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- PDB-7ee5: Crystal structure of Neu5Gc bound PltC -

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Basic information

Entry
Database: PDB / ID: 7ee5
TitleCrystal structure of Neu5Gc bound PltC
ComponentsSubtilase cytotoxin subunit B-like proteinAB5 toxin
KeywordsTOXIN / typhoid toxin
Function / homologyEnterotoxin / N-glycolyl-alpha-neuraminic acid / Subtilase cytotoxin subunit B-like protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhi str. CT18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsLiu, X.Y. / Chen, Z. / Gao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770143 China
CitationJournal: Mbio / Year: 2022
Title: Molecular Insights into the Assembly and Functional Diversification of Typhoid Toxin.
Authors: Liu, X. / Chen, Z. / Jiao, X. / Jiang, X. / Qiu, J. / You, F. / Long, H. / Cao, H. / Fowler, C.C. / Gao, X.
History
DepositionMar 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subtilase cytotoxin subunit B-like protein
B: Subtilase cytotoxin subunit B-like protein
C: Subtilase cytotoxin subunit B-like protein
D: Subtilase cytotoxin subunit B-like protein
E: Subtilase cytotoxin subunit B-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,63011
Polymers69,2925
Non-polymers2,3386
Water10,359575
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12000 Å2
ΔGint-54 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.094, 189.094, 41.207
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein
Subtilase cytotoxin subunit B-like protein / AB5 toxin / PltB homolog protein


Mass: 13858.360 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)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A716TY65
#2: Polysaccharide N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 649.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Gca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Gc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NGC / N-glycolyl-alpha-neuraminic acid / N-glycolylneuraminic acid / sialic acid / 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid / N-Glycolylneuraminic acid


Type: D-saccharide, alpha linking / Mass: 325.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19NO10 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5GcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-glycolyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5GcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5GcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 41.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 34% PEG500MME and 0.1M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.24→27.76 Å / Num. obs: 155226 / % possible obs: 99.67 % / Redundancy: 9.8 % / Biso Wilson estimate: 12.34 Å2 / CC1/2: 1 / Rrim(I) all: 0.068 / Net I/σ(I): 31.3
Reflection shellResolution: 1.24→1.285 Å / Redundancy: 7.9 % / Num. unique obs: 15252 / CC1/2: 0.93 / Rrim(I) all: 0.521

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WHT

5wht


Resolution: 1.24→27.76 Å / SU ML: 0.101 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 15.8138
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1604 7789 5.02 %
Rwork0.1382 147420 -
obs0.1393 155209 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.06 Å2
Refinement stepCycle: LAST / Resolution: 1.24→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4688 0 158 575 5421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01615042
X-RAY DIFFRACTIONf_angle_d1.9456841
X-RAY DIFFRACTIONf_chiral_restr0.1242753
X-RAY DIFFRACTIONf_plane_restr0.0123858
X-RAY DIFFRACTIONf_dihedral_angle_d18.59411747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.250.22262370.19264728X-RAY DIFFRACTION95.83
1.25-1.270.23662730.18224819X-RAY DIFFRACTION98.49
1.27-1.280.20042760.17074916X-RAY DIFFRACTION99.65
1.28-1.30.21022370.16124953X-RAY DIFFRACTION99.88
1.3-1.320.18742520.15714873X-RAY DIFFRACTION99.98
1.32-1.340.18962870.14824934X-RAY DIFFRACTION100
1.34-1.360.16772500.15094939X-RAY DIFFRACTION99.98
1.36-1.380.19042440.14294990X-RAY DIFFRACTION100
1.38-1.40.1712320.13914869X-RAY DIFFRACTION100
1.4-1.420.14892890.13394947X-RAY DIFFRACTION99.96
1.42-1.440.17272440.12934903X-RAY DIFFRACTION100
1.44-1.470.16922840.13434934X-RAY DIFFRACTION99.94
1.47-1.50.15292600.12064910X-RAY DIFFRACTION99.96
1.5-1.530.16282870.12174931X-RAY DIFFRACTION99.98
1.53-1.560.16032670.12184888X-RAY DIFFRACTION100
1.56-1.60.15822600.12424922X-RAY DIFFRACTION100
1.6-1.640.16332680.12074937X-RAY DIFFRACTION100
1.64-1.680.16162890.12584862X-RAY DIFFRACTION100
1.68-1.730.1532310.12954958X-RAY DIFFRACTION100
1.73-1.790.15352860.13274934X-RAY DIFFRACTION99.98
1.79-1.850.16352180.13244933X-RAY DIFFRACTION99.96
1.85-1.930.15852690.13164919X-RAY DIFFRACTION99.98
1.93-2.010.15682570.1294917X-RAY DIFFRACTION99.92
2.01-2.120.14712620.12574924X-RAY DIFFRACTION100
2.12-2.250.15552760.1344921X-RAY DIFFRACTION100
2.25-2.430.16272500.14114962X-RAY DIFFRACTION99.98
2.43-2.670.19312620.15344884X-RAY DIFFRACTION99.98
2.67-3.060.17722560.15564936X-RAY DIFFRACTION100
3.06-3.850.14092600.14134915X-RAY DIFFRACTION100
3.85-27.760.13162260.13244962X-RAY DIFFRACTION99.77

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