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

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Basic information

Entry
Database: PDB / ID: 2xib
TitleCRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH DEOXYFUCONOJIRIMYCIN
ComponentsALPHA-L-FUCOSIDASE
KeywordsHYDROLASE / FUCOSIDASE / METAL BINDING / INHIBITORS
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 / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / 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 / Alpha-L-fucosidase / Glycoside hydrolase, family 29 / 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
(2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL / Alpha-L-fucosidase
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 28, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references / Non-polymer description ...Database references / Non-polymer description / Other / Refinement description / 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
C: ALPHA-L-FUCOSIDASE
D: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,29319
Polymers209,6414
Non-polymers1,65215
Water12,953719
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B: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8385
Polymers52,4101
Non-polymers4274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8425
Polymers52,4101
Non-polymers4314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7464
Polymers52,4101
Non-polymers3353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8685
Polymers52,4101
Non-polymers4574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.680, 185.990, 97.630
Angle α, β, γ (deg.)90.00, 94.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 52410.367 Da / Num. of mol.: 4 / Fragment: RESIDUES 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

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Non-polymers , 5 types, 734 molecules

#2: Chemical
ChemComp-DFU / (2S,3R,4S,5R)-2-METHYLPIPERIDINE-3,4,5-TRIOL / DEOXYFUCONOJIRIMYCIN


Mass: 147.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO3
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.36 Å3/Da / Density % sol: 47.88 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.2→35 Å / Num. obs: 98203 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

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

2wvv


Resolution: 2.2→34.75 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.834 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23472 4927 5 %RANDOM
Rwork0.18505 ---
obs0.18755 93236 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.774 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å2-0.41 Å2
2--0.48 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14248 0 103 719 15070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02214768
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210177
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.93520024
X-RAY DIFFRACTIONr_angle_other_deg0.8443.00124606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79551744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40724.045712
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.179152468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6791576
X-RAY DIFFRACTIONr_chiral_restr0.0780.22024
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023128
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_it0.6171.58692
X-RAY DIFFRACTIONr_mcbond_other0.1211.53540
X-RAY DIFFRACTIONr_mcangle_it1.169213998
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.75136076
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7914.56026
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 331 -
Rwork0.243 6890 -
obs--100 %

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