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- PDB-7k7e: Crystal structure of diphtheria toxin from crystals obtained at pH 7.0 -

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Basic information

Entry
Database: PDB / ID: 7k7e
TitleCrystal structure of diphtheria toxin from crystals obtained at pH 7.0
ComponentsDiphtheria toxin
KeywordsTOXIN / diptheria toxin / pH dependent conformational changes
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / toxin activity / extracellular space / identical protein binding
Similarity search - Function
Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain
Similarity search - Domain/homology
Diphtheria toxin / Diphtheria toxin
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Rodnin, M.V. / Ladokhin, A.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-069783 United States
CitationJournal: Toxins / Year: 2020
Title: Structure of the Diphtheria Toxin at Acidic pH: Implications for the Conformational Switching of the Translocation Domain.
Authors: Rodnin, M.V. / Kashipathy, M.M. / Kyrychenko, A. / Battaile, K.P. / Lovell, S. / Ladokhin, A.S.
History
DepositionSep 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diphtheria toxin
B: Diphtheria toxin


Theoretical massNumber of molelcules
Total (without water)117,4902
Polymers117,4902
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-29 kcal/mol
Surface area40360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.378, 69.641, 73.146
Angle α, β, γ (deg.)117.480, 93.250, 98.270
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Diphtheria toxin


Mass: 58744.828 Da / Num. of mol.: 2 / Fragment: Full Length / Mutation: K51E, E148K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL23DELysS / References: UniProt: Q5PY51, UniProt: Q6NK15*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.96 % / Mosaicity: 0.25 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% (w/v) PEG 10000, 0.1 M magnesium acetate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.74 Å / Num. obs: 51695 / % possible obs: 97.7 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.7 / Num. measured all: 183332
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.3-2.373.60.7541625344560.6981.897.3
9.48-46.743.70.03427607460.99828.397.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.3data scaling
PHASERphasing
PHENIX1.14rc2_3195refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDT

1ddt


Resolution: 2.3→32.721 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.05 / Phase error: 30.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 2428 4.7 %
Rwork0.1852 49240 -
obs0.188 51668 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.67 Å2 / Biso mean: 56.3183 Å2 / Biso min: 24.31 Å2
Refinement stepCycle: final / Resolution: 2.3→32.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7591 0 0 201 7792
Biso mean---48.91 -
Num. residues----1016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097747
X-RAY DIFFRACTIONf_angle_d0.95910532
X-RAY DIFFRACTIONf_dihedral_angle_d13.054614
X-RAY DIFFRACTIONf_chiral_restr0.0531215
X-RAY DIFFRACTIONf_plane_restr0.0071360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.34690.34831650.2889285797
2.3469-2.3980.36151360.2744293997
2.398-2.45370.28621230.2533287597
2.4537-2.51510.29771280.2311289497
2.5151-2.5830.28651200.2244290697
2.583-2.6590.30041260.2197291298
2.659-2.74480.31431120.2259293698
2.7448-2.84280.28811360.2309290998
2.8428-2.95660.25161180.2273292498
2.9566-3.09110.27061240.2228293398
3.0911-3.25390.32911390.2202293198
3.2539-3.45750.27531720.2023286498
3.4575-3.72420.23211740.1756284898
3.7242-4.09830.21581740.1542286796
4.0983-4.68980.20921610.1268286098
4.6898-5.9030.17741760.1499287298
5.903-32.7210.21711440.1714291398

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