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- PDB-2rnj: NMR Structure of The S. Aureus VraR DNA Binding Domain -

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Basic information

Entry
Database: PDB / ID: 2rnj
TitleNMR Structure of The S. Aureus VraR DNA Binding Domain
ComponentsResponse regulator protein vraR
KeywordsTRANSCRIPTION / HTH LUXR-TYPE DOMAIN / DNA BINDING DOMAIN / Activator / Antibiotic resistance / Cytoplasm / DNA-binding / Phosphoprotein / PHOSPHORYLATION / Transcription regulation / Two-component regulatory system
Function / homology
Function and homology information


phosphorelay signal transduction system / response to antibiotic / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / 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. ...LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / 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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Response regulator protein VraR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing, additional refinement
AuthorsDonaldson, L.W.
CitationJournal: Biochemistry / Year: 2008
Title: The NMR Structure of the Staphylococcus aureus Response Regulator VraR DNA Binding Domain Reveals a Dynamic Relationship between It and Its Associated Receiver Domain
Authors: Donaldson, L.W.
History
DepositionJan 9, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator protein vraR


Theoretical massNumber of molelcules
Total (without water)10,3831
Polymers10,3831
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 25structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Response regulator protein vraR


Mass: 10382.875 Da / Num. of mol.: 1 / Fragment: HTH LUXR-TYPE DOMAIN, UNP residues 138-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Description: cloned as NdeI/BamHI fragment / Gene: vraR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21:DE3 / References: UniProt: Q7A2Q1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D (H)CCH-TOCSY
11113D 1H-13C NOESY
11212D (HB)CB(CGCD)HD
11312D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsContents: 10mM sodium phosphate; 750mM sodium chloride; 0.05% sodium azide; 0.3mM [U-98% 13C; U-98% 15N] protein sample; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphate1
750 mMsodium chloride1
0.05 %sodium azide1
0.3 mMprotein sample[U-98% 13C; U-98% 15N]1
Sample conditionsIonic strength: 0.5 / pH: 7.8 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian NMRS / Manufacturer: Varian / Model: NMRS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PISTACHIOEghbalnia, Bahrami, Wang, Assadi and Markleychemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing, additional refinement / Software ordinal: 1
Details: THE STRUCTURE WAS DETERMINED FROM A COMBINATION OF NOE DISTANCE RESTRAINTS AND BACKBONE DIHEDRAL ANGLE RESTRAINTS. Final refinement was performed in explicit solvent
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 10

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