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- PDB-8yk2: Blood group B alpha-1,3-galactosidase AgaBb from Bifidobacterium ... -

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Basic information

Entry
Database: PDB / ID: 8yk2
TitleBlood group B alpha-1,3-galactosidase AgaBb from Bifidobacterium bifidum, construct T7-tag_24-700
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 / membrane
Similarity search - Function
GLAA-B beta-barrel domain II / 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 / Bacterial Ig-like domain (group 2) ...GLAA-B beta-barrel domain II / 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 / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Parallel beta-helix repeat / Parallel beta-helix repeats / Bacterial Ig-like domain, group 2 / Pectin lyase fold / Pectin lyase fold/virulence factor / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Biological speciesBifidobacterium bifidum JCM 1254 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.96 Å
AuthorsKashima, T. / Akama, M. / 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 Glycosci (1999) / 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
Revision 1.1Sep 18, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)150,7057
Polymers150,3102
Non-polymers3955
Water20,8071155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Probably an artifact due to C-terminal domain interlacement. The protein is present in a monomeric form in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.557, 125.055, 196.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Alpha-galactosidase


Mass: 75155.070 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.11 Å3/Da / Density % sol: 60.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M ammonium sulfate, 0.1M HEPES pH 7.5, 0.1M NaCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 24, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→48.04 Å / Num. obs: 126369 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 25.28 Å2 / CC1/2: 1 / Net I/σ(I): 15.1
Reflection shellResolution: 1.96→1.99 Å / Num. unique obs: 6186 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.96→46.8 Å / SU ML: 0.206 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 20.0121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.212 6499 5.15 %RANDOM
Rwork0.1804 119754 --
obs0.182 126253 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.52 Å2
Refinement stepCycle: LAST / Resolution: 1.96→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9827 0 24 1155 11006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006410033
X-RAY DIFFRACTIONf_angle_d0.803113635
X-RAY DIFFRACTIONf_chiral_restr0.05951562
X-RAY DIFFRACTIONf_plane_restr0.00691783
X-RAY DIFFRACTIONf_dihedral_angle_d13.61833556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.980.27382180.24163936X-RAY DIFFRACTION100
1.98-20.26962210.24113924X-RAY DIFFRACTION100
2-2.030.28122080.2253975X-RAY DIFFRACTION100
2.03-2.050.29921840.21853983X-RAY DIFFRACTION100
2.05-2.080.2552100.21153958X-RAY DIFFRACTION100
2.08-2.110.23582130.20273890X-RAY DIFFRACTION100
2.11-2.140.24872160.20174024X-RAY DIFFRACTION100
2.14-2.170.21652060.19913898X-RAY DIFFRACTION100
2.17-2.20.2642080.19934019X-RAY DIFFRACTION100
2.2-2.240.22322410.20063895X-RAY DIFFRACTION100
2.24-2.280.23062210.19523995X-RAY DIFFRACTION100
2.28-2.320.26461960.19073937X-RAY DIFFRACTION100
2.32-2.360.22392160.18473971X-RAY DIFFRACTION100
2.36-2.410.24812420.18673925X-RAY DIFFRACTION100
2.41-2.460.22452120.18253962X-RAY DIFFRACTION100
2.46-2.520.21752050.18314032X-RAY DIFFRACTION100
2.52-2.580.23112070.18133935X-RAY DIFFRACTION100
2.58-2.650.20862090.18623992X-RAY DIFFRACTION100
2.65-2.730.23472240.19193989X-RAY DIFFRACTION100
2.73-2.820.24182190.23970X-RAY DIFFRACTION100
2.82-2.920.2592200.18993997X-RAY DIFFRACTION100
2.92-3.040.20162300.18413972X-RAY DIFFRACTION100
3.04-3.180.21932060.18854008X-RAY DIFFRACTION100
3.18-3.340.2112090.18494022X-RAY DIFFRACTION100
3.34-3.550.19542150.174020X-RAY DIFFRACTION100
3.55-3.830.19372300.15734012X-RAY DIFFRACTION100
3.83-4.210.1712160.14844061X-RAY DIFFRACTION100
4.21-4.820.15722420.13464046X-RAY DIFFRACTION99.7
4.82-6.070.18592120.17074116X-RAY DIFFRACTION99.95
6.07-46.80.20122430.19174290X-RAY DIFFRACTION99.91

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