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- PDB-6i5r: BlMnBP1 binding protein of an ABC transporter from Bifidobacteriu... -

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Basic information

Entry
Database: PDB / ID: 6i5r
TitleBlMnBP1 binding protein of an ABC transporter from Bifidobacterium animalis subsp. lactis ATCC27673 in complex with mannobiose
ComponentsSugar ABC transporter substrate-binding protein, BlMnBP1
KeywordsPROTEIN TRANSPORT / Solute Binding Protein / Mannobiose / Bifidobacterium animalis subsp. lactis ATCC27673 / Blac_00780
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 4beta-beta-mannobiose / Sugar ABC transporter substrate-binding protein, BlMnBP1
Function and homology information
Biological speciesBifidobacterium animalis subsp. lactis ATCC 27673 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsAbou Hachem, M. / Ejby, M. / Guskov, A. / Slotboom, D.J.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research4002-00297B Denmark
CitationJournal: Mol.Microbiol. / Year: 2019
Title: Two binding proteins of the ABC transporter that confers growth of Bifidobacterium animalis subsp. lactis ATCC27673 on beta-mannan possess distinct manno-oligosaccharide-binding profiles.
Authors: Ejby, M. / Guskov, A. / Pichler, M.J. / Zanten, G.C. / Schoof, E. / Saburi, W. / Slotboom, D.J. / Abou Hachem, M.
History
DepositionNov 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.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 / entity_name_com / 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_molecule_features / 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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.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

Downloads & links

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Assembly

Deposited unit
A: Sugar ABC transporter substrate-binding protein, BlMnBP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,57516
Polymers49,3171
Non-polymers1,25815
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-307 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.560, 74.500, 102.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sugar ABC transporter substrate-binding protein, BlMnBP1


Mass: 49316.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium animalis subsp. lactis ATCC 27673 (bacteria)
Gene: blac_00780 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4V8GZY6*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose / 4beta-beta-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-mannobiose
DescriptorTypeProgram
DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Mother liquor: 0.1 M MES pH 5.5, 0.05 M Zn-acetate and 18% PEG 8000 Protein conc 15 mg/ml in 10 mM MES pH 6.5 and 150 mM NaCl + 1mM Mannobiose Drops setup 1 to 1

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99985 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 1.6→48.832 Å / Num. obs: 56799 / % possible obs: 99.82 % / Redundancy: 11.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.2044 / Rpim(I) all: 0.2138 / Net I/σ(I): 8.57
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 10.8 % / Rmerge(I) obs: 2.074 / Num. unique obs: 5602 / CC1/2: 0.456 / Rpim(I) all: 0.6535 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→48.832 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.42
RfactorNum. reflection% reflection
Rfree0.2462 2840 5 %
Rwork0.2167 --
obs0.2182 56746 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.24 Å2 / Biso mean: 22.4437 Å2 / Biso min: 16.39 Å2
Refinement stepCycle: final / Resolution: 1.6→48.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 59 496 3923
Biso mean--29.08 27.76 -
Num. residues----428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62760.33881410.303926702811100
1.6276-1.65720.32741390.300926512790100
1.6572-1.6890.27951410.28226722813100
1.689-1.72350.30361380.275126402778100
1.7235-1.7610.31871410.271526682809100
1.761-1.8020.31811400.266926722812100
1.802-1.8470.25781420.248826642806100
1.847-1.8970.28531390.243726722811100
1.897-1.95280.30851450.243126542799100
1.9528-2.01580.30071370.240427012838100
2.0158-2.08790.26741350.224826662801100
2.0879-2.17150.22421470.21326822829100
2.1715-2.27030.23691500.209827032853100
2.2703-2.390.20341320.204426972829100
2.39-2.53970.27051490.21226932842100
2.5397-2.73580.24231370.209126972834100
2.7358-3.01110.23731420.200527422884100
3.0111-3.44670.21881500.187527332883100
3.4467-4.3420.19611410.189327602901100
4.342-48.85430.25441540.21742869302399

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