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- PDB-8c7k: YdaS from E. coli O157:H7 cryptic prophage CP-933P -

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Basic information

Entry
Database: PDB / ID: 8c7k
TitleYdaS from E. coli O157:H7 cryptic prophage CP-933P
ComponentsPhage antirepressor protein Cro
KeywordsDNA BINDING PROTEIN / Cro repressor / Helix-Turn-helix / Prophage
Function / homologyBacterial antitoxin YdaS / Bacterial toxin YdaS / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Phage antirepressor protein Cro
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodSOLUTION NMR / simulated annealing / torsion angle dynamics
AuthorsProlic-Kalinsek, M. / Volkov, A.N. / Loris, R.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G.0033.20N Belgium
Research Foundation - Flanders (FWO)G.0226.17N Belgium
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7.
Authors: Prolic-Kalinsek, M. / Volkov, A.N. / Hadzi, S. / Van Dyck, J. / Bervoets, I. / Charlier, D. / Loris, R.
#1: Journal: Biomolecular NMR Assignments / Year: 2020
Title: 1H, 13C, and 15N backbone and side chain chemical shift assignment of YdaS, a monomeric member of the HigA family
Authors: Prolic-Kalinsek, M. / De Bruyn, P. / Jurenas, D. / Van Melderen, L. / Loris, R. / Volkov, A.
History
DepositionJan 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 antirepressor protein Cro


Theoretical massNumber of molelcules
Total (without water)11,9221
Polymers11,9221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
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 antirepressor protein Cro


Mass: 11922.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ECs_2278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8XAD7

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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
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: 1 mM [U-100% 13C; U-100% 15N] YdaS, 20 mM sodium phosphate, 150 mM sodium chloride, 10 % [U-100% 2H] D2O, 90% H2O/10% D2O
Label: sample 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMYdaS[U-100% 13C; U-100% 15N]1
20 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
10 %D2O[U-100% 2H]1
Sample conditionsIonic strength: 165 mM / Label: condition 1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
MddNMROrekhov et al.processing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNdata analysis
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinal
simulated annealing8
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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