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- PDB-4jl1: Crystal structure of a bacterial fucosidase with a multivalent im... -

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Basic information

Entry
Database: PDB / ID: 4jl1
TitleCrystal structure of a bacterial fucosidase with a multivalent iminocyclitol 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 / 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
IMIDAZOLE / Chem-LM5 / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsWright, D.W. / Davies, G.J.
CitationJournal: EUR.J.ORG.CHEM. / Year: 2013
Title: Exploring a Multivalent Approach to alpha-L-Fucosidase Inhibition
Authors: Moreno-Clavijo, E. / Carmona, A.T. / Moreno-Varga, A.J. / Molina, L. / Wright, D.W. / Davies, G.J. / Robina, I.
History
DepositionMar 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: 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)105,93019
Polymers104,1622
Non-polymers1,76817
Water19,0061055
1
A: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,01110
Polymers52,0811
Non-polymers9309
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9199
Polymers52,0811
Non-polymers8388
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.378, 96.047, 97.204
Angle α, β, γ (deg.)90.00, 91.29, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 35 - 473 / Label seq-ID: 1 - 439

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: 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

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Non-polymers , 5 types, 1072 molecules

#2: Chemical ChemComp-LM5 / (3S,4R,5S)-N-benzyl-3,4-dihydroxy-5-methyl-D-prolinamide


Mass: 250.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18N2O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-IMD / IMIDAZOLE / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1055 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsINHIBITOR LIGAND IS N,N',N"-(1,3,5-PHENYLENETRIS(METHYLENE))TRIS-[(2S,3S,4R,5S)-3,4-DIHYDROXY-5- ...INHIBITOR LIGAND IS N,N',N"-(1,3,5-PHENYLENETRIS(METHYLENE))TRIS-[(2S,3S,4R,5S)-3,4-DIHYDROXY-5-METHYLPYRROLIDINE-2-CARBOXAMIDE]. HOWEVER, NO ADDITIONAL ATOMS COULD BE MODELLED RELIABLY FOR THIS INHIBITOR THAN WHAT ARE PRESENT IN THE PDB COORDINATES. AS SUCH, A COORDINATE SET AND MAXIMUM-LIKELIHOOD REFINEMENT DICTIONARY FOR LM5 WERE USED FOR MODELLING THIS INHIBITOR.

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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: 3.06 Å3/Da / Density % sol: 59.85 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 85% dilution of (0.13M AS, 15% PEG6K, 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: 1.68→48.707 Å / Num. all: 141254 / Num. obs: 141254 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.095 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.68-1.773.10.5011.564370206670.50199.6
1.77-1.883.30.372263790196150.37299.6
1.88-2.013.20.2662.758494183880.26699.5
2.01-2.173.20.177455369170460.17799.1
2.17-2.383.30.135.251614156540.1398.7
2.38-2.663.10.1076.144377141560.10798.7
2.66-3.073.30.087740908124190.08798.1
3.07-3.763.10.079733003105300.07997.9
3.76-5.313.30.0668.22678882060.06698.5
5.31-48.7073.20.0538.61483045730.05398.5

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Processing

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

4j27


Resolution: 1.68→48.707 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.2001 / WRfactor Rwork: 0.1701 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8371 / SU B: 2.252 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0817 / SU Rfree: 0.0822 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. LIGAND "AGLYCON" IS SOMEWHAT UNRESOLVED, ATOMS THAT DO NOT FIT DENSITY HAVE BEEN DELETED
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 7027 5 %AS PDB ENTRY 4J27
Rwork0.1649 ---
obs0.1662 141053 98.79 %-
all-141254 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.43 Å2 / Biso mean: 25.4304 Å2 / Biso min: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å2-0.46 Å2
2---0.67 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 1.68→48.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7048 0 107 1055 8210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.027555
X-RAY DIFFRACTIONr_bond_other_d0.0070.026841
X-RAY DIFFRACTIONr_angle_refined_deg1.7051.94410293
X-RAY DIFFRACTIONr_angle_other_deg1.2913.00415769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99224.178359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97151214
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1121536
X-RAY DIFFRACTIONr_chiral_restr0.1210.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218580
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021834
X-RAY DIFFRACTIONr_mcbond_it1.9782.2453576
X-RAY DIFFRACTIONr_mcbond_other1.9772.2453576
X-RAY DIFFRACTIONr_mcangle_it2.7253.3564474
Refine LS restraints NCS

Ens-ID: 1 / Number: 26894 / 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: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 507 -
Rwork0.289 9929 -
all-10436 -
obs--99.55 %

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