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- PDB-9ill: monomeric SarA-E89Q in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 9ill
Titlemonomeric SarA-E89Q in complex with DNA
Components
  • DNA
  • Transcriptional regulator SarA
KeywordsDNA BINDING PROTEIN / winged-helix protein / complex structure
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
DNA / DNA (> 10) / Transcriptional regulator SarA
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
synthetic construct (others)
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: Biomol.NMR Assign / Year: 2023
Title: solution Structure of the monomeric SarA in complex with DNA
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
B: DNA
C: DNA


Theoretical massNumber of molelcules
Total (without water)24,8273
Polymers24,8273
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: 13795.796 Da / Num. of mol.: 1 / Mutation: E89Q
Source method: isolated from a genetically manipulated source
Details: truncation of residue 20-124
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: sarA, SA0573 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7A732
#2: DNA chain DNA


Mass: 5515.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestN
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
111isotropic12D 1H-13C HSQC
121isotropic12D 1H-15N HSQC
131isotropic12D 1H-1H NOESY XF
141isotropic23D HN(CO)CA
151isotropic23D CBCA(CO)NH
161isotropic23D HNCA
191isotropic23D CCHCOSY
181isotropic23D CCHTOCSY
171isotropic23D HBHA(CO)NH
1121isotropic23D (H)CCH-COSY
1111isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY
1131isotropic13D 1H-13C NOESY aromatic
1141isotropic13D XFCNOESY

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Sample preparation

DetailsType: solution
Contents: 10 mM sodium phosphate, 10 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_SarAmo in complex with unlabled DNA / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphatenatural abundance1
10 mMNaClnatural abundance1
90 %H2Onatural abundance1
10 %D2O[U-99% 2H]1
0.01 %DSSnatural abundance1
0.01 %sodium azidenatural abundance1
5 %EDTA-free Protease Inhibitor Cocktailnatural abundance1
Sample conditionsIonic strength: 20 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE6002

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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: 2
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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