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- PDB-7wnr: Data-driven HADDOCK model of mycobacterial nMazE6-operator DNA complex -

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Basic information

Entry
Database: PDB / ID: 7wnr
TitleData-driven HADDOCK model of mycobacterial nMazE6-operator DNA complex
Components
  • Antitoxin MazE6
  • DNA (5'-D(P*CP*CP*GP*GP*TP*TP*AP*TP*AP*CP*TP*AP*TP*CP*TP*GP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*CP*AP*GP*AP*TP*AP*GP*TP*AP*TP*AP*AP*CP*CP*GP*G)-3')
KeywordsANTITOXIN/DNA / HADDOCK model / mycobacterial TA system / MazEF6 / MazE6-DNA complex / ANTITOXIN / ANTITOXIN-DNA complex
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
DNA / DNA (> 10) / Antitoxin MazE6
Similarity search - Component
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 19, 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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(P*CP*CP*GP*GP*TP*TP*AP*TP*AP*CP*TP*AP*TP*CP*TP*GP*TP*A)-3')
D: DNA (5'-D(P*TP*AP*CP*AP*GP*AP*TP*AP*GP*TP*AP*TP*AP*AP*CP*CP*GP*G)-3')
B: Antitoxin MazE6
C: Antitoxin MazE6


Theoretical massNumber of molelcules
Total (without water)22,7154
Polymers22,7154
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6560 Å2
ΔGint-40 kcal/mol
Surface area11750 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 200structures with favorable non-bond energy
RepresentativeModel #1fewest violations

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Components

#1: DNA chain DNA (5'-D(P*CP*CP*GP*GP*TP*TP*AP*TP*AP*CP*TP*AP*TP*CP*TP*GP*TP*A)-3')


Mass: 5481.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Production host: chemical production metagenome (others)
#2: DNA chain DNA (5'-D(P*TP*AP*CP*AP*GP*AP*TP*AP*GP*TP*AP*TP*AP*AP*CP*CP*GP*G)-3')


Mass: 5548.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Production host: chemical production metagenome (others)
#3: 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
181isotropic12D 1H-1H NOESY
193isotropic113C, 15N simultaneousEdited 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
X-PLOR NIH3.1Schwieters, Kuszewski, Tjandra and Clorerefinement
HADDOCKBonvinstructure calculation
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 200 / Conformers submitted total number: 4

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