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

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Basic information

Entry
Database: PDB / ID: 9wfh
TitleCarbohydrate-binding module 32 of LnbB from Bifidobacterium bifidum, ligand free form, multiple small-wedge data set
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
DepositionAug 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,9714
Polymers38,8912
Non-polymers802
Water2,450136
1
A: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4852
Polymers19,4451
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4852
Polymers19,4451
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.780, 54.780, 202.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Lacto-N-biosidase / LNBase


Mass: 19445.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum JCM 1254 (bacteria)
Gene: lnbB / Plasmid: PET28B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CONDONPLUS-RIL / References: UniProt: B3TLD6, lacto-N-biosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.96 Å3/Da / Density % sol: 37.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: TRIS-HCL, AMMONIUM SULFATE, PH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2024
RadiationMonochromator: LIQUID-NITROGEN-COOLED SI DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 21990 / % possible obs: 99.9 % / Redundancy: 45.5 % / Biso Wilson estimate: 17.86 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.1823 / Rrim(I) all: 0.1844 / Net I/σ(I): 8.84
Reflection shellResolution: 2→2.09 Å / Redundancy: 40.4 % / Rmerge(I) obs: 1.038 / Mean I/σ(I) obs: 0.82 / Num. unique obs: 2654 / CC1/2: 0.618 / Rrim(I) all: 1.051 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.25 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.554 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24034 1071 4.9 %RANDOM
Rwork0.22447 ---
obs0.22527 20822 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å20 Å2-0 Å2
2--2.17 Å20 Å2
3----4.34 Å2
Refinement stepCycle: 1 / Resolution: 2→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 2 136 2568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0122496
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162243
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.7733427
X-RAY DIFFRACTIONr_angle_other_deg0.5111.7375171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.165321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.91552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70510344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022989
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
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_it1.7522.0961290
X-RAY DIFFRACTIONr_mcbond_other1.7512.0961290
X-RAY DIFFRACTIONr_mcangle_it3.0283.7471609
X-RAY DIFFRACTIONr_mcangle_other3.0273.751610
X-RAY DIFFRACTIONr_scbond_it2.0612.2181206
X-RAY DIFFRACTIONr_scbond_other2.062.2211207
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4743.9751819
X-RAY DIFFRACTIONr_long_range_B_refined5.19520.572787
X-RAY DIFFRACTIONr_long_range_B_other5.17220.422776
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 81 -
Rwork0.352 1491 -
obs--100 %

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