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- PDB-3mo4: The crystal structure of an alpha-(1-3,4)-fucosidase from Bifidob... -

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Basic information

Entry
Database: PDB / ID: 3mo4
TitleThe crystal structure of an alpha-(1-3,4)-fucosidase from Bifidobacterium longum subsp. infantis ATCC 15697
ComponentsAlpha-1,3/4-fucosidase
KeywordsHYDROLASE / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome
Similarity search - Function
Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls ...Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / TYROSINE / Alpha-1,3/4-fucosidase, putative
Similarity search - Component
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsTan, K. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Appl.Environ.Microbiol. / Year: 2012
Title: Bifidobacterium longum subsp. infantis ATCC 15697 alpha-fucosidases are active on fucosylated human milk oligosaccharides.
Authors: Sela, D.A. / Garrido, D. / Lerno, L. / Wu, S. / Tan, K. / Eom, H.J. / Joachimiak, A. / Lebrilla, C.B. / Mills, D.A.
History
DepositionApr 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1,3/4-fucosidase
B: Alpha-1,3/4-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7214
Polymers107,4942
Non-polymers2272
Water14,646813
1
A: Alpha-1,3/4-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9282
Polymers53,7471
Non-polymers1811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-1,3/4-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7932
Polymers53,7471
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.610, 106.094, 122.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. The molecule is likely monomeric.

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Components

#1: Protein Alpha-1,3/4-fucosidase


Mass: 53747.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (bacteria)
Strain: ATCC 15697 / Gene: Blon_2336 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B7GNN8
#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.8M succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2010 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.9→42 Å / Num. all: 84888 / Num. obs: 84888 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4205 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→41.934 Å / SU ML: 0.23 / σ(F): 0.02 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 4023 5.01 %random
Rwork0.162 ---
all0.1642 80222 --
obs0.1642 80222 94.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.07 Å2 / ksol: 0.356 e/Å3
Refinement stepCycle: LAST / Resolution: 1.901→41.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7158 0 16 813 7987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067451
X-RAY DIFFRACTIONf_angle_d1.00310163
X-RAY DIFFRACTIONf_dihedral_angle_d17.6042696
X-RAY DIFFRACTIONf_chiral_restr0.0681088
X-RAY DIFFRACTIONf_plane_restr0.0051346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9009-1.96890.26243570.20676641X-RAY DIFFRACTION83
1.9689-2.04770.24823600.19467137X-RAY DIFFRACTION89
2.0477-2.14090.26273740.17567365X-RAY DIFFRACTION92
2.1409-2.25370.23333860.16597484X-RAY DIFFRACTION93
2.2537-2.39490.22984030.16287586X-RAY DIFFRACTION94
2.3949-2.57980.2354080.16297742X-RAY DIFFRACTION96
2.5798-2.83940.2234280.17657842X-RAY DIFFRACTION97
2.8394-3.25010.214250.17617998X-RAY DIFFRACTION99
3.2501-4.09420.15834230.13528120X-RAY DIFFRACTION99
4.0942-41.94460.17364590.1458284X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.64210.027-0.2580.27840.02060.3549-0.06-0.0317-0.14150.02150.00270.01540.0418-0.0360.05070.0832-0.0070.00630.09870.01410.110573.920239.249436.0236
20.3602-0.145-0.21820.46570.24560.3125-0.00360.02020.0263-0.04080.0159-0.0236-0.04330.0062-0.01030.09120.0040.00120.07860.02210.0912
Refinement TLS groupSelection details: chain B

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