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- PDB-4wsj: Crystal structure of a bacterial fucodiase in complex with 1-((1R... -

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Basic information

Entry
Database: PDB / ID: 4wsj
TitleCrystal structure of a bacterial fucodiase in complex with 1-((1R,2R,3R,4R,5R,6R)-2,3,4-trihydroxy-5-methyl-7-azabicyclo[4.1.0]heptan-7-yl)ethan-1-one
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-3U3 / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsDavies, G.J. / Wright, D.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilA0067812 United Kingdom
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 5, 2014Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 2.0Aug 30, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Apr 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 2.2Jan 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 2.3Oct 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
B: Alpha-L-fucosidase
C: Alpha-L-fucosidase
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,38613
Polymers206,0934
Non-polymers1,2939
Water29,1481618
1
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9194
Polymers51,5231
Non-polymers3953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9194
Polymers51,5231
Non-polymers3953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8233
Polymers51,5231
Non-polymers2992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7272
Polymers51,5231
Non-polymers2031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.480, 186.980, 98.190
Angle α, β, γ (deg.)90.000, 94.170, 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
11ALAALAAA35 - 4721 - 438
21ALAALABB35 - 4721 - 438
12ARGARGAA35 - 4701 - 436
22ARGARGCC35 - 4701 - 436
13ALAALAAA35 - 4721 - 438
23ALAALADD35 - 4721 - 438
14ARGARGBB35 - 4701 - 436
24ARGARGCC35 - 4701 - 436
15LYSLYSBB35 - 4731 - 439
25LYSLYSDD35 - 4731 - 439
16ARGARGCC35 - 4701 - 436
26ARGARGDD35 - 4701 - 436

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Alpha-L-fucosidase


Mass: 51523.309 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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-3U3 / N-[(1S,2R,3R,4S,5R)-3,4,5-trihydroxy-2-methylcyclohexyl]acetamide


Mass: 203.236 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H17NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1618 / 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: 50.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M HEPES pH 7.5

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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: Oct 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.64→93.49 Å / Num. obs: 238023 / % possible obs: 98.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDRejects% possible all
1.64-1.684.20.6781098.6
7.33-93.494.10.0341098.2

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Processing

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

4jfv


Resolution: 1.64→93.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1946 / WRfactor Rwork: 0.1645 / FOM work R set: 0.8595 / SU B: 1.967 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0858 / SU Rfree: 0.0862 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 11927 5 %RANDOM
Rwork0.1642 226036 --
obs0.1657 226036 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.39 Å2 / Biso mean: 25.202 Å2 / Biso min: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å2-0.09 Å2
2--0.36 Å20 Å2
3----0.81 Å2
Refinement stepCycle: final / Resolution: 1.64→93.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14062 0 81 1618 15761
Biso mean--24.32 35.33 -
Num. residues----1761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214584
X-RAY DIFFRACTIONr_bond_other_d0.0090.0213095
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9319867
X-RAY DIFFRACTIONr_angle_other_deg1.4463.00230114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97851760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3924.174690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66152271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9621564
X-RAY DIFFRACTIONr_chiral_restr0.1160.22053
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02116600
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023492
X-RAY DIFFRACTIONr_mcbond_it2.2282.3477043
X-RAY DIFFRACTIONr_mcbond_other2.2282.3467042
X-RAY DIFFRACTIONr_mcangle_it2.8423.5158796
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A261840.07
12B261840.07
21A258850.07
22C258850.07
31A260400.06
32D260400.06
41B262410.07
42C262410.07
51B260390.07
52D260390.07
61C259140.07
62D259140.07
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 852 -
Rwork0.272 16847 -
all-17699 -
obs--98.55 %

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