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- PDB-4jfu: Crystal structure of a bacterial fucosidase with iminosugar inhibitor -

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Basic information

Entry
Database: PDB / ID: 4jfu
TitleCrystal structure of a bacterial fucosidase with iminosugar inhibitor
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 / 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
IMIDAZOLE / Chem-K80 / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 1.1Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,67017
Polymers104,1622
Non-polymers1,50915
Water19,7801098
1
A: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,98710
Polymers52,0811
Non-polymers9069
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6847
Polymers52,0811
Non-polymers6036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.030, 95.400, 96.930
Angle α, β, γ (deg.)90.000, 90.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein alpha-L-fucosidase


Mass: 52080.930 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 1113 molecules

#2: Chemical ChemComp-K80 / (2S,3R,4S,5S)-2-methyl-5-(4-methylphenyl)pyrrolidine-3,4-diol


Mass: 207.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17NO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1098 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.16 M ammonium sulfate, 20% PEG 6K, 0.1M imidazole pH 7, 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: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.659→55.385 Å / Num. all: 145075 / Num. obs: 145075 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.047 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.66-1.752.90.1614.560208210780.16199.1
1.75-1.852.80.1215.856307199230.12199.4
1.85-1.982.80.0956.652705188910.09599.4
1.98-2.1430.087.552224174470.0899.2
2.14-2.352.80.0797.444454161260.07999
2.35-2.6230.0649.243304145910.06499.6
2.62-3.032.90.05111.937280128840.05199.2
3.03-3.7130.03815.433118108910.03899.5
3.71-5.252.80.03615.92398985070.03699.6
5.25-56.06130.02713.71413047370.02799.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J27

4j27


Resolution: 1.66→55.385 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.1929 / WRfactor Rwork: 0.1629 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8775 / SU B: 1.638 / SU ML: 0.054 / SU R Cruickshank DPI: 0.073 / SU Rfree: 0.0741 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY. THE MOLECULAR REPLACEMENT WAS NOT USED, COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS ...Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY. THE MOLECULAR REPLACEMENT WAS NOT USED, COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS CELL OF 4JFU TO BUILD A STARTING MODEL DIRECTLY. THE RFREE FLAG FROM 4J27 WAS USED FOR THIS DATASET.
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 7225 5 %AS 4J27
Rwork0.1521 ---
obs0.1534 144771 99.08 %-
all-145075 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.72 Å2 / Biso mean: 26.2193 Å2 / Biso min: 14.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20 Å2-0.83 Å2
2--1.18 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 1.66→55.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7058 0 100 1098 8256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.027510
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9410233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5855922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14624.15359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.848151212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9921537
X-RAY DIFFRACTIONr_chiral_restr0.1190.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215846
X-RAY DIFFRACTIONr_mcbond_it1.6382.3113559
X-RAY DIFFRACTIONr_mcangle_it2.2873.4564459
X-RAY DIFFRACTIONr_scbond_it2.4952.513951
LS refinement shellResolution: 1.66→1.702 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 535 -
Rwork0.223 10085 -
all-10620 -
obs--98.55 %

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