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- PDB-5bxt: LNBase in complex with LNB-NHAcAUS -

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Basic information

Entry
Database: PDB / ID: 5bxt
TitleLNBase in complex with LNB-NHAcAUS
ComponentsLacto-N-biosidase
KeywordsHYDROLASE / TIM barrel / distal gut / Human milk oligosaccharides / Inhibitor
Function / homology
Function and homology information


lacto-N-biosidase / lacto-N-biosidase activity / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process / plasma membrane
Similarity search - Function
Ricin-type beta-trefoil lectin domain-like / Beta-hexosaminidase / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Bacterial Ig-like domain (group 2) / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 ...Ricin-type beta-trefoil lectin domain-like / Beta-hexosaminidase / Invasin/intimin cell-adhesion fragments / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Bacterial Ig-like domain (group 2) / Chitobiase/beta-hexosaminidase domain 2-like / Chitobiase; domain 2 / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-4WS / beta-D-galactopyranose / Lacto-N-biosidase
Similarity search - Component
Biological speciesBifidobacterium bifidum JCM 1254 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsIto, T. / Arakawa, T. / Fushinobu, S.
Citation
Journal: Chem.Commun.(Camb.) / Year: 2015
Title: Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis
Authors: Hattie, M. / Ito, T. / Debowski, A.W. / Arakawa, T. / Katayama, T. / Yamamoto, K. / Fushinobu, S. / Stubbs, K.A.
#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 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)145,08611
Polymers143,7842
Non-polymers1,3019
Water16,123895
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A: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5916
Polymers71,8921
Non-polymers6995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-19 kcal/mol
Surface area25260 Å2
MethodPISA
2
B: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4955
Polymers71,8921
Non-polymers6034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-9 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.985, 131.513, 104.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-818-

HOH

21B-984-

HOH

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Components

#1: Protein Lacto-N-biosidase /


Mass: 71892.227 Da / Num. of mol.: 2 / Fragment: UNP residues 41-663
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum JCM 1254 (bacteria)
Gene: lnbB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: B3TLD6, lacto-N-biosidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-4WS / N-{[(1R,2R,3R,7S,7aR)-1,2,7-trihydroxyhexahydro-1H-pyrrolizin-3-yl]methyl}acetamide


Mass: 230.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N2O4
#4: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 895 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M potassium sodium tartate tetrahydrate, 0.1M sodium citrate, 2.0M ammonium sulfate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 148686 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 25.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.26 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4H04

4h04


Resolution: 1.8→30.42 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.308 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20942 7449 5 %RANDOM
Rwork0.17685 ---
obs0.17848 141159 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9952 0 79 895 10926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0210254
X-RAY DIFFRACTIONr_bond_other_d0.0010.029522
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.95413928
X-RAY DIFFRACTIONr_angle_other_deg2.458321958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23451265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89224.852474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.251151721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.991552
X-RAY DIFFRACTIONr_chiral_restr0.1420.21526
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111663
X-RAY DIFFRACTIONr_gen_planes_other0.0140.022325
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_it1.8221.6345066
X-RAY DIFFRACTIONr_mcbond_other1.8221.6345065
X-RAY DIFFRACTIONr_mcangle_it2.5742.4426329
X-RAY DIFFRACTIONr_mcangle_other2.5742.4426330
X-RAY DIFFRACTIONr_scbond_it2.461.8525188
X-RAY DIFFRACTIONr_scbond_other2.4511.8465169
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7682.6597570
X-RAY DIFFRACTIONr_long_range_B_refined5.3514.04312630
X-RAY DIFFRACTIONr_long_range_B_other5.37513.62912213
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 556 -
Rwork0.222 10184 -
obs--98.94 %

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