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- PDB-2zxa: alpha-L-fucosidase complexed with inhibitor, FNJ-acetyl -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2zxa
Titlealpha-L-fucosidase complexed with inhibitor, FNJ-acetyl
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
Chem-ZXA / Alpha-L-fucosidase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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 22, 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)106,6384
Polymers106,2022
Non-polymers4372
Water7,026390
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)319,91512
Polymers318,6066
Non-polymers1,3106
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 area12280 Å2
ΔGint-27 kcal/mol
Surface area93290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.562, 180.562, 169.345
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-525-

HOH

21A-559-

HOH

31A-585-

HOH

41A-632-

HOH

51A-660-

HOH

61B-595-

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-ZXA / N-{[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methylpiperidin-2-yl]methyl}acetamide


Mass: 218.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 50.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 17% PEG 5000 MME, 0.1M Tris-HCl, pH 8.2, 5% Jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2008
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→30 Å / Num. all: 33764 / Num. obs: 33755 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.3
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3336 / % possible all: 100

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Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB enrty 2zwz

2zwz


Resolution: 2.57→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 1613 -RANDOM
Rwork0.1612 ---
all0.1644 33810 --
obs0.1644 32595 96.4 %-
Solvent computationBsol: 61.472 Å2
Displacement parametersBiso max: 111.56 Å2 / Biso mean: 33.595 Å2 / Biso min: 10.29 Å2
Baniso -1Baniso -2Baniso -3
1-2.567 Å2-2.856 Å20 Å2
2--2.567 Å20 Å2
3----5.134 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.57→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7296 0 30 390 7716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.97219
X-RAY DIFFRACTIONc_bond_d0.021827
LS refinement shellResolution: 2.57→2.66 Å / Rfactor Rfree error: 0.0827
RfactorNum. reflection% reflection
Rfree0.2565 141 -
Rwork0.1738 --
obs-2992 89.42 %

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