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

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Basic information

Entry
Database: PDB / ID: 8ibt
TitleCrystal structure of GH42 beta-galactosidase BiBga42A from Bifidobacterium longum subspecies infantis E318S mutant in complex with lacto-N-tetraose
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
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,9454
Polymers157,5302
Non-polymers1,4152
Water11,710650
1
A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules

A: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,4176
Polymers236,2943
Non-polymers2,1233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area20100 Å2
ΔGint-27 kcal/mol
Surface area65050 Å2
MethodPISA
2
B: Beta-galactosidase
hetero molecules

B: Beta-galactosidase
hetero molecules

B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,4176
Polymers236,2943
Non-polymers2,1233
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 area20310 Å2
ΔGint-26 kcal/mol
Surface area64010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.432, 166.432, 149.459
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-852-

HOH

21B-863-

HOH

31B-879-

HOH

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Components

#1: Protein Beta-galactosidase


Mass: 78764.820 Da / Num. of mol.: 2 / Mutation: E318S
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: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3-2/a4-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / Source method: isolated from a natural source / Formula: H2O
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: 3.8 Å3/Da / Density % sol: 67.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 5 mM MES-NaOH buffer (pH 5.8), 0.1 M KSCN, 30% PEG MME 2000, 20% ethylene glycol, 50 mM lacto-N-tetraose

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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: Jan 27, 2014
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: 2.2→48.04 Å / Num. obs: 121062 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 24.96 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.074 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.916 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5977 / CC1/2: 0.633 / Rpim(I) all: 0.362 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSJan 10, 2022data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17493 6036 5 %RANDOM
Rwork0.1463 ---
obs0.14773 115024 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.356 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å2-0 Å2-0 Å2
2---3.83 Å2-0 Å2
3---7.66 Å2
Refinement stepCycle: 1 / Resolution: 2.2→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10965 0 96 650 11711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01211381
X-RAY DIFFRACTIONr_bond_other_d0.0020.01610201
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.64615528
X-RAY DIFFRACTIONr_angle_other_deg0.9981.57623492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.37951384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.661568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.567101701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.21657
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213448
X-RAY DIFFRACTIONr_gen_planes_other0.0210.022704
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_it3.1982.8335545
X-RAY DIFFRACTIONr_mcbond_other3.1982.8335545
X-RAY DIFFRACTIONr_mcangle_it4.0645.0746926
X-RAY DIFFRACTIONr_mcangle_other4.0685.0756927
X-RAY DIFFRACTIONr_scbond_it4.4773.1165836
X-RAY DIFFRACTIONr_scbond_other4.4763.1165837
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1595.5558603
X-RAY DIFFRACTIONr_long_range_B_refined6.87727.7113141
X-RAY DIFFRACTIONr_long_range_B_other6.87727.7213142
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 463 -
Rwork0.284 8429 -
obs--99.83 %

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