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- PDB-9dlu: Solution structure of Staphylococcus aureus response regulator Ar... -

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Basic information

Entry
Database: PDB / ID: 9dlu
TitleSolution structure of Staphylococcus aureus response regulator ArlR DNA-binding domain
ComponentsResponse regulator ArlR
KeywordsDNA BINDING PROTEIN / Two-component regulatory system ArlRS / Response regulator ArlR
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Response regulator ArlR
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsRafid Feisal, M. / Hwang, P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-04105 Canada
CitationJournal: To Be Published
Title: Structure and dynamics of Staphylococcus aureus response regulator ArlR DNA-binding domain by solution NMR
Authors: Rafid Feisal, M. / Mercier, P. / Mak, K.Y.L. / Liu, P.B. / Wen, Y. / Hwang, P.M.
History
DepositionSep 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator ArlR


Theoretical massNumber of molelcules
Total (without water)12,4211
Polymers12,4211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Confirmed by, Ouyang, Zhenlin, et al. "Deciphering the activation and recognition mechanisms of Staphylococcus aureus response regulator ArlR." Nucleic Acids Research 47.21 ...Evidence: gel filtration, Confirmed by, Ouyang, Zhenlin, et al. "Deciphering the activation and recognition mechanisms of Staphylococcus aureus response regulator ArlR." Nucleic Acids Research 47.21 (2019): 11418-11429., NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Response regulator ArlR


Mass: 12421.122 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: arlR, SAOUHSC_01420 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KJN4
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-15N HSQC
122isotropic22D 1H-15N HSQC
131isotropic22D 1H-13C HSQC
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
161isotropic13D HN(CA)CO
171isotropic13D HNCO
182isotropic23D 1H-15N NOESY
191isotropic23D 1H-13C NOESY
1101isotropic23D C(CO)NH
1113isotropic13D 1H-13C NOESY aromatic
1123isotropic12D 1H-13C HSQC aromatic
1131isotropic23D H-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-13C; U-15N] DNA-binding domain of the Staphylococcus aureus response regulator ArlR, 10 mM imidazole, 300 mM sodium chloride, 0.5 mM [U-2H] d6-DSS, 90% H2O/10% D2O0.5 mM, [U-13C; U-15N] ArlR DNA-binding domain protein, 10 mM Imidazole, pH 6.7 to 6.8, 300 mM NaCl, 5 mM d6-DSSsample_1_13C_15N_labeled90% H2O/10% D2O
solution20.5 mM [U-15N] DNA-binding domain of the Staphylococcus aureus response regulator ArlR, 10 mM imidazole, 300 mM sodium chloride, 0.5 mM [U-2H] d6-DSS, 90% H2O/10% D2O0.5 mM, [U-15N] ArlR DNA-binding domain protein, 10 mM Imidazole, pH 6.7, 300 mM NaCl, 5 mM d6-DSSsample_2_15N_labeled90% H2O/10% D2O
solution30.5 mM [U-30% 13C; U-100% 15N] DNA-binding domain of the Staphylococcus aureus response regulator ArlR, 10 mM imidazole, 100 mM potassium chloride, 0.5 mM [U-2H] d6-DSS, 100% D2O0.4 mM, [U-30% 13C; U-15N] ArlR DNA binding domain protein, in 10 mM imidazole, pH 6.70, 100 mM KCl, 100% D2Osample_3_(30%)13C_15N_labeled100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDNA-binding domain of the Staphylococcus aureus response regulator ArlR[U-13C; U-15N]1
10 mMimidazolenatural abundance1
300 mMsodium chloridenatural abundance1
0.5 mMd6-DSS[U-2H]1
0.5 mMDNA-binding domain of the Staphylococcus aureus response regulator ArlR[U-15N]2
10 mMimidazolenatural abundance2
300 mMsodium chloridenatural abundance2
0.5 mMd6-DSS[U-2H]2
0.5 mMDNA-binding domain of the Staphylococcus aureus response regulator ArlR[U-30% 13C; U-100% 15N]3
10 mMimidazolenatural abundance3
100 mMpotassium chloridenatural abundance3
0.5 mMd6-DSS[U-2H]3
Sample conditionsDetails: pH 6.7 - 6.8, 30 degrees Celsius / Ionic strength: 300 mM / Label: SampleConditions_1 / pH: 6.7 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
NMRViewJohnson, One Moon Scientificpeak picking
ARIALinge, O'Donoghue and Nilgesrefinement
VNMRVariancollection
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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