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- PDB-7nkv: PaaR2 regulator N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 7nkv
TitlePaaR2 regulator N-terminal domain
ComponentsPhage repressor protein CI
KeywordsDNA BINDING PROTEIN / cryptic prophage CP933-P / CI repressor / toxin-antitoxin
Function / homologyPhage repressor protein CI
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsProlic-Kalinsek, M. / Loris, R. / Volkov, A.N.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G003320N Belgium
Research Foundation - Flanders (FWO)G.0226.17N Belgium
CitationJournal: To Be Published
Title: Regulation of the Escherichia coli paaR2-paaA2-ParD2 toxin-antitoxin system
Authors: Prolic-Kalinsek, M. / De Bruyn, P. / Volkov, A.N. / Charlier, D. / Loris, R.
History
DepositionFeb 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 19, 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: Phage repressor protein CI


Theoretical massNumber of molelcules
Total (without water)8,7851
Polymers8,7851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4940 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Phage repressor protein CI


Mass: 8784.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ECs_2279 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8XAD6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D HN(COCA)CB
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D HBHA(CO)NH
171isotropic13D (H)CCH-TOCSY
181isotropic13D (H)CCH-TOCSY
191isotropic12D 1H-13C HSQC aliphatic
1101isotropic12D 1H-13C HSQC aromatic
1111isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic
1141isotropic12D (HB)CB(CGCD)HD
1151isotropic12D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsType: solution
Contents: 20 mM sodium phosphate, 50 mM sodium chloride, 10 % v/v [U-100% 2H] D2O, 1 mM [U-100% 13C; U-100% 15N] PaaR2, 90% H2O/10% D2O
Label: sample1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
10 % v/vD2O[U-100% 2H]1
1 mMPaaR2[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 65 mM / Label: condition1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
qMDDOrekhov, Vprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
CcpNmr AnalysisCCPNpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinal
simulated annealing9
torsion angle dynamics10
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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