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- PDB-8ibr: Crystal structure of GH42 beta-galactosidase BiBga42A from Bifido... -

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Basic information

Entry
Database: PDB / ID: 8ibr
TitleCrystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis in complex with glycerol
ComponentsBeta-galactosidase
KeywordsHYDROLASE / Glycoside Hydrolase family 42
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase-like / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Beta-galactosidase
Similarity search - Component
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHidaka, M. / Fushinobu, S. / Gotoh, A. / Katayama, T.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15H04481 Japan
Japan Society for the Promotion of Science (JSPS)17K19231 Japan
Japan Society for the Promotion of Science (JSPS)21H02116 Japan
Japan Society for the Promotion of Science (JSPS)15F15091 Japan
Japan Society for the Promotion of Science (JSPS)24380053 Japan
Japan Society for the Promotion of Science (JSPS)19H00929 Japan
Citation
Journal: Microbiome Res Rep / Year: 2023
Title: Substrate recognition mode of a glycoside hydrolase family 42 beta-galactosidase from Bifidobacterium longum subspecies infantis ( Bi Bga42A) revealed by crystallographic and mutational analyses.
Authors: Gotoh, A. / Hidaka, M. / Sakurama, H. / Nishimoto, M. / Kitaoka, M. / Sakanaka, M. / Fushinobu, S. / Katayama, T.
#1: Journal: Glycobiology / Year: 2012
Title: Bifidobacterium longum subsp. infantis uses two different beta-galactosidases for selectively degrading type-1 and type-2 human milk oligosaccharides.
Authors: Yoshida, E. / Sakurama, H. / Kiyohara, M. / Nakajima, M. / Kitaoka, M. / Ashida, H. / Hirose, J. / Katayama, T. / Yamamoto, K. / Kumagai, H.
History
DepositionFeb 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0053
Polymers78,8071
Non-polymers1982
Water12,070670
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,0159
Polymers236,4213
Non-polymers5956
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area17080 Å2
ΔGint-58 kcal/mol
Surface area64280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.642, 145.642, 66.845
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-958-

HOH

21A-984-

HOH

31A-1111-

HOH

41A-1546-

HOH

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Components

#1: Protein Beta-galactosidase


Mass: 78806.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (strain ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12) (bacteria)
Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Gene: Blon_2016 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): delta-lacZ / References: UniProt: B7GUD7, beta-galactosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M KSCN, 30% PEG MME 2000, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.67 Å / Num. obs: 85479 / % possible obs: 95.5 % / Redundancy: 9.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.04 / Net I/σ(I): 16.3
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2985 / CC1/2: 0.784 / Rpim(I) all: 0.511 / % possible all: 63.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSJan 10, 2022data reduction
pointless1.12.8data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.91 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18567 4302 5 %RANDOM
Rwork0.16108 ---
obs0.16235 81166 95.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.969 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å2-0.67 Å2-0 Å2
2---1.34 Å2-0 Å2
3---4.35 Å2
Refinement stepCycle: 1 / Resolution: 1.7→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5472 0 13 670 6155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0125648
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165071
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6437700
X-RAY DIFFRACTIONr_angle_other_deg0.8891.57611671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7585692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.428534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18110852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026718
X-RAY DIFFRACTIONr_gen_planes_other0.0170.021350
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_it1.4391.3562765
X-RAY DIFFRACTIONr_mcbond_other1.4381.3562765
X-RAY DIFFRACTIONr_mcangle_it2.1652.4343455
X-RAY DIFFRACTIONr_mcangle_other2.1652.4353456
X-RAY DIFFRACTIONr_scbond_it2.3841.5812883
X-RAY DIFFRACTIONr_scbond_other2.3831.5822884
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7442.784245
X-RAY DIFFRACTIONr_long_range_B_refined5.1214.176631
X-RAY DIFFRACTIONr_long_range_B_other5.1214.176632
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 213 -
Rwork0.292 4307 -
obs--68.92 %

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