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- PDB-2wvt: Crystal structure of an alpha-L-fucosidase GH29 from Bacteroides ... -

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Basic information

Entry
Database: PDB / ID: 2wvt
TitleCrystal structure of an alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron in complex with a novel iminosugar fucosidase inhibitor
ComponentsALPHA-L-FUCOSIDASE
KeywordsHYDROLASE / ALPHA-L-FUCOSE / GLYCOSIDE HYDROLASE FAMILY 29
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-FHN / IMIDAZOLE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLammerts van Bueren, A. / Ardevol, A. / Fayers-Kerr, J. / Luo, B. / Zhang, Y. / Sollogoub, M. / Bleriot, Y. / Rovira, C. / Davies, G.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Analysis of the Reaction Coordinate of Alpha-L-Fucosidases: A Combined Structural and Quantum Mechanical Approach.
Authors: Lammerts Van Bueren, A. / Ardevol, A. / Fayers-Kerr, J. / Luo, B. / Zhang, Y. / Sollogoub, M. / Bleriot, Y. / Rovira, C. / Davies, G.J.
History
DepositionOct 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: ALPHA-L-FUCOSIDASE
B: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,78713
Polymers102,6622
Non-polymers1,12511
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint2.8 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.830, 85.160, 121.285
Angle α, β, γ (deg.)90.00, 108.73, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein ALPHA-L-FUCOSIDASE


Mass: 51331.121 Da / Num. of mol.: 2 / Fragment: RESIDUES 31-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Strain: VPI-5482 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q8A3I4
#2: Chemical ChemComp-FHN / (2S,3R,5R,6S)-3,4,5-TRIHYDROXY-2,6-BIS(HYDROXYMETHYL)PIPERIDINIUM


Mass: 194.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16NO5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.38 Å3/Da / Density % sol: 47.87 % / Description: NONE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.8→48 Å / Num. obs: 93456 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.7

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WVV

2wvv


Resolution: 1.8→90.93 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.471 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24508 4690 5 %RANDOM
Rwork0.20748 ---
obs0.20936 88765 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.158 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å2-1.16 Å2
2--2.37 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→90.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7163 0 76 455 7694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227429
X-RAY DIFFRACTIONr_bond_other_d0.0010.025153
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.93810058
X-RAY DIFFRACTIONr_angle_other_deg0.8613.00112445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87224.045356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.947151246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7421538
X-RAY DIFFRACTIONr_chiral_restr0.0820.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218198
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021586
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.71.54356
X-RAY DIFFRACTIONr_mcbond_other0.1861.51777
X-RAY DIFFRACTIONr_mcangle_it1.24727019
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93633073
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0244.53038
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 354 -
Rwork0.305 6518 -
obs--99.74 %

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