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- PDB-2jzy: Solution structure of C-terminal effector domain of putative two-... -

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Basic information

Entry
Database: PDB / ID: 2jzy
TitleSolution structure of C-terminal effector domain of putative two-component-system response regulator involved in copper resistance from Klebsiella pneumoniae
ComponentsTranscriptional regulatory protein PcoR
KeywordsTRANSCRIPTION / two-component-system response regulator / effector domain / DNA-binding / Phosphoprotein / Plasmid / Transcription regulation / Two-component regulatory system
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional regulatory protein PcoR, heavy metal response / 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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Transcriptional regulatory protein PcoR, heavy metal response / 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 / 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
Transcriptional regulatory protein PcoR
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics
AuthorsHung, K. / Fang, P. / Chang, C. / Tsai, S. / Huang, T.
CitationJournal: To be Published
Title: Solution structure of C-terminal effector domain of putative two-component-system response regulator involved in copper resistance from Klebsiella pneumoniae
Authors: Hung, K. / Fang, P. / Lin, Y. / Chang, C. / Tsai, S. / Huang, T.
History
DepositionJan 22, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulatory protein PcoR


Theoretical massNumber of molelcules
Total (without water)12,9321
Polymers12,9321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional regulatory protein PcoR


Mass: 12931.965 Da / Num. of mol.: 1 / Fragment: sequence database residues 126-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: pcoR / Production host: Escherichia coli (E. coli) / References: UniProt: Q6U5P9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CO)CA
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D 1H-15N NOESY
1713D HNCO
1813D HCACO
1913D 1H-13C NOESY
11013D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-13C; U-15N] C-terminal domain of TCS response regulator, 20 mM Tris, 150 mM NaCl, 150 mM Glu, 150 mM Arg, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMC-terminal domain of TCS response regulator[U-13C; U-15N]1
20 mMTris1
150 mMNaCl1
150 mMGlu1
150 mMArg1
Sample conditionsIonic strength: 150mM NaCl and 150mM Glu/Arg. / pH: 7.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker DRXBrukerDRX6002

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Processing

NMR softwareName: CYANA / Version: 2.1 / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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