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- PDB-6p4m: Salmonella typhi PltB Homopentamer with Neu5Ac-alpha-2-3-Gal-beta... -

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Basic information

Entry
Database: PDB / ID: 6p4m
TitleSalmonella typhi PltB Homopentamer with Neu5Ac-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans
ComponentsPutative pertussis-like toxin subunit
KeywordsTOXIN / PltB
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Bordetella 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 / Mainly Beta
Similarity search - Domain/homology
3'-sialyl-N-acetyllactosamine / Pertussis-like toxin subunit
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsNguyen, T. / Milano, S.K. / Hillpot, E.C. / 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: Cell Host Microbe / Year: 2020
Title: Salmonella Typhoid Toxin PltB Subunit and Its Non-typhoidal Salmonella Ortholog Confer Differential Host Adaptation and Virulence.
Authors: Lee, S. / Yang, Y.A. / Milano, S.K. / Nguyen, T. / Ahn, C. / Sim, J.H. / Thompson, A.J. / Hillpot, E.C. / Yoo, G. / Paulson, J.C. / Song, J.
History
DepositionMay 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
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 / 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_validate_close_contact / 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.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 5, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 / _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: Putative pertussis-like toxin subunit
B: Putative pertussis-like toxin subunit
C: Putative pertussis-like toxin subunit
D: Putative pertussis-like toxin subunit
E: Putative pertussis-like toxin subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,59814
Polymers81,5275
Non-polymers6,0719
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18470 Å2
ΔGint9 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.706, 97.745, 105.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative pertussis-like toxin subunit / PltB Protein


Mass: 16305.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
Gene: STY1891, t1107 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Z6A3
#2: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 674.604 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-N-acetyllactosamine
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_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-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 26% PEG1500, Sodium actetate 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-D / Wavelength: 1.87 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.87 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 66141 / % possible obs: 99.3 % / Redundancy: 4.6 % / Net I/σ(I): 21.8
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 3078

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Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
HKL-2000717data reduction
HKL-2000717data scaling
PHENIX1.10.1-2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.802→39.825 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 17.36
RfactorNum. reflection% reflection
Rfree0.1932 2002 3.04 %
Rwork0.1688 --
obs0.1695 65771 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.802→39.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4425 0 414 359 5198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074993
X-RAY DIFFRACTIONf_angle_d1.2046868
X-RAY DIFFRACTIONf_dihedral_angle_d2.9092825
X-RAY DIFFRACTIONf_chiral_restr0.071835
X-RAY DIFFRACTIONf_plane_restr0.006814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8021-1.84720.24781410.19524254X-RAY DIFFRACTION94
1.8472-1.89710.21621320.17844472X-RAY DIFFRACTION99
1.8971-1.9530.20181440.17014532X-RAY DIFFRACTION100
1.953-2.0160.23061410.16454513X-RAY DIFFRACTION100
2.016-2.0880.18981460.1664535X-RAY DIFFRACTION100
2.088-2.17160.19251350.16464545X-RAY DIFFRACTION100
2.1716-2.27050.18791470.15944514X-RAY DIFFRACTION100
2.2705-2.39010.18911410.1684577X-RAY DIFFRACTION100
2.3901-2.53990.19491480.17284543X-RAY DIFFRACTION100
2.5399-2.73590.22471350.17554579X-RAY DIFFRACTION100
2.7359-3.01120.19131580.18624583X-RAY DIFFRACTION100
3.0112-3.44670.21191390.18084610X-RAY DIFFRACTION100
3.4467-4.34160.16131450.15384663X-RAY DIFFRACTION100
4.3416-39.83450.17731500.15984849X-RAY DIFFRACTION100

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