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- PDB-4jfv: Crystal structure of a bacterial fucosidase with iminosugar inhib... -

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Basic information

Entry
Database: PDB / ID: 4jfv
TitleCrystal structure of a bacterial fucosidase with iminosugar inhibitor (2S,3S,4R,5S)-2-[N-(methylferrocene)]aminoethyl-5-methylpyrrolidine-3,4-diol
Componentsalpha-L-fucosidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / alpha-L-fucosidase / HYDROLASE-HYDROLASE INHIBITOR complex
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-H57 / IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsWright, D.W. / Davies, G.J.
CitationJournal: Chemistry / Year: 2013
Title: alpha-L-fucosidase inhibition by pyrrolidine-ferrocene hybrids: rationalization of ligand-binding properties by structural studies.
Authors: Hottin, A. / Wright, D.W. / Steenackers, A. / Delannoy, P. / Dubar, F. / Biot, C. / Davies, G.J. / Behr, J.B.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Non-polymer description
Revision 1.2Sep 20, 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_ncs_dom_lim / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)210,99724
Polymers208,3244
Non-polymers2,67320
Water13,187732
1
A: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9779
Polymers52,0811
Non-polymers8968
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7436
Polymers52,0811
Non-polymers6625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6044
Polymers52,0811
Non-polymers5233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6735
Polymers52,0811
Non-polymers5924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.540, 187.001, 97.671
Angle α, β, γ (deg.)90.00, 94.19, 90.00
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
11LYSLYSAA35 - 4731 - 439
21LYSLYSBB35 - 4731 - 439
12ALAALAAA35 - 4711 - 437
22ALAALACC35 - 4711 - 437
13ALAALAAA35 - 4721 - 438
23ALAALADD35 - 4721 - 438
14ALAALABB35 - 4711 - 437
24ALAALACC35 - 4711 - 437
15ALAALABB35 - 4721 - 438
25ALAALADD35 - 4721 - 438
16ALAALACC35 - 4711 - 437
26ALAALADD35 - 4711 - 437

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
alpha-L-fucosidase


Mass: 52080.930 Da / Num. of mol.: 4 / Fragment: RESIDUES 35-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Plasmid: pET-YSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-H57 / (3alpha)-[({2-[(2S,3S,4R,5S)-3,4-dihydroxy-5-methylpyrrolidin-2-yl]ethyl}amino)methyl]ferrocene / (2S,3S,4R,5S)-2-[N-(methylferrocene)]aminoethyl-5-methylpyrrolidine-3,4-diol


Mass: 358.256 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H26FeN2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.13M ammonium sulfate, 16% PEG 6K, 0.1M imidazole pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.714→97.409 Å / Num. all: 155289 / Num. obs: 155289 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.072 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.88-1.983.50.4341.777017222780.43495
1.98-2.13.70.2892.279515212270.28996
2.1-2.254.20.2153.585936205480.21598.7
2.25-2.434.20.147579060190230.14797.9
2.43-2.664.10.1086.671229172160.10896.6
2.66-2.973.60.076953273149840.07692.8
2.97-3.434.30.0610.660627141180.0699.3
3.43-4.24.20.0512.350453119540.0599.1
4.2-5.953.70.04213.63255987710.04294.2
5.95-38.8784.70.04610.92405451700.04699.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WVV

2wvv


Resolution: 1.88→97.409 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2239 / WRfactor Rwork: 0.1918 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8394 / SU B: 3.698 / SU ML: 0.107 / SU R Cruickshank DPI: 0.1526 / SU Rfree: 0.1372 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY LIGAND AGLYCON HAS HIGH THERMAL FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 7806 5 %AS 2WVV
Rwork0.1899 ---
obs0.1915 155246 96.58 %-
all-155289 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.95 Å2 / Biso mean: 31.1146 Å2 / Biso min: 11.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å2-0.31 Å2
2---0.33 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.88→97.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14109 0 172 732 15013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01914780
X-RAY DIFFRACTIONr_bond_other_d0.0090.0213349
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.95120286
X-RAY DIFFRACTIONr_angle_other_deg1.322.99730737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87251766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57524.066696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.437152336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8181570
X-RAY DIFFRACTIONr_chiral_restr0.1050.22042
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02116790
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023598
X-RAY DIFFRACTIONr_mcbond_it2.8022.9157037
X-RAY DIFFRACTIONr_mcbond_other2.8022.9157036
X-RAY DIFFRACTIONr_mcangle_it3.6684.368791
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A265670.07
12B265670.07
21A263740.07
22C263740.07
31A263390.06
32D263390.06
41B270400.07
42C270400.07
51B269330.07
52D269330.07
61C268490.07
62D268490.07
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 577 -
Rwork0.271 10920 -
all-11497 -
obs--97.15 %

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