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

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Basic information

Entry
Database: PDB / ID: 4jft
TitleCrystal structure of a bacterial fucosidase with iminosugar inhibitor N-desmethyl-4-epi-(+)-Codonopsinine
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-1KN / 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 1.1Sep 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,86819
Polymers104,1622
Non-polymers1,70617
Water7,296405
1
A: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,98010
Polymers52,0811
Non-polymers8999
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8889
Polymers52,0811
Non-polymers8078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.495, 94.646, 96.905
Angle α, β, γ (deg.)90.000, 90.870, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 35 - 472 / Label seq-ID: 1 - 438

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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, 422 molecules

#2: Chemical ChemComp-1KN / (2S,3S,4R,5S)-2-(4-methoxyphenyl)-5-methylpyrrolidine-3,4-diol / N-desmethyl-4-epi-(+)-Codonopsinine


Mass: 223.268 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17NO3
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 69.085 Da / Num. of mol.: 6 / 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.: 405 / 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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.13 M ammonium sulfate, 12% PEG 6K, 0.1 M 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: 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: 1.56→96.894 Å / Num. all: 70382 / Num. obs: 70382 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.08 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.214.40.4771.645672103490.47799.7
2.21-2.354.30.3372.24233997510.33799.5
2.35-2.514.30.24633883890910.24698.9
2.51-2.714.10.1774.13467184150.17798.1
2.71-2.973.80.144.62886476950.1497.7
2.97-3.324.30.0996.13078870960.09999.3
3.32-3.834.40.0629.52761963000.06299.7
3.83-4.74.20.0415.62232253420.0499.5
4.7-6.644.10.03318.61643940460.03397.6
6.64-28.9634.50.02523.91039222970.02598.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J27

4j27


Resolution: 2.1→96.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1934 / WRfactor Rwork: 0.1584 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8003 / SU B: 5.895 / SU ML: 0.143 / SU R Cruickshank DPI: 0.1762 / SU Rfree: 0.1566 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. THE COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS CELL OF 4JFT TO BUILD A STARTING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. THE COORDINATES FROM 4J27 WERE CONVERTED INTO THE (ALMOST) ISOMORPHOUS CELL OF 4JFT TO BUILD A STARTING MODEL DIRECTLY. THE RFREE FLAG FROM 4J27 WAS USED FOR THIS DATASET.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 3540 5 %AS 4J27
Rwork0.1806 ---
obs0.1825 70362 98.76 %-
all-70382 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.31 Å2 / Biso mean: 39.888 Å2 / Biso min: 22.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å2-0.86 Å2
2--3.29 Å20 Å2
3----4.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→96.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7005 0 112 405 7522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.027371
X-RAY DIFFRACTIONr_bond_other_d0.0050.026634
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.93910023
X-RAY DIFFRACTIONr_angle_other_deg1.0473.00215254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66324.212349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.631151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6561533
X-RAY DIFFRACTIONr_chiral_restr0.0960.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218364
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021789
X-RAY DIFFRACTIONr_mcbond_it2.9473.8073515
X-RAY DIFFRACTIONr_mcbond_other2.9473.8063514
X-RAY DIFFRACTIONr_mcangle_it3.8775.7024393
Refine LS restraints NCS

Ens-ID: 1 / Number: 26522 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 242 -
Rwork0.288 5022 -
all-5264 -
obs--99.4 %

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