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- PDB-2zx5: alpha-L-fucosidase complexed with inhibitor, F10 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2zx5
Titlealpha-L-fucosidase complexed with inhibitor, F10
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 / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / 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 / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / 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-ZX5 / Alpha-L-fucosidase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsWu, H.-J. / Ko, T.-P. / Ho, C.-W. / Lin, C.-H. / Wang, A.H.-J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Structural basis of alpha-fucosidase inhibition by iminocyclitols with K(i) values in the micro- to picomolar range.
Authors: Wu, H.J. / Ho, C.W. / Ko, T.P. / Popat, S.D. / Lin, C.H. / Wang, A.H.
History
DepositionDec 19, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8974
Polymers106,2022
Non-polymers6952
Water6,107339
1
A: Alpha-L-fucosidase, putative
B: Alpha-L-fucosidase, putative
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)320,69012
Polymers318,6066
Non-polymers2,0846
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 area12110 Å2
ΔGint-33 kcal/mol
Surface area92710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.520, 180.520, 169.266
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-537-

HOH

21A-559-

HOH

31A-604-

HOH

41A-620-

HOH

51A-621-

HOH

61B-554-

HOH

71B-610-

HOH

81B-611-

HOH

91B-617-

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: Chemical ChemComp-ZX5 / 3-(1H-indol-3-yl)-N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}propanamide


Mass: 347.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H25N3O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 15% PEG 5000 MME, 0.1M HEPES, pH 7.2, 5% Jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 14, 2007 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. all: 30844 / Num. obs: 30844 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 11.19 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 10.3
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3050 / % possible all: 100

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB enrty 2ZWZ

2zwz


Resolution: 2.65→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1521 -RANDOM
Rwork0.1908 ---
all0.1941 30844 --
obs0.1941 30649 99.4 %-
Solvent computationBsol: 65.024 Å2
Displacement parametersBiso max: 131.33 Å2 / Biso mean: 42.638 Å2 / Biso min: 17.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.618 Å2-3.265 Å20 Å2
2--2.618 Å20 Å2
3----5.236 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7278 0 50 339 7667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.90623
X-RAY DIFFRACTIONc_bond_d0.018792
LS refinement shellResolution: 2.65→2.74 Å / Rfactor Rfree error: 0.0947
RfactorNum. reflection% reflection
Rfree0.2889 162 -
Rwork0.1941 --
obs-3005 98.69 %

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