153359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.31415144
X-RAY DIFFRACTIONr_chiral_restr0.1010.22689
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0224316
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024204
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_it2.9583.15610164
X-RAY DIFFRACTIONr_mcbond_other2.9583.15510163
X-RAY DIFFRACTIONr_mcangle_it4.1734.71912700
X-RAY DIFFRACTIONr_mcangle_other4.1734.7212701
X-RAY DIFFRACTIONr_scbond_it4.2283.72111487
X-RAY DIFFRACTIONr_scbond_other4.2263.72111487
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3675.37116678
X-RAY DIFFRACTIONr_long_range_B_refined7.66737.38224864
X-RAY DIFFRACTIONr_long_range_B_other7.66737.38524865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å
RfactorNum. reflection% reflection
Rfree0.375 573 -
Rwork0.341 11477 -
obs--98.78 %

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