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- PDB-2mru: Structure of truncated EcMazE-DNA complex -

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Basic information

Entry
Database: PDB / ID: 2mru
TitleStructure of truncated EcMazE-DNA complex
Components
  • Antitoxin MazE
  • DNA (5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / MazE / antitoxin / DNA-binding domain / protein-DNA complex / transcription / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


toxin sequestering activity / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / double-stranded DNA binding / protein-containing complex binding / regulation of DNA-templated transcription / protein homodimerization activity / protein-containing complex / DNA binding
Similarity search - Function
: / SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Antitoxin MazE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsZorzini, V. / Buts, L. / Loris, R. / van Nuland, N.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Escherichia coli antitoxin MazE as transcription factor: insights into MazE-DNA binding.
Authors: Zorzini, V. / Buts, L. / Schrank, E. / Sterckx, Y.G. / Respondek, M. / Engelberg-Kulka, H. / Loris, R. / Zangger, K. / van Nuland, N.A.
History
DepositionJul 15, 2014Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 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 MazE
B: Antitoxin MazE
X: DNA (5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3')
Y: DNA (5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)24,5284
Polymers24,5284
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)7 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Antitoxin MazE


Mass: 7675.703 Da / Num. of mol.: 2 / Fragment: DNA-binding domain (UNP RESIDUES 2-50)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b2783, BN896_2518, chpAI, chpR, JW2754, mazE / Production host: Escherichia coli (E. coli) / References: UniProt: P0AE72
#2: DNA chain DNA (5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3')


Mass: 4624.020 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3')


Mass: 4552.986 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.33-0.4 mM [U-99% 13C; U-99% 15N] entity_1-1, 0-0.4 mM DNA (5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3')-2, 0-0.4 mM DNA (5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3')- ...Contents: 0.33-0.4 mM [U-99% 13C; U-99% 15N] entity_1-1, 0-0.4 mM DNA (5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3')-2, 0-0.4 mM DNA (5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3')-3, 50 mM potassium phosphate-4, 50 mM sodium chloride-5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-99% 13C; U-99% 15N]0.33-0.41
mMDNA (5'-D(*CP*GP*TP*GP*AP*TP*AP*TP*AP*TP*AP*GP*TP*GP*C)-3')-20-0.41
mMDNA (5'-D(P*GP*CP*AP*CP*TP*AP*TP*AP*TP*AP*TP*CP*AP*CP*G)-3')-30-0.41
50 mMpotassium phosphate-41
50 mMsodium chloride-51
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CcpNMRCCPNdata analysis
HADDOCKAlexandre Bonvinstructure solution
HADDOCKAlexandre Bonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Haddock runs under CNS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 7 / Representative conformer: 1

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