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- PDB-4h04: Lacto-N-biosidase from Bifidobacterium bifidum -

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Basic information

Entry
Database: PDB / ID: 4h04
TitleLacto-N-biosidase from Bifidobacterium bifidum
ComponentsLacto-N-biosidase
KeywordsHYDROLASE / Tim Barrel / 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 / Beta-hexosaminidase, bacterial type, N-terminal ...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 / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, 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 / 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
Biological speciesBifidobacterium bifidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsIto, T. / Katayama, T. / Wada, J. / Suzuki, R. / Ashida, H. / Wakagi, T. / Yamamoto, K. / 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
DepositionSep 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)145,32012
Polymers143,7842
Non-polymers1,53510
Water23,9061327
1
A: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6606
Polymers71,8921
Non-polymers7685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6606
Polymers71,8921
Non-polymers7685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-14 kcal/mol
Surface area46730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.815, 131.033, 104.409
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-801-

HOH

21B-801-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 662
2114B1 - 661

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.990574, -0.136679, 0.009065), (-0.136688, 0.990614, -0.000389), (-0.008926, -0.001624, -0.999959)115.7412, 7.9246, 55.15983

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Components

#1: Protein Lacto-N-biosidase


Mass: 71892.227 Da / Num. of mol.: 2 / Fragment: GH20 domain, UNP residues 41-663
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium bifidum (bacteria) / Strain: JCM1254 / Gene: lnbB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3)-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.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1327 / 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: 2.78 Å3/Da / Density % sol: 55.73 %
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, 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 315r / Detector: CCD / Date: Dec 22, 2008
RadiationMonochromator: Numerical link type Si(111) 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. all: 148755 / Num. obs: 148717 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.079 / Net I/σ(I): 27.64
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 4.67 / Num. unique all: 14688 / Rsym value: 0.281 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→47.51 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.813 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19135 7448 5 %RANDOM
Rwork0.15503 ---
all0.1571 141195 --
obs0.15685 141195 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.139 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.099 Å0.098 Å
Refinement stepCycle: LAST / Resolution: 1.8→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9932 0 92 1327 11351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0210238
X-RAY DIFFRACTIONr_angle_refined_deg2.5031.95513904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12751263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91624.873472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79151719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7841552
X-RAY DIFFRACTIONr_chiral_restr0.2940.21523
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0217764
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4963 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.370.5
MEDIUM THERMAL2.072
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 475 -
Rwork0.203 9810 -
obs-9810 98.97 %

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