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- PDB-4wsk: Crystal structure of a bacterial fucosidase with phenyl((1R,2R,3R... -

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Basic information

Entry
Database: PDB / ID: 4wsk
TitleCrystal structure of a bacterial fucosidase with phenyl((1R,2R,3R,4R,5R,6R)-2,3,4-trihydroxy-5-methyl-7-azabicyclo[4.1.0]heptan-7-yl)methanone
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / Fucosidase Complex Covalent Inhibitor
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-3U2 / IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsDavies, G.J.
CitationJournal: Chem Sci / Year: 2015
Title: In vitroandin vivocomparative and competitive activity-based protein profiling of GH29 alpha-l-fucosidases.
Authors: Jiang, J. / Kallemeijn, W.W. / Wright, D.W. / van den Nieuwendijk, A.M.C.H. / Rohde, V.C. / Folch, E.C. / van den Elst, H. / Florea, B.I. / Scheij, S. / Donker-Koopman, W.E. / Verhoek, M. / ...Authors: Jiang, J. / Kallemeijn, W.W. / Wright, D.W. / van den Nieuwendijk, A.M.C.H. / Rohde, V.C. / Folch, E.C. / van den Elst, H. / Florea, B.I. / Scheij, S. / Donker-Koopman, W.E. / Verhoek, M. / Li, N. / Schurmann, M. / Mink, D. / Boot, R.G. / Codee, J.D.C. / van der Marel, G.A. / Davies, G.J. / Aerts, J.M.F.G. / Overkleeft, H.S.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 10, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 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
B: Alpha-L-fucosidase
C: Alpha-L-fucosidase
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,16517
Polymers216,5174
Non-polymers1,64913
Water21,6901204
1
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6565
Polymers54,1291
Non-polymers5274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6565
Polymers54,1291
Non-polymers5274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5604
Polymers54,1291
Non-polymers4303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2943
Polymers54,1291
Non-polymers1652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.650, 186.520, 98.150
Angle α, β, γ (deg.)90.000, 94.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA35 - 47824 - 467
21ILEILEBB35 - 47824 - 467
12ILEILEAA35 - 47824 - 467
22ILEILECC35 - 47824 - 467
13TYRTYRAA35 - 47924 - 468
23TYRTYRDD35 - 47924 - 468
14ILEILEBB35 - 47824 - 467
24ILEILECC35 - 47824 - 467
15ILEILEBB35 - 47824 - 467
25ILEILEDD35 - 47824 - 467
16ILEILECC35 - 47824 - 467
26ILEILEDD35 - 47824 - 467

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Alpha-L-fucosidase


Mass: 54129.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2970 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A3I4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-3U2 / N-[(1S,2R,3R,4S,5R)-3,4,5-trihydroxy-2-methylcyclohexyl]benzamide


Mass: 265.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H19NO4
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1204 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M imidazole pH 7.0, 0.2 M ammonium sulfate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.92→53.2 Å / Num. obs: 199312 / % possible obs: 96.9 % / Redundancy: 4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.058 / Net I/σ(I): 7 / Num. measured all: 579846 / Scaling rejects: 80
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.92-1.953.70.9091.82640771780.5440.53996.7
10.52-53.23.90.06116.737009440.9680.03898.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimless0.2.17data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JFV

4jfv


Resolution: 1.92→97.89 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2384 / WRfactor Rwork: 0.1871 / FOM work R set: 0.8148 / SU B: 4.222 / SU ML: 0.12 / SU R Cruickshank DPI: 0.1623 / SU Rfree: 0.1533 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 7350 5 %RANDOM
Rwork0.1824 139018 --
obs0.1849 139018 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.86 Å2 / Biso mean: 31.583 Å2 / Biso min: 11.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å2-0.75 Å2
2--0.58 Å20 Å2
3----1.4 Å2
Refinement stepCycle: final / Resolution: 1.92→97.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14236 0 96 1204 15536
Biso mean--46.06 36.89 -
Num. residues----1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214801
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.93220142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25151794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44724.182691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.503152332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7941563
X-RAY DIFFRACTIONr_chiral_restr0.1330.22076
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111480
X-RAY DIFFRACTIONr_mcbond_it2.8833.0717143
X-RAY DIFFRACTIONr_mcangle_it3.8344.5888927
X-RAY DIFFRACTIONr_scbond_it3.6373.2337658
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6050.07
12B6050.07
21A6050.06
22C6050.06
31A6100.09
32D6100.09
41B6050.08
42C6050.08
51B6090.09
52D6090.09
61C6070.07
62D6070.07
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 515 -
Rwork0.262 10163 -
all-10678 -
obs--95.75 %

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