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- PDB-6tyo: Salmonella Typhi PltB Homopentamer with Neu-5NAc-4OAc-alpha-2-3-G... -

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Basic information

Entry
Database: PDB / ID: 6tyo
TitleSalmonella Typhi PltB Homopentamer with Neu-5NAc-4OAc-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans
ComponentsPertussis-like toxin subunit
KeywordsTOXIN / PltB
Function / homologyBordetella pertussis toxin B, subunit 2/3, C-terminal / Pertussis toxin, subunit 2 and 3, C-terminal domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / extracellular region / Mainly Beta / Pertussis-like toxin subunit
Function and homology information
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsNguyen, T. / Milano, S.K. / Yang, Y.A. / Song, J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI137345 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI139625 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI141514 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R03 AI135767 United States
CitationJournal: Plos Pathog. / Year: 2020
Title: The role of 9-O-acetylated glycan receptor moieties in the typhoid toxin binding and intoxication.
Authors: Nguyen, T. / Lee, S. / Yang, Y.A. / Ahn, C. / Sim, J.H. / Kei, T.G. / Barnard, K.N. / Yu, H. / Millano, S.K. / Chen, X. / Parrish, C.R. / Song, J.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pertussis-like toxin subunit
B: Pertussis-like toxin subunit
C: Pertussis-like toxin subunit
D: Pertussis-like toxin subunit
E: Pertussis-like toxin subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,39810
Polymers62,8155
Non-polymers3,5835
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-21 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.580, 98.208, 104.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein
Pertussis-like toxin subunit / Subtilase cytotoxin subunit B / PltB


Mass: 12563.042 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria)
Gene: STY1891, t1107, ABP05_22510, AXU46_23480, E2E79_23180, E2E83_22990, E2F00_23020, E2F08_23180, E2F09_23155, E2F13_22745, PltB
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Z6A3
#2: Polysaccharide
4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-3)-beta-D- ...4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.641 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_4*OCC/3=O_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup4Ac5Ac]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 26% PEG 1500 0.1M Sodium Acetate pH 4.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.87 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.87 Å / Relative weight: 1
ReflectionResolution: 2.04→40 Å / Num. obs: 45598 / % possible obs: 99.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 37.4
Reflection shellResolution: 2.04→2.09 Å / Rmerge(I) obs: 0.148 / Num. unique obs: 3219

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RHR

4rhr


Resolution: 2.04→40 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1976 --
Rwork0.1607 --
obs-45598 99.8 %
Displacement parametersBiso mean: 17.16 Å2
Refinement stepCycle: LAST / Resolution: 2.04→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4425 0 245 398 5068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784800
X-RAY DIFFRACTIONf_angle_d1.07626575
X-RAY DIFFRACTIONf_chiral_restr0.0595770
X-RAY DIFFRACTIONf_plane_restr0.0051805
X-RAY DIFFRACTIONf_dihedral_angle_d11.13882665

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