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- PDB-9vak: Carbohydrate-binding module 32 of LnbB from Bifidobacterium bifid... -

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Basic information

Entry
Database: PDB / ID: 9vak
TitleCarbohydrate-binding module 32 of LnbB from Bifidobacterium bifidum, LNB complex
ComponentsLacto-N-biosidase
KeywordsSUGAR BINDING PROTEIN / Carbohydrate Binding Module Family 32 domain
Function / homology
Function and homology information


lacto-N-biosidase / lacto-N-biosidase activity / beta-N-acetylhexosaminidase activity / carbohydrate metabolic process / plasma membrane
Similarity search - Function
: / Beta-hexosaminidase / Ricin-type beta-trefoil lectin domain-like / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 ...: / Beta-hexosaminidase / Ricin-type beta-trefoil lectin domain-like / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Beta-hexosaminidase-like, domain 2 / F5/8 type C domain / Ricin B, lectin domain / Coagulation factor 5/8 C-terminal domain / Ricin B-like lectins / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesBifidobacterium bifidum JCM 1254 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, X. / Kashima, T. / Fushinobu, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H00322 Japan
Citation
Journal: Febs Lett. / Year: 2025
Title: Structural insights into lacto-N-biose I recognition by a family 32 carbohydrate-binding module from Bifidobacterium bifidum.
Authors: Zhang, X. / Sunagawa, N. / Kashima, T. / Igarashi, K. / Miyanaga, A. / Fushinobu, S.
#1: Journal: J Biol Chem / Year: 2013
Title: Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum.
Authors: Ito, T. / Katayama, T. / Hattie, M. / Sakurama, H. / Wada, J. / Suzuki, R. / Ashida, H. / Wakagi, T. / Yamamoto, K. / Stubbs, K.A. / Fushinobu, S.
History
DepositionJun 3, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 2.0Nov 19, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity_poly / pdbx_branch_scheme / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_ls_restr / refine_ls_shell / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _entity_poly.pdbx_strand_id / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.pdb_asym_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id
Description: Ligand identity / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Lacto-N-biosidase
A: Lacto-N-biosidase
C: Lacto-N-biosidase
D: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,47512
Polymers77,7814
Non-polymers1,6948
Water6,846380
1
B: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8693
Polymers19,4451
Non-polymers4232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8693
Polymers19,4451
Non-polymers4232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8693
Polymers19,4451
Non-polymers4232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8693
Polymers19,4451
Non-polymers4232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.489, 105.802, 122.102
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)

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Components

#1: Protein
Lacto-N-biosidase / LNBase


Mass: 19445.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum JCM 1254 (bacteria)
Gene: lnbB / Plasmid: pET38b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CondonPlus-RIL / References: UniProt: B3TLD6, lacto-N-biosidase
#2: Polysaccharide
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Lithium chloride, HEPES-NaOH, PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.012 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 22, 2024
RadiationMonochromator: Cryo-cooled channel-cut Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.012 Å / Relative weight: 1
ReflectionResolution: 2→48.54 Å / Num. obs: 50324 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.05 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.086 / Rrim(I) all: 0.226 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 7 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3663 / CC1/2: 0.721 / Rpim(I) all: 0.376 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.54 Å / SU ML: 0.2139 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 20.3248
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2296 2559 5.09 %
Rwork0.1981 47707 -
obs0.1997 50266 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.81 Å2
Refinement stepCycle: LAST / Resolution: 2→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 108 380 5360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675108
X-RAY DIFFRACTIONf_angle_d0.77827012
X-RAY DIFFRACTIONf_chiral_restr0.0547812
X-RAY DIFFRACTIONf_plane_restr0.0047900
X-RAY DIFFRACTIONf_dihedral_angle_d14.73521860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.30861400.24392642X-RAY DIFFRACTION100
2.04-2.080.25161380.24082576X-RAY DIFFRACTION100
2.08-2.130.26221410.232621X-RAY DIFFRACTION100
2.13-2.170.24371460.22042612X-RAY DIFFRACTION100
2.17-2.230.26411370.20932590X-RAY DIFFRACTION100
2.23-2.290.26561660.20732583X-RAY DIFFRACTION100
2.29-2.360.26791450.20932647X-RAY DIFFRACTION100
2.36-2.430.27071240.21012630X-RAY DIFFRACTION100
2.43-2.520.25951440.22092642X-RAY DIFFRACTION100
2.52-2.620.251170.20722626X-RAY DIFFRACTION99.96
2.62-2.740.26721440.21072649X-RAY DIFFRACTION100
2.74-2.880.23751480.20232626X-RAY DIFFRACTION100
2.88-3.060.21511300.2062675X-RAY DIFFRACTION100
3.07-3.30.19491370.19232674X-RAY DIFFRACTION99.96
3.3-3.630.22921560.18262653X-RAY DIFFRACTION100
3.63-4.160.19071580.17192664X-RAY DIFFRACTION100
4.16-5.240.19011460.16792729X-RAY DIFFRACTION100
5.24-48.540.20451420.18822868X-RAY DIFFRACTION100

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