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- PDB-6fix: antitoxin GraA in complex with its operator -

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Basic information

Entry
Database: PDB / ID: 6fix
Titleantitoxin GraA in complex with its operator
Components
  • (DNA (30-MER)) x 2
  • XRE family transcriptional regulator
KeywordsANTITOXIN / GraA / HigA / operator / DNA / GraT / HigB
Function / homology
Function and homology information


Toxin-antitoxin system, antidote protein, HigA / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / XRE family transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsTalavera, A. / Loris, R.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Fonds voor Wetenschappelijk Onderzoek VlaanderenG.0135.15N, GOC1213N, G.0090.11N Belgium
Vrije Universiteit BrusselOZR2232 to SH, SPR13 Belgium
BioStruct-X1673, 6131 Belgium
Citation
Journal: Nat Commun / Year: 2019
Title: A dual role in regulation and toxicity for the disordered N-terminus of the toxin GraT.
Authors: Ariel Talavera / Hedvig Tamman / Andres Ainelo / Albert Konijnenberg / San Hadži / Frank Sobott / Abel Garcia-Pino / Rita Hõrak / Remy Loris /
Abstract: Bacterial toxin-antitoxin (TA) modules are tightly regulated to maintain growth in favorable conditions or growth arrest during stress. A typical regulatory strategy involves the antitoxin binding ...Bacterial toxin-antitoxin (TA) modules are tightly regulated to maintain growth in favorable conditions or growth arrest during stress. A typical regulatory strategy involves the antitoxin binding and repressing its own promoter while the toxin often acts as a co-repressor. Here we show that Pseudomonas putida graTA-encoded antitoxin GraA and toxin GraT differ from other TA proteins in the sense that not the antitoxin but the toxin possesses a flexible region. GraA auto-represses the graTA promoter: two GraA dimers bind cooperatively at opposite sides of the operator sequence. Contrary to other TA modules, GraT is a de-repressor of the graTA promoter as its N-terminal disordered segment prevents the binding of the GraTA complex to the operator. Removal of this region restores operator binding and abrogates Gr aT toxicity. GraTA represents a TA module where a flexible region in the toxin rather than in the antitoxin controls operon expression and toxin activity.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Production, biophysical characterization and crystallization of Pseudomonas putida GraA and its complexes with GraT and the graTA operator.
Authors: Talavera, A. / Tamman, H. / Ainelo, A. / Hadaei, S. / Garcia-Pino, A. / Horak, R. / Konijnenberg, A. / Loris, R.
History
DepositionJan 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 2.0Feb 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Polymer sequence / Structure summary
Category: entity / entity_poly ...entity / entity_poly / pdbx_seq_map_depositor_info / struct_asym
Item: _entity.formula_weight / _entity_poly.type ..._entity.formula_weight / _entity_poly.type / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_asym.pdbx_type
Revision 2.1Mar 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.2May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XRE family transcriptional regulator
B: XRE family transcriptional regulator
C: DNA (30-MER)
D: XRE family transcriptional regulator
E: XRE family transcriptional regulator
F: DNA (30-MER)


Theoretical massNumber of molelcules
Total (without water)65,7166
Polymers65,7166
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11950 Å2
ΔGint-107 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.550, 105.550, 149.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
XRE family transcriptional regulator


Mass: 11746.399 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: AYO08_18510 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A179R2V1
#2: DNA chain DNA (30-MER)


Mass: 9512.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida (bacteria)
#3: DNA chain DNA (30-MER)


Mass: 9217.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida (bacteria)

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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: 7.33 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M sodium acetate pH 4.5, 50% PEG 400

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.793→43.853 Å / Num. obs: 18427 / % possible obs: 99.54 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.1271 / Net I/σ(I): 8.84
Reflection shellResolution: 3.793→3.929 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.692 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 1797 / CC1/2: 0.39 / % possible all: 95.69

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→43.853 Å / SU ML: 0.74 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 38.6
RfactorNum. reflection% reflection
Rfree0.2857 920 5 %
Rwork0.246 --
obs0.248 18387 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.8→43.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 1230 0 0 4036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064217
X-RAY DIFFRACTIONf_angle_d1.0765964
X-RAY DIFFRACTIONf_dihedral_angle_d23.4921632
X-RAY DIFFRACTIONf_chiral_restr0.043687
X-RAY DIFFRACTIONf_plane_restr0.006582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8004-4.00060.43031320.382507X-RAY DIFFRACTION100
4.0006-4.25110.35741310.33982494X-RAY DIFFRACTION100
4.2511-4.5790.37761320.30222498X-RAY DIFFRACTION100
4.579-5.03920.34471310.30272496X-RAY DIFFRACTION100
5.0392-5.7670.31641310.28532495X-RAY DIFFRACTION100
5.767-7.26050.29281310.27742470X-RAY DIFFRACTION100
7.2605-43.85580.21061320.16562507X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 119.1349 Å / Origin y: 7.5571 Å / Origin z: -4.1854 Å
111213212223313233
T1.0854 Å20.1932 Å20.0071 Å2-1.0215 Å20.0447 Å2--1.4079 Å2
L0.624 °2-1.5827 °20.3316 °2-1.5789 °2-0.611 °2--0.0816 °2
S-0.1499 Å °-0.1497 Å °-0.3847 Å °0.1871 Å °-0.1503 Å °-0.1412 Å °-0.0107 Å °0.1634 Å °0.1982 Å °
Refinement TLS groupSelection details: all

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