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- PDB-5gqf: Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium ... -

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Basic information

Entry
Database: PDB / ID: 5gqf
TitleCrystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, lacto-N-biose complex
ComponentsLacto-N-biosidase
KeywordsHYDROLASE / beta-helix
Function / homology
Function and homology information


membrane / metal ion binding
Similarity search - Function
Long Rib domain / Long Rib domain / FIVAR domain / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
Biological speciesBifidobacterium longum subsp. longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 Å
AuthorsYamada, C. / Arakawa, T. / Katayama, T. / Fushinobu, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries and Food Industry25010A Japan
JSPS16J09251 Japan
Citation
Journal: Cell Chem Biol / Year: 2017
Title: Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum
Authors: Yamada, C. / Gotoh, A. / Sakanaka, M. / Hattie, M. / Stubbs, K.A. / Katayama-Ikegami, A. / Hirose, J. / Kurihara, S. / Arakawa, T. / Kitaoka, M. / Okuda, S. / Katayama, T. / Fushinobu, S.
#1: Journal: J. Biol. Chem. / Year: 2013
Title: Lacto-N-biosidase encoded by a novel gene of Bifidobacterium longum subspecies longum shows unique substrate specificity and requires a designated chaperone for its active expression.
Authors: Sakurama, H. / Kiyohara, M. / Wada, J. / Honda, Y. / Yamaguchi, M. / Fukiya, S. / Yokota, A. / Ashida, H. / Kumagai, H. / Kitaoka, M. / Yamamoto, K. / Katayama, T.
History
DepositionAug 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Oct 18, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)133,1088
Polymers132,1812
Non-polymers9276
Water19,9971110
1
A: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5544
Polymers66,0901
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area20020 Å2
MethodPISA
2
B: Lacto-N-biosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5544
Polymers66,0901
Non-polymers4643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area20190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.035, 143.625, 146.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lacto-N-biosidase /


Mass: 66090.375 Da / Num. of mol.: 2 / Fragment: UNP residues 31-625
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. longum (bacteria)
Strain: JCM1217 / Gene: lnbX / Plasmid: pTK2385 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): delta-lacZ (DE3)/pRARE2 / References: UniProt: A0A024QYS6, 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-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1110 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M ammonium fluoride, 0.1 M MES-NaOH, 20-21% (v/v) PEG3350, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 3, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→102.45 Å / Num. obs: 116978 / % possible obs: 96.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 23.1
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2 / CC1/2: 0.811 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.82→102.45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.267 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23575 1991 1.7 %RANDOM
Rwork0.18126 ---
obs0.18218 114879 96.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.297 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.82→102.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8936 0 56 1110 10102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0199188
X-RAY DIFFRACTIONr_bond_other_d0.0060.028094
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.92512526
X-RAY DIFFRACTIONr_angle_other_deg1.079318592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.83951162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.03125.378476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.801151350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3381538
X-RAY DIFFRACTIONr_chiral_restr0.1230.21346
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022210
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_it3.2413.4034654
X-RAY DIFFRACTIONr_mcbond_other3.243.4024653
X-RAY DIFFRACTIONr_mcangle_it3.8575.0835814
X-RAY DIFFRACTIONr_mcangle_other3.8585.0845815
X-RAY DIFFRACTIONr_scbond_it3.5793.5734534
X-RAY DIFFRACTIONr_scbond_other3.5783.5734535
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7085.2846713
X-RAY DIFFRACTIONr_long_range_B_refined6.06141.46711024
X-RAY DIFFRACTIONr_long_range_B_other5.87740.68810674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 144 -
Rwork0.271 8346 -
obs--95.63 %

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