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- PDB-2k4j: ArsR DNA Binding Domain -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2k4j
TitleArsR DNA Binding Domain
ComponentsPutative TRANSCRIPTIONAL REGULATORTranscriptional regulation
KeywordsTRANSCRIPTION / Response regulator / Helicobacter pylori / acid resistance / DNA-binding / Phosphoprotein / Transcription regulation
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / 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 profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / 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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative TRANSCRIPTIONAL REGULATOR
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
AuthorsGupta, S.S. / Cover, T.L. / Krezel, A.M.
CitationJournal: To be Published
Title: ArsR DNA Binding Domain
Authors: Gupta, S.S. / Cover, T.L. / Krezel, A.M.
History
DepositionJun 11, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative TRANSCRIPTIONAL REGULATOR


Theoretical massNumber of molelcules
Total (without water)13,3031
Polymers13,3031
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Putative TRANSCRIPTIONAL REGULATOR / Transcriptional regulation


Mass: 13303.024 Da / Num. of mol.: 1 / Fragment: DNA binding domain, UNP residue 123-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Species: pylori / Strain: J99 / Gene: jhp_0152 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZMR6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D CBCANH
1413D HCC-TOCSY
1513D HHC-TOCSY
1613D H(CC)(CO)NH
1713D HCC(CO)NH
1813D HBHA(CO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] entity, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: entity / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.56 / pH: 7.6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CSI2Wishart, DS and Sykes, BDdata analysis
MOLMOL2K.2Koradi, Billeter and Wuthrichstructure visualization
ProcheckNMR3.5.4Laskowski and MacArthurdata analysis
Procheck3.5.4Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
TopSpin2Bruker Biospinprocessing
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddardpeak picking
Sparky3.114Goddardprocessing
Insight IIv2005.03Accelrys Software Inc.data analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
Details: CYANA based refinement, energy minimization with AMBER program
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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