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- PDB-4pcs: Crystal structure of a bacterial fucosidase with iminosugar (2S,3... -

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Basic information

Entry
Database: PDB / ID: 4pcs
TitleCrystal structure of a bacterial fucosidase with iminosugar (2S,3S,4R,5S)-3,4-dihydroxy-2-[2'-phenyl]ethynyl-5-methylpyrrolidine
ComponentsAlpha-L-fucosidase
KeywordsHYDROLASE / a-L-fucosidase enzyme inhibition
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-2M7 / IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsDavies, G.J. / Wright, D.W. / 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 16, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Jan 21, 2015Group: Database references
Revision 1.4Dec 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)205,35020
Polymers203,4904
Non-polymers1,86016
Water10,593588
1
A: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4206
Polymers50,8731
Non-polymers5485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4206
Polymers50,8731
Non-polymers5485
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2554
Polymers50,8731
Non-polymers3823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2554
Polymers50,8731
Non-polymers3823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.370, 188.280, 97.930
Angle α, β, γ (deg.)90.000, 94.100, 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
11LYSLYSAA35 - 4731 - 439
21LYSLYSBB35 - 4731 - 439
12ARGARGAA35 - 4701 - 436
22ARGARGCC35 - 4701 - 436
13ARGARGAA35 - 4701 - 436
23ARGARGDD35 - 4701 - 436
14ARGARGBB35 - 4701 - 436
24ARGARGCC35 - 4701 - 436
15ARGARGBB35 - 4701 - 436
25ARGARGDD35 - 4701 - 436
16ALAALACC35 - 4711 - 437
26ALAALADD35 - 4711 - 437

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Alpha-L-fucosidase


Mass: 50872.570 Da / Num. of mol.: 4 / Fragment: Residues 35-473
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: 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.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-2M7 / (2S,3R,4S,5S)-2-methyl-5-(phenylethynyl)pyrrolidine-3,4-diol


Mass: 217.264 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H15NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.16 M AS, 14% PEG 6000 0.1 M imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.77→39.25 Å / Num. obs: 187759 / % possible obs: 95.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.062 / Net I/σ(I): 6 / Num. measured all: 751195 / Scaling rejects: 546
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.77-1.841.720.73702793530.96996.7
9.72-39.254.60.0328.7555712110.01698.4

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Processing

Software
NameVersionClassification
iMOSFLM0.1.27data reduction
PDB_EXTRACT3.14data extraction
REFMAC5.8.0033refinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wvv

2wvv


Resolution: 1.77→39.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2484 / WRfactor Rwork: 0.212 / FOM work R set: 0.6936 / SU B: 5.627 / SU ML: 0.156 / SU R Cruickshank DPI: 0.1451 / SU Rfree: 0.1379 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 9469 5 %RANDOM
Rwork0.2236 178165 --
obs0.2255 187634 95.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.08 Å2 / Biso mean: 35.533 Å2 / Biso min: 14.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å2-0.62 Å2
2--0.33 Å20 Å2
3----2.69 Å2
Refinement stepCycle: final / Resolution: 1.77→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14157 0 124 588 14869
Biso mean--50.72 32.19 -
Num. residues----1752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214738
X-RAY DIFFRACTIONr_bond_other_d0.0070.0213384
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.93620022
X-RAY DIFFRACTIONr_angle_other_deg1.0873.00230809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6851758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42424.076709
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.009152381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0021574
X-RAY DIFFRACTIONr_chiral_restr0.0910.22039
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02116691
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023567
X-RAY DIFFRACTIONr_mcbond_it2.7673.4327014
X-RAY DIFFRACTIONr_mcbond_other2.7663.4327013
X-RAY DIFFRACTIONr_mcangle_it3.8325.1368763
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A272310.05
12B272310.05
21A269830.06
22C269830.06
31A264690.05
32D264690.05
41B271500.06
42C271500.06
51B265580.05
52D265580.05
61C266540.05
62D266540.05
LS refinement shellResolution: 1.774→1.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 668 -
Rwork0.426 13385 -
all-14053 -
obs--96.45 %

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