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- PDB-8qnq: Structure of the toxin-antitoxin NatRT complex from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 8qnq
TitleStructure of the toxin-antitoxin NatRT complex from Pseudomonas aeruginosa. NatTE29D mutant
Components
  • Antitoxin Xre/MbcA/ParS-like toxin-binding domain-containing protein
  • RES domain-containing protein
KeywordsTOXIN / RES domain NADase NAD+ Pseudomonas aeruginosa
Function / homologyAntitoxin Xre/MbcA/ParS-like, toxin-binding domain / Antitoxin Xre/MbcA/ParS C-terminal toxin-binding domain / RES domain / RES domain / RES / PHOSPHATE ION / RES domain-containing protein / Antitoxin Xre/MbcA/ParS-like toxin-binding domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.386 Å
AuthorsDias Teixeira, R. / Hiller, S. / Jenal, U.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_189253 Switzerland
Swiss National Science Foundation51NF40_180541 Switzerland
CitationJournal: Embo J. / Year: 2024
Title: Toxin-mediated depletion of NAD and NADP drives persister formation in a human pathogen.
Authors: Santi, I. / Dias Teixeira, R. / Manfredi, P. / Hernandez Gonzalez, H. / Spiess, D.C. / Mas, G. / Klotz, A. / Kaczmarczyk, A. / Zamboni, N. / Hiller, S. / Jenal, U.
History
DepositionSep 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antitoxin Xre/MbcA/ParS-like toxin-binding domain-containing protein
B: Antitoxin Xre/MbcA/ParS-like toxin-binding domain-containing protein
C: RES domain-containing protein
D: Antitoxin Xre/MbcA/ParS-like toxin-binding domain-containing protein
E: Antitoxin Xre/MbcA/ParS-like toxin-binding domain-containing protein
F: RES domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,76810
Polymers116,3886
Non-polymers3804
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18720 Å2
ΔGint-113 kcal/mol
Surface area38870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.422, 107.706, 93.528
Angle α, β, γ (deg.)90.00, 104.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Antitoxin Xre/MbcA/ParS-like toxin-binding domain-containing protein


Mass: 14186.486 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA1029 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I4U5
#2: Protein RES domain-containing protein


Mass: 29820.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA1030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4U4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: in 0.2 M sodium/potassium phosphate pH 7.5, 0.1 M HEPES 7.5, 22.5 % v/v, PEG Smear Medium, 10 % v/v Glycerol from condition G11 of BCS screen (Molecular dimensions)

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→90.72 Å / Num. obs: 39257 / % possible obs: 92.5 % / Redundancy: 6.9 % / CC1/2: 0.97 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.094 / Rrim(I) all: 0.24 / Net I/σ(I): 11.8
Reflection shellResolution: 2.38→2.42 Å / Rmerge(I) obs: 1.34 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2102 / CC1/2: 0.665 / Rpim(I) all: 0.54 / Rrim(I) all: 1.45 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.386→53.853 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 1971 5.03 %
Rwork0.2338 --
obs0.2356 39149 92.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.386→53.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7730 0 20 62 7812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047926
X-RAY DIFFRACTIONf_angle_d0.70410760
X-RAY DIFFRACTIONf_dihedral_angle_d4.5794778
X-RAY DIFFRACTIONf_chiral_restr0.0511191
X-RAY DIFFRACTIONf_plane_restr0.0041393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3861-2.44580.36391610.31962832X-RAY DIFFRACTION99
2.4458-2.51190.36711430.3042831X-RAY DIFFRACTION98
2.5119-2.58580.36791370.32322800X-RAY DIFFRACTION98
2.5858-2.66930.4067920.31121663X-RAY DIFFRACTION93
2.6693-2.76470.3523820.30531459X-RAY DIFFRACTION83
2.7647-2.87540.31541530.28772828X-RAY DIFFRACTION99
2.8754-3.00620.32771420.28462859X-RAY DIFFRACTION99
3.0062-3.16470.31741500.2822847X-RAY DIFFRACTION99
3.1647-3.3630.30511530.26542850X-RAY DIFFRACTION99
3.363-3.62260.2911440.24382780X-RAY DIFFRACTION97
3.6226-3.9870.23081680.21752786X-RAY DIFFRACTION97
3.987-4.56370.23771710.1882837X-RAY DIFFRACTION99
4.5637-5.74870.22331430.19312894X-RAY DIFFRACTION99
5.7487-53.8530.20621320.18462912X-RAY DIFFRACTION98

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