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- PDB-4jl2: Crystal structure of a bacterial fucosidase with a monovalent imi... -

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Basic information

Entry
Database: PDB / ID: 4jl2
TitleCrystal structure of a bacterial fucosidase with a monovalent 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: 1.7 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_ref_seq_dif / 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_ref_seq_dif.details / _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)105,69417
Polymers104,1642
Non-polymers1,53015
Water20,3571130
1
A: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9209
Polymers52,0821
Non-polymers8388
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7748
Polymers52,0821
Non-polymers6927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.520, 95.350, 97.160
Angle α, β, γ (deg.)90.00, 90.13, 90.00
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 - 471 / Label seq-ID: 1 - 437

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: 52081.980 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, 1145 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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1130 / 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 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 90% dilution of 0.11M 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: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.566→97.16 Å / Num. all: 135078 / Num. obs: 135078 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.096 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.793.80.5411.474271196450.541100
1.79-1.93.80.362.170541186020.36100
1.9-2.033.80.2273.366560174990.227100
2.03-2.193.80.1584.762067162890.158100
2.19-2.43.80.1136.657322150020.113100
2.4-2.693.80.0838.652116136040.083100
2.69-3.13.80.0699.546009119910.069100
3.1-3.83.80.0639.439070101730.063100
3.8-5.383.80.04811.83025878980.048100
5.38-30.6663.70.03317.41640543750.03399.5

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Processing

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

4j27


Resolution: 1.7→97.16 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1635 / WRfactor Rwork: 0.1195 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9065 / SU B: 3.651 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0852 / SU Rfree: 0.0741 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. INHIBITOR AGLYCON IN B-CHAIN HAS PARTIAL OCCUPANCY, MISSING ATOMS REMOVED
RfactorNum. reflection% reflectionSelection details
Rfree0.1669 6741 5 %RANDOM
Rwork0.1225 ---
obs0.1248 135052 99.92 %-
all-135078 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.43 Å2 / Biso mean: 18.0864 Å2 / Biso min: 6.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0.35 Å2
2--0.44 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→97.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7051 0 96 1130 8277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.027570
X-RAY DIFFRACTIONr_bond_other_d0.0040.026881
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.94110334
X-RAY DIFFRACTIONr_angle_other_deg0.9953.00215869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6585946
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53824.185356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.905151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9931535
X-RAY DIFFRACTIONr_chiral_restr0.0860.21061
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218652
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021839
X-RAY DIFFRACTIONr_mcbond_it2.2061.4543598
X-RAY DIFFRACTIONr_mcbond_other2.2061.4543598
X-RAY DIFFRACTIONr_mcangle_it2.6952.1914513
X-RAY DIFFRACTIONr_rigid_bond_restr10.8314451
X-RAY DIFFRACTIONr_sphericity_free38.1525309
X-RAY DIFFRACTIONr_sphericity_bonded11.194515022
Refine LS restraints NCS

Ens-ID: 1 / Number: 27092 / 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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 483 -
Rwork0.219 9459 -
all-9942 -
obs--99.87 %

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