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

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Basic information

Entry
Database: PDB / ID: 2wvv
TitleCrystal structure of an alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron
Components(ALPHA-L-FUCOSIDASE) x 2
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
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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

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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)209,56516
Polymers208,3244
Non-polymers1,24112
Water19,6181089
1
B: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4835
Polymers52,0811
Non-polymers4024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2953
Polymers52,0811
Non-polymers2142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4875
Polymers52,0811
Non-polymers4064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ALPHA-L-FUCOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2993
Polymers52,0811
Non-polymers2182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.880, 186.870, 97.860
Angle α, β, γ (deg.)90.00, 94.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACDB

#1: Protein ALPHA-L-FUCOSIDASE /


Mass: 52080.930 Da / Num. of mol.: 3 / Fragment: RESIDUES 35-484
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: Protein ALPHA-L-FUCOSIDASE /


Mass: 52080.930 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-484
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

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Non-polymers , 4 types, 1101 molecules

#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1089 / 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: 2.45 Å3/Da / Density % sol: 55.6 % / 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: 1.73→48 Å / Num. obs: 208289 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→97.56 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.351 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22454 10463 5 %RANDOM
Rwork0.19228 ---
obs0.1939 197776 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.782 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20.18 Å2
2---0.4 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.73→97.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14389 0 76 1089 15554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02214906
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.93520209
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40951766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95223.972720
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.232152507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.271580
X-RAY DIFFRACTIONr_chiral_restr0.0860.22033
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111472
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6431.58796
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.212214165
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.97836110
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1934.56040
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: 1.726→1.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 733 -
Rwork0.327 14198 -
obs--96.67 %

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