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- PDB-7k7d: Crystal structure of diphtheria toxin from crystals obtained at pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 7k7d
TitleCrystal structure of diphtheria toxin from crystals obtained at pH 6.0
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: 2.1 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)GM-069783 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 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 23, 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
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-30 kcal/mol
Surface area40320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.439, 69.605, 73.122
Angle α, β, γ (deg.)117.900, 93.860, 97.930
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.: 227 / 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: 2.6 Å3/Da / Density % sol: 52.75 % / Mosaicity: 0.15 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% (w/v) PEG 10000, 0.1 M magnesium acetate, 0.1 M MES

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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: 2.1→46.57 Å / Num. obs: 67346 / % possible obs: 97.4 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.7 / Num. measured all: 236012
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.1-2.153.50.6961558845020.7531.896.9
9.85-46.573.60.02924086610.99833.498.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.1data scaling
PHASERphasing
PHENIX1.14rc3_3208refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDT

1ddt


Resolution: 2.1→36.427 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 31.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 3175 4.72 %
Rwork0.2104 64135 -
obs0.2126 67310 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.77 Å2 / Biso mean: 56.0176 Å2 / Biso min: 27.59 Å2
Refinement stepCycle: final / Resolution: 2.1→36.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7491 0 0 227 7718
Biso mean---48.41 -
Num. residues----1012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017645
X-RAY DIFFRACTIONf_angle_d0.94110399
X-RAY DIFFRACTIONf_dihedral_angle_d12.6864543
X-RAY DIFFRACTIONf_chiral_restr0.0541209
X-RAY DIFFRACTIONf_plane_restr0.0071338
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1001-2.13140.34881430.2973272797
2.1314-2.16470.31051440.2836282197
2.1647-2.20020.33341400.277270697
2.2002-2.23810.36711240.2728284597
2.2381-2.27880.31711720.2729273597
2.2788-2.32260.341370.2568281998
2.3226-2.370.30281390.2517275997
2.37-2.42160.29721480.2544277197
2.4216-2.47790.30831350.2528281298
2.4779-2.53980.27811500.2541278598
2.5398-2.60850.30531720.2359276298
2.6085-2.68520.29751480.2448280197
2.6852-2.77190.30621510.2426278298
2.7719-2.87090.26921370.2369278898
2.8709-2.98580.31691180.2372279598
2.9858-3.12160.27531080.234286298
3.1216-3.28610.30031060.2316282598
3.2861-3.49180.27991210.2252288698
3.4918-3.76120.24681180.2037273097
3.7612-4.13920.2351280.1763277596
4.1392-4.7370.19861430.1563277297
4.737-5.96390.21481660.1721278498
5.9639-36.4270.21411270.1897279397

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