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- PDB-6hzy: Crystal structure of a bacterial fucosidase with inhibitor FucPUG -

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Basic information

Entry
Database: PDB / ID: 6hzy
TitleCrystal structure of a bacterial fucosidase with inhibitor FucPUG
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE
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 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Alpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-GYZ / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWu, L. / Davies, G.J. / Stubbs, K.A. / Coyle, T. / Debowski, A.W.
Funding support Australia, United Kingdom, 3items
OrganizationGrant numberCountry
Australian Research CouncilFT100100291 Australia
National Health and Medical Research Council (Australia)APP1073250 Australia
European Research CouncilERC-2012-AdG-322942 United Kingdom
CitationJournal: Chembiochem / Year: 2019
Title: Synthetic and Crystallographic Insight into Exploiting sp2Hybridization in the Development of alpha-l-Fucosidase Inhibitors.
Authors: Coyle, T. / Wu, L. / Debowski, A.W. / Davies, G.J. / Stubbs, K.A.
History
DepositionOct 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)111,98028
Polymers109,6602
Non-polymers2,32026
Water13,727762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-59 kcal/mol
Surface area35730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.925, 84.602, 121.737
Angle α, β, γ (deg.)90.00, 109.00, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-771-

HOH

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Components

#1: Protein Alpha-L-fucosidase


Mass: 54829.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_2970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A3I4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GYZ / [(~{Z})-[(3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-ylidene]amino] ~{N}-phenylcarbamate


Mass: 296.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N2O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Imidazole pH 7.0 0.125 Ammonium Sulfate 16% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→49.61 Å / Num. obs: 109676 / % possible obs: 99.3 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.03 / Net I/σ(I): 11.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5379 / CC1/2: 0.952 / Rpim(I) all: 0.197 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pee

4pee


Resolution: 1.7→49.65 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.486 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25393 5431 5 %RANDOM
Rwork0.20766 ---
obs0.21006 104238 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.593 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å2-1.53 Å2
2--3.59 Å20 Å2
3----1.86 Å2
Refinement stepCycle: 1 / Resolution: 1.7→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7153 0 145 762 8060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137543
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176813
X-RAY DIFFRACTIONr_angle_refined_deg1.61.66210199
X-RAY DIFFRACTIONr_angle_other_deg1.3191.59215825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9565885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91222.581399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.687151267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5741540
X-RAY DIFFRACTIONr_chiral_restr0.0790.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028349
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021679
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_it2.4612.9213528
X-RAY DIFFRACTIONr_mcbond_other2.462.923527
X-RAY DIFFRACTIONr_mcangle_it3.2274.3764417
X-RAY DIFFRACTIONr_mcangle_other3.2274.3774418
X-RAY DIFFRACTIONr_scbond_it2.793.1994015
X-RAY DIFFRACTIONr_scbond_other2.7713.1823988
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0174.6475741
X-RAY DIFFRACTIONr_long_range_B_refined5.70434.3389083
X-RAY DIFFRACTIONr_long_range_B_other5.63533.898904
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 411 -
Rwork0.308 7650 -
obs--98.11 %

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