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- PDB-2kz8: Solution NMR structure of MqsA, a protein from E. coli, containin... -

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Basic information

Entry
Database: PDB / ID: 2kz8
TitleSolution NMR structure of MqsA, a protein from E. coli, containing a Zinc finger, N-terminal and a Helix Turn-Helix C-terminal domain
ComponentsUncharacterized HTH-type transcriptional regulator ygiT
KeywordsTRANSCRIPTION / Zinc finger / Helix turn helix / YgiT / MqsA
Function / homology
Function and homology information


toxin-antitoxin complex / single-species biofilm formation / sequence-specific DNA binding / regulation of DNA-templated transcription / protein homodimerization activity / metal ion binding
Similarity search - Function
Antitoxin MqsA / Zinc finger, MqsA-type / Antitoxin MqsA/HigA-2 / Antitoxin component of bacterial toxin-antitoxin system, MqsA / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsPapadopoulos, E. / Vlamis-Gardikas, A. / Graslund, A. / Billeter, M. / Holmgren, A. / Collet, J.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: Solution structure and biophysical properties of MqsA, a Zn-containing antitoxin from Escherichia coli
Authors: Papadopoulos, E. / Collet, J.F. / Vukojevic, V. / Billeter, M. / Holmgren, A. / Graslund, A. / Vlamis-Gardikas, A.
History
DepositionJun 14, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2012Group: Structure summary
Revision 1.3Jul 25, 2012Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized HTH-type transcriptional regulator ygiT


Theoretical massNumber of molelcules
Total (without water)14,7281
Polymers14,7281
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)20 / 100structures with acceptable covalent geometry
RepresentativeModel #1fewest violations

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Components

#1: Protein Uncharacterized HTH-type transcriptional regulator ygiT


Mass: 14728.140 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ygiT, b3021, JW2989 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46864

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCA
1313D HN(CA)CB
1413D HNCO
1513D CBCA(CO)NH
1613D HBHA(CO)NH
1713D C(CO)NH
1813D H(CCO)NH

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Sample preparation

DetailsContents: 1mM [U-100% 13C; U-100% 15N] Ygit, 95% H2O/5% D2O / Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: Ygit / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 25 / pH: 5 / Pressure: 0.7 atm / Temperature: 37 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
CYANA3.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 3 7 CYCLES OF CYANA - CANDID. A) KEEPING MANUAL ASSIGNEMENTS B) ALLOWING MANUAL ASSIGNEMENTS TO VARIATE C) ADDING EXTRA CSVALUES FROM STATISTICAL TABLES. IF THE N-TERMINUS DOMAIN IS ALIGNED ...Details: 3 7 CYCLES OF CYANA - CANDID. A) KEEPING MANUAL ASSIGNEMENTS B) ALLOWING MANUAL ASSIGNEMENTS TO VARIATE C) ADDING EXTRA CSVALUES FROM STATISTICAL TABLES. IF THE N-TERMINUS DOMAIN IS ALIGNED IT LOOKS STRUCTURED AND THE C-TERMINUS ROTATES. THE TWO ALIGNMENTS GIVE A SOMEHOW DIFFERENT IMPRESSION ABOUT THE PROTEIN AND VERIFY THAT EACH DOMAIN IS INDIVIDUALLY STRUCTURED. THERE ARE TWO B-SHEETS ONE WITH 4 STRANDS AND ONE WITH TWO LONG STRANDS. THE 4 STRANDS MIGHT BELONG TO THE SAME SHEET OR THEY MAY BE TWO TIMES TWO STRANDS OR A SMALL B-BARREL. THEY BIND AND THEY ARE STABILIZED BY ZN.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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