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- PDB-7wj0: Solution structure of N-terminal domain (nMazE6) of mycobacterial... -

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Basic information

Entry
Database: PDB / ID: 7wj0
TitleSolution structure of N-terminal domain (nMazE6) of mycobacterial antitoxin MazE6 from MazEF6 TA system
ComponentsAntitoxin MazE6
KeywordsANTITOXIN / RHH domain / mycobacterial TA system / MazEF6 / DNA binding domain
Function / homology
Function and homology information


detoxification / toxin sequestering activity / negative regulation of growth / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / Arc-type ribbon-helix-helix / Ribbon-helix-helix
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsKumari, K. / Sarma, S.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: Commun Biol / Year: 2022
Title: Structural and mutational analysis of MazE6-operator DNA complex provide insights into autoregulation of toxin-antitoxin systems.
Authors: Kumari, K. / Sarma, S.P.
History
DepositionJan 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antitoxin MazE6
B: Antitoxin MazE6


Theoretical massNumber of molelcules
Total (without water)11,6852
Polymers11,6852
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2820 Å2
ΔGint-20 kcal/mol
Surface area7240 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Antitoxin MazE6


Mass: 5842.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: mazE6, mazE-mt3, Rv1991A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WJ87

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
123isotropic13D HN(CA)CB
133isotropic13D CC(CO)NH
143isotropic13D HNCO
153isotropic13D HN(CA)CO
163isotropic13D H(CCO)NH
171isotropic12D 1H-1H TOCSY
191isotropic12D 1H-1H NOESY
183isotropic113C, 15N simultaneous edited NOESY
1103isotropic13D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM NA nMazE6, 20 mM NA potassium phosphate, 20 mM NA Sodium chloride, 1 mM NA EDTA, 0.01 % NA Sodium Azide, 0.2 mM NA DSS, 10 % [U-99% 2H] D2O, 90% H2O/10% D2OUnlabeled-nMazE690% H2O/10% D2O
solution20.4 mM [U-99% 15N] nMazE6, 20 mM NA potassium phosphate, 20 mM NA Sodium chloride, 1 mM NA EDTA, 0.01 % NA Sodium Azide, 0.2 mM NA DSS, 10 % [U-99% 2H] D2O, 90% H2O/10% D2O15N-nMazE690% H2O/10% D2O
solution30.4 mM [U-99% 13C; U-99% 15N] nMazE6, 20 mM NA potassium phosphate, 20 mM NA Sodium chloride, 1 mM NA EDTA, 0.01 % NA Sodium Azide, 0.2 mM NA DSS, 10 % [U-99% 2H] D2O, 90% H2O/10% D2O13C,15N-nMazE690% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMnMazE6NA1
20 mMpotassium phosphateNA1
20 mMSodium chlorideNA1
1 mMEDTANA1
0.01 %Sodium AzideNA1
0.2 mMDSSNA1
10 %D2O[U-99% 2H]1
0.4 mMnMazE6[U-99% 15N]2
20 mMpotassium phosphateNA2
20 mMSodium chlorideNA2
1 mMEDTANA2
0.01 %Sodium AzideNA2
0.2 mMDSSNA2
10 %D2O[U-99% 2H]2
0.4 mMnMazE6[U-99% 13C; U-99% 15N]3
20 mMpotassium phosphateNA3
20 mMSodium chlorideNA3
1 mMEDTANA3
0.01 %Sodium AzideNA3
0.2 mMDSSNA3
10 %D2O[U-99% 2H]3
Sample conditionsIonic strength: 100 mM / Label: Condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent Agilent DDS2 600 / Manufacturer: Agilent / Model: Agilent DDS2 600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ4.2Agilentcollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNpeak picking
X-PLOR NIH3.1Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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