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- PDB-6i5w: BlMnBP1 binding protein of an ABC transporter from Bifidobacteriu... -

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Basic information

Entry
Database: PDB / ID: 6i5w
TitleBlMnBP1 binding protein of an ABC transporter from Bifidobacterium animalis subsp. lactis ATCC27673 in complex with mannobiose
ComponentsSolute Binding Protein BlMnBP1, Blac_00780 in complex with mannopentaose
KeywordsPROTEIN TRANSPORT / Solute Binding Protein / Mannopentaose / Bifidobacterium animalis subsp. lactis ATCC27673 / Blac_00780
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACETATE ION / Solute Binding Protein BlMnBP1, Blac_00780 in complex with mannopentaose
Function and homology information
Biological speciesBifidobacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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: 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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _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.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_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute Binding Protein BlMnBP1, Blac_00780 in complex with mannopentaose
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,15026
Polymers47,7961
Non-polymers2,35425
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-364 kcal/mol
Surface area17380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.520, 73.250, 103.610
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 Solute Binding Protein BlMnBP1, Blac_00780 in complex with mannopentaose


Mass: 47795.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium (bacteria) / Strain: animalis lactis / Gene: Blac_00780 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4V8GZY8*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Mother liquor, 0.1 M MES pH 5.5, 0.05 M Zn-acetate and 18% PEG 8000. Protein,15 mg/ml in 10 mM MES pH 6.5 and 150 mM NaCl. Drops set up 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: ESRF / Beamline: ID30B / Wavelength: 0.9989 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9989 Å / Relative weight: 1
ReflectionResolution: 1.9→47.551 Å / Num. obs: 32748 / % possible obs: 99.51 % / Redundancy: 13.3 % / Biso Wilson estimate: 57.28 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.09
Reflection shellResolution: 1.9→2 Å / Mean I/σ(I) obs: 0.94 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→47.551 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.49
RfactorNum. reflection% reflection
Rfree0.2731 1638 5 %
Rwork0.2103 --
obs0.2134 32748 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 214.49 Å2 / Biso mean: 46.5309 Å2 / Biso min: 18.77 Å2
Refinement stepCycle: final / Resolution: 1.9→47.551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 175 103 3637
Biso mean--56.53 40.41 -
Num. residues----427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.9560.4191340.419925372671100
1.956-2.01920.39851340.378625552689100
2.0192-2.09140.35151350.348725662701100
2.0914-2.17510.39741350.328625562691100
2.1751-2.27410.33541350.287425702705100
2.2741-2.3940.31741340.25825382672100
2.394-2.5440.3111380.235726112749100
2.544-2.74040.30711350.210225612696100
2.7404-3.01610.29631360.197826092745100
3.0161-3.45240.23821360.17992590272699
3.4524-4.34920.21461390.151126432782100
4.3492-47.56560.23271470.176327742921100

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