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- PDB-2zwy: alpha-L-fucosidase -

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Basic information

Entry
Database: PDB / ID: 2zwy
Titlealpha-L-fucosidase
ComponentsAlpha-L-fucosidase, putative
KeywordsHYDROLASE / Tim Barrel
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
Alpha-L-fucosidase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWu, H.-J. / Ko, T.-P. / Ho, C.-W. / Lin, C.-H. / Wang, A.H.-J.
CitationJournal: To be Published
Title: Structural Basis of alpha-Fucosidase Inhibition by Iminocyclitols with Ki Ranging from Micro- to Picomolar
Authors: Wu, H.-J. / Ho, C.-W. / Ko, T.P. / Popat, S.D. / Lin, C.-H. / Wang, A.H.-J.
History
DepositionDec 18, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-L-fucosidase, putative
B: Alpha-L-fucosidase, putative


Theoretical massNumber of molelcules
Total (without water)106,2022
Polymers106,2022
Non-polymers00
Water5,134285
1
A: Alpha-L-fucosidase, putative
B: Alpha-L-fucosidase, putative

A: Alpha-L-fucosidase, putative
B: Alpha-L-fucosidase, putative

A: Alpha-L-fucosidase, putative
B: Alpha-L-fucosidase, putative


Theoretical massNumber of molelcules
Total (without water)318,6066
Polymers318,6066
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12450 Å2
ΔGint-33 kcal/mol
Surface area94210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.593, 180.593, 169.408
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-500-

HOH

21A-575-

HOH

31A-578-

HOH

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Components

#1: Protein Alpha-L-fucosidase, putative


Mass: 53100.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYE2, alpha-L-fucosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 14% PEG 5000 MME, 0.1M Tris-HCl, pH 8.0, 6% Jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2008
RadiationMonochromator: LN2-cooled, fixed-exit double crystal Si (111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 27735 / Num. obs: 27723 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 8.4 % / Rmerge(I) obs: 0.108 / Rsym value: 0.609 / Net I/σ(I): 20.2
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2751 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB enrty 1HL8

1hl8


Resolution: 2.75→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1271 -RANDOM
Rwork0.1687 ---
all0.1716 27681 --
obs0.1716 26388 95.3 %-
Solvent computationBsol: 47.08 Å2
Displacement parametersBiso max: 90.13 Å2 / Biso mean: 43.02 Å2 / Biso min: 14.26 Å2
Baniso -1Baniso -2Baniso -3
1-3.903 Å2-4.069 Å20 Å2
2--3.903 Å20 Å2
3----7.806 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7296 0 0 285 7581
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.03013
X-RAY DIFFRACTIONc_bond_d0.019861
LS refinement shellResolution: 2.75→2.85 Å / Rfactor Rfree error: 0.09
RfactorNum. reflection% reflection
Rfree0.3442 120 -
Rwork0.2538 --
obs-2396 83.34 %

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