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- PDB-4jaw: Crystal Structure of Lacto-N-Biosidase from Bifidobacterium bifid... -

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Basic information

Entry
Database: PDB / ID: 4jaw
TitleCrystal Structure of Lacto-N-Biosidase from Bifidobacterium bifidum complexed with LNB-thiazoline
ComponentsLacto-N-biosidase
KeywordsHYDROLASE / alpha/beta-domain / Tim Barrel / beta-Trefoil / Membrane-anchored extracellular
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 / Ricin B, lectin domain / F5/8 type C 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
beta-D-galactopyranose / Chem-NGT / Lacto-N-biosidase
Similarity search - Component
Biological speciesBifidobacterium bifidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsIto, T. / Katayama, T. / Stubbs, K.A. / Fushinobu, S.
Citation
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.
#1: Journal: Appl.Environ.Microbiol. / Year: 2008
Title: Bifidobacterium bifidum lacto-N-biosidase, a critical enzyme for the degradation of human milk oligosaccharides with a type 1 structure.
Authors: Wada, J. / Ando, T. / Kiyohara, M. / Ashida, H. / Kitaoka, M. / Yamaguchi, M. / Kumagai, H. / Katayama, T. / Yamamoto, K.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)145,25613
Polymers143,7842
Non-polymers1,47111
Water7,260403
1
A: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6767
Polymers71,8921
Non-polymers7846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5806
Polymers71,8921
Non-polymers6885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-15 kcal/mol
Surface area47270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.524, 131.557, 104.762
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-950-

HOH

21B-939-

HOH

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Components

#1: Protein Lacto-N-biosidase /


Mass: 71892.227 Da / Num. of mol.: 2 / Fragment: UNP Residue 41-663
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Strain: JCM1254 / Gene: lnbB / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL / References: UniProt: B3TLD6, lacto-N-biosidase
#2: 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: isolated from a genetically manipulated source
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
#3: Chemical ChemComp-NGT / 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL


Mass: 219.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO4S
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate, 2.0M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Nov 25, 2012
RadiationMonochromator: Si(111), numerical link type double crystal monochromator
Protocol: 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: 150089 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.102 / Net I/σ(I): 23.97
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.85 / Num. unique all: 7436 / Rsym value: 0.485 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.6.0117phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4H04

4h04


Resolution: 1.8→43.61 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.879 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21306 7499 5 %RANDOM
Rwork0.18178 ---
all0.18335 150089 --
obs0.18335 141665 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.513 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.106 Å0.107 Å
Refinement stepCycle: LAST / Resolution: 1.8→43.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9932 0 85 403 10420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0210236
X-RAY DIFFRACTIONr_angle_refined_deg2.3651.95513898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17851263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2724.873472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.646151719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0641552
X-RAY DIFFRACTIONr_chiral_restr0.2750.21520
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0217762
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 522 -
Rwork0.194 9905 -
obs--100 %

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