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- PDB-2zwz: alpha-L-fucosidase complexed with inhibitor, Core1 -

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Basic information

Entry
Database: PDB / ID: 2zwz
Titlealpha-L-fucosidase complexed with inhibitor, Core1
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-ZWZ / Alpha-L-fucosidase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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 1.2Nov 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)106,5544
Polymers106,2022
Non-polymers3522
Water9,134507
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)319,66312
Polymers318,6066
Non-polymers1,0576
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 area12180 Å2
ΔGint-29 kcal/mol
Surface area92770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.693, 180.693, 169.375
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-476-

HOH

21A-639-

HOH

31A-663-

HOH

41A-669-

HOH

51A-694-

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-ZWZ / (2R,3R,4R,5R,6S)-2-(aminomethyl)-6-methylpiperidine-3,4,5-triol


Mass: 176.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 14% PEG 5000 MME, 0.1M HEPES, pH 7.4, 4% 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: BL13C1 / Wavelength: 0.97315 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 9, 2007 / Details: Vertically focusing mirror
RadiationMonochromator: horizontally focusing single crystal Si(111) bent monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97315 Å / Relative weight: 1
ReflectionResolution: 2.36→30 Å / Num. all: 43512 / Num. obs: 43077 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.4
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4281 / % possible all: 99.7

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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: 2.36→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 2066 -RANDOM
Rwork0.1594 ---
all0.162 43646 --
obs0.162 41233 94.5 %-
Solvent computationBsol: 61.256 Å2
Displacement parametersBiso max: 102.1 Å2 / Biso mean: 35.125 Å2 / Biso min: 12.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.156 Å2-2.623 Å20 Å2
2--1.156 Å20 Å2
3----2.311 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.36→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7278 0 24 507 7809
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.85617
X-RAY DIFFRACTIONc_bond_d0.019395
LS refinement shellResolution: 2.36→2.44 Å / Rfactor Rfree error: 0.0336
RfactorNum. reflection% reflection
Rfree0.2214 177 -
Rwork0.1878 --
obs-3756 86.86 %

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