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- PDB-8yk3: Blood group B alpha-1,3-galactosidase AgaBb from Bifidobacterium ... -

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Basic information

Entry
Database: PDB / ID: 8yk3
TitleBlood group B alpha-1,3-galactosidase AgaBb from Bifidobacterium bifidum, construct T7-tag_24-673
ComponentsAlpha-galactosidase
KeywordsHYDROLASE / Blood group B antigen / Glycoside hydrolase / ligand free
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metabolic process / membrane
Similarity search - Function
Cadherin-like beta sandwich domain / Cadherin-like beta sandwich domain / Glycosyl hydrolase family 98, putative carbohydrate-binding module / NPCBM domain superfamily / NPCBM/NEW2 domain / NPCBM / Right handed beta helix domain / Right handed beta helix region / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) ...Cadherin-like beta sandwich domain / Cadherin-like beta sandwich domain / Glycosyl hydrolase family 98, putative carbohydrate-binding module / NPCBM domain superfamily / NPCBM/NEW2 domain / NPCBM / Right handed beta helix domain / Right handed beta helix region / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain, group 2 / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
alpha-D-galactopyranose / Alpha-galactosidase
Similarity search - Component
Biological speciesBifidobacterium bifidum JCM 1254 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKashima, T. / Ashida, H. / Fushinobu, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24380053 Japan
Japan Society for the Promotion of Science (JSPS)23H00322 Japan
CitationJournal: J.Appl.Glyosci. / Year: 2024
Title: Crystal Structure of Bifidobacterium bifidum Glycoside Hydrolase Family 110 alpha-Galactosidase Specific for Blood Group B Antigen
Authors: Kashima, T. / Akama, M. / Wakinaka, T. / Arakawa, T. / Ashida, H. / Fushinobu, S.
History
DepositionMar 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-galactosidase
B: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,9228
Polymers145,1812
Non-polymers7426
Water00
1
A: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9575
Polymers72,5901
Non-polymers3664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30 Å2
ΔGint-0 kcal/mol
Surface area22580 Å2
MethodPISA
2
B: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9663
Polymers72,5901
Non-polymers3752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.340, 73.154, 177.968
Angle α, β, γ (deg.)90.000, 91.380, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Alpha-galactosidase


Mass: 72590.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum JCM 1254 (bacteria)
Gene: agabb, GBA83_07165 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2
References: UniProt: L8B3G2, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% (w/v) PEG 20000, 0.1M MES-NaOH pH 6.5 (Seed condition: 10% (w/v) PEG 6000, 0.1M citric acid pH 5.0, 4 degrees celsius)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 29, 2020
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3.5→47.88 Å / Num. obs: 20905 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.82 Å2 / CC1/2: 0.76 / Net I/σ(I): 2.9
Reflection shellResolution: 3.5→3.83 Å / Num. unique obs: 4934 / CC1/2: 0.35

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→47.88 Å / SU ML: 0.5648 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 27.7232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2848 1111 5.32 %RANDOM
Rwork0.2028 19773 --
obs0.2072 20884 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.8 Å2
Refinement stepCycle: LAST / Resolution: 3.5→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9432 0 48 0 9480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019661
X-RAY DIFFRACTIONf_angle_d1.048413121
X-RAY DIFFRACTIONf_chiral_restr0.05771501
X-RAY DIFFRACTIONf_plane_restr0.0081709
X-RAY DIFFRACTIONf_dihedral_angle_d14.88913484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.660.33971420.25732421X-RAY DIFFRACTION100
3.66-3.850.35161380.24912462X-RAY DIFFRACTION99.81
3.85-4.090.31091620.22692420X-RAY DIFFRACTION99.88
4.09-4.40.28831100.20222481X-RAY DIFFRACTION99.96
4.4-4.850.24311140.16692514X-RAY DIFFRACTION99.81
4.85-5.550.24361600.16422424X-RAY DIFFRACTION99.96
5.55-6.990.29451370.19022505X-RAY DIFFRACTION100
6.99-47.880.22551480.17272546X-RAY DIFFRACTION99.96

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