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- PDB-2eab: Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifi... -

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Basic information

Entry
Database: PDB / ID: 2eab
TitleCrystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum (apo form)
ComponentsAlpha-fucosidase
KeywordsHYDROLASE / FUCOSIDASE / GLYCOSIDE HYDROLASE
Function / homology
Function and homology information


carbohydrate metabolic process / membrane / metal ion binding
Similarity search - Function
: / Glycoside hydrolase family 95, C-terminal domain / Glycosyl hydrolase family 95, N-terminal domain / Glycosyl hydrolase family 65, N-terminal domain / putative glycoside hydrolase family protein from bacillus halodurans / Bacterial Ig-like domain (group 3) / Ig-like domain, bacterial type / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 ...: / Glycoside hydrolase family 95, C-terminal domain / Glycosyl hydrolase family 95, N-terminal domain / Glycosyl hydrolase family 65, N-terminal domain / putative glycoside hydrolase family protein from bacillus halodurans / Bacterial Ig-like domain (group 3) / Ig-like domain, bacterial type / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Glycosyltransferase - #10 / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Golgi alpha-mannosidase II / Distorted Sandwich / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBifidobacterium bifidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.12 Å
AuthorsNagae, M. / Tsuchiya, A. / Katayama, T. / Yamamoto, K. / Wakatsuki, S. / Kato, R.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum
Authors: Nagae, M. / Tsuchiya, A. / Katayama, T. / Yamamoto, K. / Wakatsuki, S. / Kato, R.
History
DepositionJan 31, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: 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-fucosidase
B: Alpha-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,25620
Polymers193,9422
Non-polymers1,31418
Water60,9453383
1
A: Alpha-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,62810
Polymers96,9711
Non-polymers6579
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,62810
Polymers96,9711
Non-polymers6579
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.183, 112.035, 98.317
Angle α, β, γ (deg.)90.00, 94.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-fucosidase /


Mass: 96971.203 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 0-898
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Plasmid: PET3-A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6JV24, EC: 3.2.1.63
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3383 / 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: 51.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M TRIS (PH 7.5), 10% ISOPROPANOL, 10% PEG6000, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SYNCHROTRONSSRL BL9-220.9792, 0.97936, 0.91837
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 29, 2005
ADSC QUANTUM 2102CCDJun 29, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97921
30.979361
40.918371
ReflectionResolution: 1.12→50 Å / Num. obs: 643080 / % possible obs: 91.1 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 30
Reflection shellResolution: 1.12→1.16 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.5 / % possible all: 77.6

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.12→35.05 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.422 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.189 33894 5 %RANDOM
Rwork0.175 ---
obs0.176 643080 91.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.12→35.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13475 0 82 3383 16940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02113831
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.93518783
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84251765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27125.289641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.133152143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5931552
X-RAY DIFFRACTIONr_chiral_restr0.0750.22032
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210678
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.27670
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.29620
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0730.23157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0740.2137
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4421.58888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.734213896
X-RAY DIFFRACTIONr_scbond_it1.23835727
X-RAY DIFFRACTIONr_scangle_it1.7914.54887
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.12→1.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 2235 -
Rwork0.263 42213 -
obs--81.55 %

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