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- PDB-6fuv: Structure of a manno-oligosaccharide specific solute binding prot... -

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Basic information

Entry
Database: PDB / ID: 6fuv
TitleStructure of a manno-oligosaccharide specific solute binding protein, BlMnBP2 from Bifidobacterium animalis subsp. lactis ATCC 27673 in complex with mannotriose
ComponentsSolute Binding Protein, BlMnBP1 in complex with mannotriose
KeywordsTRANSPORT PROTEIN / ABC-transporter / beta-mannotriose / Solute Binding Protein
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACETATE ION / TRIETHYLENE GLYCOL / Solute Binding Protein, BlMnBP1 in complex with mannotriose
Function and homology information
Biological speciesBifidobacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.001 Å
AuthorsEjby, M. / Abou Hachem, M. / Guskov, A. / Slotboom, D.J.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent ResearchDFF-4002-00297 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
DepositionFeb 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 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 / 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 / struct_asym / struct_conn / 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.pdbx_synonyms / _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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 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: Solute Binding Protein, BlMnBP1 in complex with mannotriose
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4049
Polymers47,5871
Non-polymers1,8178
Water8,557475
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint15 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.170, 64.590, 133.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Solute Binding Protein, BlMnBP1 in complex with mannotriose


Mass: 47586.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NCBI-ProteinID: AGW84383 / Source: (gene. exp.) Bifidobacterium (bacteria) / Gene: Blac_00785
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A4V8GZV8*PLUS
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 482 molecules

#3: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#5: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C14H30O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Reservoir: 0.1 M MES pH 5.5, 0.05 M Zn-acetate and 18% PEG 8000 Protein 15 mg/ml in 20 mM MES pH 6.5, 150 mM NaCl + 1 mM Mannotriose. Drops ratio 1/1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2→40.585 Å / Num. obs: 28205 / % possible obs: 90.3 % / Redundancy: 3.027 % / Biso Wilson estimate: 21.25 Å2 / CC1/2: 0.968 / Rmerge(I) obs: 0.2288 / Rpim(I) all: 0.1501 / Χ2: 0.872 / Net I/σ(I): 4.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible allRrim(I) all
2-2.0732.0991.1370.6416570.3880.776553.66
2.1-2.52.8560.71.4298430.61890.70.848
2.5-33.2470.372366240.84899.20.446
3-43.3740.1467.5753800.97699.40.174
4-63.2560.08711.7727970.98998.80.104
6-102.9210.07412.359630.99298.20.09
10-40.5852.920.04418.342890.99695.10.054

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.86 Å40.58 Å
Translation6.86 Å40.58 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.12_2829phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.001→40.585 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.59
RfactorNum. reflection% reflection
Rfree0.2506 1411 5 %
Rwork0.1783 --
obs0.1819 28200 90.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.17 Å2 / Biso mean: 24.1145 Å2 / Biso min: 5.3 Å2
Refinement stepCycle: final / Resolution: 2.001→40.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 271 475 4092
Biso mean--31.37 29.73 -
Num. residues----427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0009-2.07240.3206830.26151575165854
2.0724-2.15540.33561030.26221953205667
2.1554-2.25350.33891340.24852549268388
2.2535-2.37230.31871530.21612910306399
2.3723-2.52090.29041540.191629193073100
2.5209-2.71550.26391540.177229193073100
2.7155-2.98870.20331530.17312912306599
2.9887-3.4210.25651570.15829793136100
3.421-4.30930.20031560.12842972312899
4.3093-40.59320.22391640.17993101326598

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