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- PDB-9ilk: monomeric SarA, truncation of residue 20-124 -

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Basic information

Entry
Database: PDB / ID: 9ilk
Titlemonomeric SarA, truncation of residue 20-124
ComponentsTranscriptional regulator SarA
KeywordsDNA BINDING PROTEIN / S.aureus / DNA-binding / winged-helix
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
Transcriptional regulator SarA/Rot / : / Transcriptional regulator SarA/Rot / : / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulator SarA
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsXia, B. / Fu, D.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: To Be Published
Title: Solution Structure of the monomeric DNA-binding domain of SarA
Authors: Xia, B. / Fu, D.H.
History
DepositionJun 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator SarA


Theoretical massNumber of molelcules
Total (without water)13,7971
Polymers13,7971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional regulator SarA / Staphylococcal accessory regulator A


Mass: 13796.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: truncation of residues 20-124 of SarA
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: sarA, SA0573 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7A732
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic22D 1H-15N HSQC
122isotropic22D 1H-13C HSQC
132isotropic23D 1H-15N NOESY
142isotropic23D 1H-13C NOESY aromatic
152isotropic23D 1H-13C NOESY
162isotropic13D CBCA(CO)NH
172isotropic13D HN(CA)CB
182isotropic13D (H)CCH-COSY
192isotropic13D (H)CCH-TOCSY
1102isotropic13D CCH-COSY
1112isotropic13D CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 50 mM sodium phosphate, 50 mM NaCl, 90 % H2O, 10 % [U-99% 2H] D2O, 0.01 % DSS, 0.01 % sodium azide, 5 % EDTA-free Protease Inhibitor Cocktail, 90% H2O/10% D2O
Label: 15N, 13C_monomeric SarA / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphatenatural abundance2
50 mMNaClnatural abundance2
90 %H2Onatural abundance2
10 %D2O[U-99% 2H]2
0.01 %DSSnatural abundance2
0.01 %sodium azidenatural abundance2
5 %EDTA-free Protease Inhibitor Cocktailnatural abundance2
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure calculation
DYANAGuntert, Braun and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificpeak picking
TALOS-NYang Shen, Ad Baxdata analysis
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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