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- PDB-2xii: CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES ... -

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Basic information

Entry
Database: PDB / ID: 2xii
TitleCRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH AN EXTENDED 9-FLUORENONE IMINOSUGAR INHIBITOR
ComponentsALPHA-L-FUCOSIDASE
KeywordsHYDROLASE / FUCOSE
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-TA9 / TYROSINE / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLammerts van Bueren, A. / Popat, S.D. / Lin, C.H. / Davies, G.J.
CitationJournal: Chembiochem / Year: 2010
Title: Structural and Thermodynamic Analyses of Alpha-L-Fucosidase Inhibitors.
Authors: Lammerts Van Bueren, A. / Popat, S.D. / Lin, C.H. / Davies, G.J.
History
DepositionJun 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 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

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)106,42411
Polymers104,8212
Non-polymers1,6049
Water12,538696
1
A: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2626
Polymers52,4101
Non-polymers8525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1625
Polymers52,4101
Non-polymers7524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.466, 85.080, 120.210
Angle α, β, γ (deg.)90.00, 108.52, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALPHA-L-FUCOSIDASE / / FUCOSIDASE / GLYCOSIDE HYDROLASE / ALPHA-L-FUCOSIDE FUCOHYDROLASE


Mass: 52410.367 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, 32-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A3I4, alpha-L-fucosidase

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Non-polymers , 5 types, 705 molecules

#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical ChemComp-TA9 / 9-oxo-N-[[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyl-piperidin-2-yl]methyl]fluorene-1-carboxamide


Mass: 382.410 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22N2O5
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 696 / 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: 2.42 Å3/Da / Density % sol: 49.09 % / Description: NONE
Crystal growDetails: 20% PEG-6000, 0.15M AMMONIUM SULFATE, 0.1M IMIDAZOLE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→45 Å / Num. obs: 92257 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WVT

2wvt


Resolution: 1.8→45.15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.079 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22308 4633 5 %RANDOM
Rwork0.18716 ---
obs0.18895 87624 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.537 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-1.04 Å2
2--1.27 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7163 0 108 696 7967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227493
X-RAY DIFFRACTIONr_bond_other_d0.0010.025169
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.94310164
X-RAY DIFFRACTIONr_angle_other_deg0.8893.00112471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9345877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9523.944360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.562151258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9531540
X-RAY DIFFRACTIONr_chiral_restr0.0860.21020
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218278
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_it0.7731.54372
X-RAY DIFFRACTIONr_mcbond_other0.2021.51781
X-RAY DIFFRACTIONr_mcangle_it1.38127042
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.18933121
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4794.53121
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
Rfree0.284 349 -
Rwork0.274 6421 -
obs--100 %

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