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- PDB-8g0f: Crystal structure of diphtheria toxin H223Q/H257Q double mutant (... -

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Basic information

Entry
Database: PDB / ID: 8g0f
TitleCrystal structure of diphtheria toxin H223Q/H257Q double mutant (pH 5.5)
ComponentsDiphtheria toxin
KeywordsTOXIN / diptheria toxin / pH dependent conformational changes
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase activity / toxin activity / extracellular space
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
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Ladokhin, A.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: Toxins / Year: 2023
Title: Histidine Protonation and Conformational Switching in Diphtheria Toxin Translocation Domain.
Authors: Rodnin, M.V. / Vasques-Montes, V. / Kyrychenko, A. / Oliveira, N.F.B. / Kashipathy, M.M. / Battaile, K.P. / Douglas, J. / Lovell, S. / Machuqueiro, M. / Ladokhin, A.S.
History
DepositionJan 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diphtheria toxin
B: Diphtheria toxin


Theoretical massNumber of molelcules
Total (without water)117,4502
Polymers117,4502
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-29 kcal/mol
Surface area40340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.548, 69.471, 72.879
Angle α, β, γ (deg.)117.99, 93.87, 99.34
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Diphtheria toxin


Mass: 58724.797 Da / Num. of mol.: 2 / Mutation: K51E, E148K, H223Q, H257Q
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% (w/v) PEG 2000 MME, 100 mM sodium citrate tribasic, 200 mM sodium malonate

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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: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→46.78 Å / Num. obs: 52984 / % possible obs: 95.8 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.047 / Rrim(I) all: 0.088 / Χ2: 0.92 / Net I/σ(I): 9.7 / Num. measured all: 182683
Reflection shellResolution: 2.25→2.32 Å / % possible obs: 96.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.727 / Num. measured all: 15664 / Num. unique obs: 4660 / CC1/2: 0.692 / Rpim(I) all: 0.469 / Rrim(I) all: 0.869 / Χ2: 0.81 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→36.31 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 2608 4.92 %
Rwork0.1904 --
obs0.1937 52961 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7506 0 0 167 7673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017654
X-RAY DIFFRACTIONf_angle_d0.96910419
X-RAY DIFFRACTIONf_dihedral_angle_d14.4912649
X-RAY DIFFRACTIONf_chiral_restr0.0521222
X-RAY DIFFRACTIONf_plane_restr0.0071343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.32111210.27532700X-RAY DIFFRACTION96
2.3-2.340.34071400.2462701X-RAY DIFFRACTION97
2.34-2.390.2631470.24912655X-RAY DIFFRACTION97
2.39-2.440.29581140.24422708X-RAY DIFFRACTION97
2.44-2.50.32731170.24752739X-RAY DIFFRACTION98
2.5-2.560.35351660.25772660X-RAY DIFFRACTION97
2.56-2.630.30471360.24082724X-RAY DIFFRACTION98
2.63-2.70.33611280.2452238X-RAY DIFFRACTION81
2.71-2.790.33331450.22732738X-RAY DIFFRACTION98
2.79-2.890.30281200.2342733X-RAY DIFFRACTION98
2.89-3.010.33031360.2372686X-RAY DIFFRACTION98
3.01-3.140.31221530.23942706X-RAY DIFFRACTION98
3.14-3.310.30871520.21262719X-RAY DIFFRACTION98
3.31-3.520.26351110.19562301X-RAY DIFFRACTION84
3.52-3.790.24171700.17412648X-RAY DIFFRACTION97
3.79-4.170.21381490.15292669X-RAY DIFFRACTION97
4.17-4.770.1791360.12922690X-RAY DIFFRACTION97
4.77-6.010.21861740.15862630X-RAY DIFFRACTION96
6.01-36.310.2156930.16862708X-RAY DIFFRACTION96

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