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

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Basic information

Entry
Database: PDB / ID: 4jfw
TitleCrystal structure of a bacterial fucosidase with iminosugar inhibitor (2S,3S,4R,5S)-2-[N-(propylferrocene)]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-H58 / IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)210,81819
Polymers208,3244
Non-polymers2,49415
Water3,873215
1
A: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6324
Polymers52,0811
Non-polymers5513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7285
Polymers52,0811
Non-polymers6484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7285
Polymers52,0811
Non-polymers6484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7285
Polymers52,0811
Non-polymers6484
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.507, 189.982, 97.540
Angle α, β, γ (deg.)90.000, 94.090, 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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYSAA35 - 4731 - 439
21GLUGLULYSLYSBB35 - 4731 - 439
12GLUGLULYSLYSAA35 - 4731 - 439
22GLUGLULYSLYSCC35 - 4731 - 439
13ILEILEALAALAAA36 - 4722 - 438
23ILEILEALAALADD36 - 4722 - 438
14GLUGLULYSLYSBB35 - 4731 - 439
24GLUGLULYSLYSCC35 - 4731 - 439
15ILEILEALAALABB36 - 4722 - 438
25ILEILEALAALADD36 - 4722 - 438
16ILEILEALAALACC36 - 4722 - 438
26ILEILEALAALADD36 - 4722 - 438

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: UNP 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-H58 / (3alpha)-[3-({2-[(2S,3S,4R,5S)-3,4-dihydroxy-5-methylpyrrolidin-2-yl]ethyl}amino)propyl]ferrocene / (2S,3S,4R,5S)-2-[N-(propylferrocene)]aminoethyl-5-methylpyrrolidine-3,4-diol


Mass: 386.309 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H30FeN2O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#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.: 215 / 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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.12M ammonium sulfate, 14% PEG 6K, 0.1M 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: I03 / Wavelength: 1.2 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.72→97.272 Å / Num. all: 118860 / Num. obs: 118860 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.086 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.216.10.7331105056172740.73399.9
2.21-2.356.20.4531.6101718164310.45399.9
2.35-2.516.30.3112.397617153760.31199.8
2.51-2.716.10.1993.588181144070.19999.9
2.71-2.976.30.137582695132170.13799.9
2.97-3.326.30.0976.675195119570.09799.8
3.32-3.836.40.0768.267250105070.07699.9
3.83-4.76.40.05910.55732989360.05999.9
4.7-6.646.40.051124433669050.051100
6.64-67.9226.30.0429.52430138500.04299.9

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Processing

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

2wvv


Resolution: 2.1→97.272 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2387 / WRfactor Rwork: 0.2006 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7346 / SU B: 8.097 / SU ML: 0.193 / SU R Cruickshank DPI: 0.223 / SU Rfree: 0.1853 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY LIGAND AGLYCON HAS HIGH THERMAL FACTORS, PRESENCE OF IRON CONFIRMED BY ANOMALOUS DIFFERENCE
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 5986 5 %AS 2WVV
Rwork0.2069 ---
obs0.2087 112918 99.79 %-
all-118546 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 187.26 Å2 / Biso mean: 54.2889 Å2 / Biso min: 28.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-2.14 Å2
2--4.28 Å20 Å2
3----3.91 Å2
Refinement stepCycle: LAST / Resolution: 2.1→97.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13859 0 155 215 14229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01914475
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212815
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.94119939
X-RAY DIFFRACTIONr_angle_other_deg1.0512.9929388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63451751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22123.905676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.891152125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1941571
X-RAY DIFFRACTIONr_chiral_restr0.0860.22034
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02116531
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023547
X-RAY DIFFRACTIONr_mcbond_it4.3135.2537016
X-RAY DIFFRACTIONr_mcbond_other4.3135.2527015
X-RAY DIFFRACTIONr_mcangle_it5.9827.8738763
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A259610.06
12B259610.06
21A260020.05
22C260020.05
31A258480.05
32D258480.05
41B257940.05
42C257940.05
51B254740.05
52D254740.05
61C253730.05
62D253730.05
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 438 -
Rwork0.379 8305 -
all-8743 -
obs--99.82 %

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