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- PDB-8g0g: Crystal structure of diphtheria toxin H223Q/H257Q double mutant (... -

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Basic information

Entry
Database: PDB / ID: 8g0g
TitleCrystal structure of diphtheria toxin H223Q/H257Q double mutant (pH 4.5)
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
ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE / Diphtheria toxin
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diphtheria toxin
B: Diphtheria toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7564
Polymers117,4502
Non-polymers1,3072
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-38 kcal/mol
Surface area40280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.360, 69.399, 69.670
Angle α, β, γ (deg.)64.51, 76.51, 81.19
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: Chemical ChemComp-APU / ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE


Mass: 653.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25N7O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 20% (w/v) PEG 4000, 100 mM sodium citrate

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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
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.57 Å / Num. obs: 63799 / % possible obs: 96.1 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.043 / Rrim(I) all: 0.081 / Χ2: 1.01 / Net I/σ(I): 9.7 / Num. measured all: 217428
Reflection shellResolution: 2.1→2.15 Å / % possible obs: 96.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.65 / Num. measured all: 15203 / Num. unique obs: 4499 / CC1/2: 0.703 / Rpim(I) all: 0.418 / Rrim(I) all: 0.776 / Χ2: 1.12 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→37 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 3134 4.91 %
Rwork0.1897 --
obs0.1921 63775 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7621 0 86 280 7987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097863
X-RAY DIFFRACTIONf_angle_d0.90610702
X-RAY DIFFRACTIONf_dihedral_angle_d14.4052746
X-RAY DIFFRACTIONf_chiral_restr0.051234
X-RAY DIFFRACTIONf_plane_restr0.0071374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.3291440.2752730X-RAY DIFFRACTION97
2.13-2.170.25641570.26112820X-RAY DIFFRACTION97
2.17-2.210.34441380.24552750X-RAY DIFFRACTION97
2.21-2.250.30351380.25632781X-RAY DIFFRACTION95
2.25-2.290.29051170.24572070X-RAY DIFFRACTION95
2.29-2.340.291510.2292814X-RAY DIFFRACTION97
2.34-2.390.28311750.22852782X-RAY DIFFRACTION97
2.39-2.440.28811530.22732747X-RAY DIFFRACTION97
2.44-2.50.29091430.22152823X-RAY DIFFRACTION98
2.5-2.570.26351450.22032847X-RAY DIFFRACTION98
2.57-2.650.29371250.22252790X-RAY DIFFRACTION98
2.65-2.730.30341370.21342799X-RAY DIFFRACTION98
2.73-2.830.25721520.21272797X-RAY DIFFRACTION98
2.83-2.940.27441480.21162827X-RAY DIFFRACTION98
2.94-3.080.27081460.2192811X-RAY DIFFRACTION98
3.08-3.240.24611180.21132817X-RAY DIFFRACTION97
3.24-3.440.24891490.1892771X-RAY DIFFRACTION97
3.44-3.710.24731420.18032790X-RAY DIFFRACTION97
3.71-4.080.20891340.1632809X-RAY DIFFRACTION97
4.08-4.670.15891490.13922738X-RAY DIFFRACTION96
4.67-5.870.22241320.15322771X-RAY DIFFRACTION96
5.88-370.20431410.1752757X-RAY DIFFRACTION96

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