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- PDB-4pee: Crystal structure of a bacterial fucosidase with inhibitor 1-phen... -

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Basic information

Entry
Database: PDB / ID: 4pee
TitleCrystal structure of a bacterial fucosidase with inhibitor 1-phenyl-4-[(2S,3S,4R,5S)-3,4-dihydroxy-5-methylpyrrolidin-2-yl]triazole
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE
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-2OX / IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.95 Å
AuthorsWright, D.W. / Davies, G.J. / Behr, J.B.
CitationJournal: Chembiochem / Year: 2015
Title: Exploiting the Hydrophobic Terrain in Fucosidases with Aryl-Substituted Pyrrolidine Iminosugars.
Authors: Hottin, A. / Wright, D.W. / Davies, G.J. / Behr, J.B.
History
DepositionApr 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)209,06520
Polymers207,0064
Non-polymers2,05916
Water16,069892
1
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2735
Polymers51,7521
Non-polymers5224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2735
Polymers51,7521
Non-polymers5224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2735
Polymers51,7521
Non-polymers5224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2465
Polymers51,7521
Non-polymers4954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.040, 187.590, 97.700
Angle α, β, γ (deg.)90.000, 94.260, 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: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA35 - 4792 - 446
21TYRTYRBB35 - 4792 - 446
12ILEILEAA35 - 4782 - 445
22ILEILECC35 - 4782 - 445
13ILEILEAA35 - 4782 - 445
23ILEILEDD35 - 4782 - 445
14ILEILEBB35 - 4782 - 445
24ILEILECC35 - 4782 - 445
15ILEILEBB35 - 4782 - 445
25ILEILEDD35 - 4782 - 445
16ILEILECC35 - 4782 - 445
26ILEILEDD35 - 4782 - 445

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Alpha-L-fucosidase / fucosidase 2970


Mass: 51751.586 Da / Num. of mol.: 4 / Fragment: Residues 35-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2970 / Plasmid: pET-YSBLIC3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A3I4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-2OX / (2S,3R,4S,5S)-2-methyl-5-(1-phenyl-1H-1,2,3-triazol-4-yl)pyrrolidine-3,4-diol


Mass: 260.292 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C13H16N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.2 M ammonium sulfate, 0.1 M imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.95→55.89 Å / Num. obs: 143082 / % possible obs: 98.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.047 / Net I/σ(I): 8.8 / Num. measured all: 554820 / Scaling rejects: 59
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.9 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.95-1.980.8271.72735570140.47497.4
10.68-55.890.04722.136209220.02698.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimless0.2.17data scaling
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: 4JFV

4jfv


Resolution: 1.95→97.43 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.1933 / FOM work R set: 0.801 / SU B: 4.826 / SU ML: 0.131 / SU R Cruickshank DPI: 0.1728 / SU Rfree: 0.1536 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY PDB entry 4JFV has an almost isomorphous space group to 4PEE. Coordinates of 4JFV (ligand/ion atoms omitted) ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY PDB entry 4JFV has an almost isomorphous space group to 4PEE. Coordinates of 4JFV (ligand/ion atoms omitted) were scaled to the slightly different 4PEE unit cell using coordconv before refinement with REFMAC to generate an initial model of 4PEE. Rfree flags from the 4JFV refinement were used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 7202 5 %RANDOM
Rwork0.1907 135815 --
obs0.1926 143017 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.13 Å2 / Biso mean: 37.86 Å2 / Biso min: 17.01 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å2-1.07 Å2
2---0.95 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 1.95→97.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14284 0 136 892 15312
Biso mean--55.91 39.93 -
Num. residues----1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214878
X-RAY DIFFRACTIONr_bond_other_d0.0080.0213414
X-RAY DIFFRACTIONr_angle_refined_deg1.531.93720236
X-RAY DIFFRACTIONr_angle_other_deg1.2543.00230848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80451788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53523.969703
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.844152350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5831574
X-RAY DIFFRACTIONr_chiral_restr0.0980.22068
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02116904
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023608
X-RAY DIFFRACTIONr_mcbond_it3.3173.6637134
X-RAY DIFFRACTIONr_mcbond_other3.3143.6637133
X-RAY DIFFRACTIONr_mcangle_it4.3845.4778913
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A268110.07
12B268110.07
21A264340.07
22C264340.07
31A263620.07
32D263620.07
41B272290.07
42C272290.07
51B270970.07
52D270970.07
61C269010.06
62D269010.06
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 511 -
Rwork0.3 9958 -
all-10469 -
obs--97.1 %

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