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- PDB-6hur: 2'-fucosyllactose and 3-fucosyllactose binding protein from Bifid... -

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Basic information

Entry
Database: PDB / ID: 6hur
Title2'-fucosyllactose and 3-fucosyllactose binding protein from Bifidobacterium longum infantis, bound with 2'-fucosyllactose
ComponentsABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / Solute Binding Protein / 2'-Fucosyllactose / Bifidobacterium longum infantis / ABC-transporter
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / beta-D-glucopyranose / ABC transporter substrate-binding protein
Function and homology information
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.297 Å
AuthorsEjby, M. / Abou Hachem, M. / Lo Leggio, L. / Katayama, T. / Sakanaka, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-4002-00297 Denmark
CitationJournal: Sci Adv / Year: 2019
Title: Evolutionary adaptation in fucosyllactose uptake systems supports bifidobacteria-infant symbiosis.
Authors: Sakanaka, M. / Hansen, M.E. / Gotoh, A. / Katoh, T. / Yoshida, K. / Odamaki, T. / Yachi, H. / Sugiyama, Y. / Kurihara, S. / Hirose, J. / Urashima, T. / Xiao, J.Z. / Kitaoka, M. / Fukiya, S. ...Authors: Sakanaka, M. / Hansen, M.E. / Gotoh, A. / Katoh, T. / Yoshida, K. / Odamaki, T. / Yachi, H. / Sugiyama, Y. / Kurihara, S. / Hirose, J. / Urashima, T. / Xiao, J.Z. / Kitaoka, M. / Fukiya, S. / Yokota, A. / Lo Leggio, L. / Abou Hachem, M. / Katayama, T.
History
DepositionOct 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 15, 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

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,63011
Polymers48,1231
Non-polymers1,50610
Water8,845491
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: surface plasmon resonance, gel filtration, homology, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-99 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.000, 134.000, 59.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ABC transporter substrate-binding protein


Mass: 48123.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (bacteria)
Gene: BFS25_04965 / Plasmid: pETM-11 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0A1S2VYK0

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 499 molecules

#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: Zn
#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Drop ratio 1:1 protein: 100 mg/mL in 10 mM MES pH 6.5 and 150 mM NaCl Mother liqour: 0.1 M MES pH 6.5, 25 % PEG-500MME and 10 mM ZnSO4
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid Nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.297→41.61 Å / Num. obs: 98453 / % possible obs: 99.42 % / Redundancy: 4.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06549 / Rpim(I) all: 0.03582 / Rrim(I) all: 0.07486 / Net I/σ(I): 10.43
Reflection shellResolution: 1.297→1.343 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.03 / Num. unique obs: 9625 / CC1/2: 0.475 / % possible all: 97.39

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSVERSION Jan 26, 2018 BUILT=20180126data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180126data scaling
CootV. 0.8.9.1model building
PHENIX1.13_2998model building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.297→41.61 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1706 --
Rwork0.1513 --
obs-98453 99.42 %
Displacement parametersBiso max: 107.82 Å2 / Biso mean: 19.95 Å2 / Biso min: 11.01 Å2
Refinement stepCycle: LAST / Resolution: 1.297→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 82 491 3960

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