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- PDB-1fr0: SOLUTION STRUCTURE OF THE HISTIDINE-CONTAINING PHOSPHOTRANSFER DO... -

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Basic information

Entry
Database: PDB / ID: 1fr0
TitleSOLUTION STRUCTURE OF THE HISTIDINE-CONTAINING PHOSPHOTRANSFER DOMAIN OF ANAEROBIC SENSOR KINASE ARCB FROM ESCHERICHIA COLI.
ComponentsARCB
KeywordsTRANSFERASE / four-helix bundle motif / anaerobic sensor kinase
Function / homology
Function and homology information


peptidyl-histidine phosphorylation / plasma membrane => GO:0005886 / response to oxygen levels / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / protein autophosphorylation / regulation of DNA-templated transcription / signal transduction / ATP binding ...peptidyl-histidine phosphorylation / plasma membrane => GO:0005886 / response to oxygen levels / histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / protein autophosphorylation / regulation of DNA-templated transcription / signal transduction / ATP binding / plasma membrane / cytosol
Similarity search - Function
Signal transduction histidine kinase, hybrid-type, aerobic respiration control ArcB / Aerobic respiration control sensor protein ArcB, transmembrane domain superfamily / Histidine kinase receptor ArcB, transmembrane domain / Histidine kinase receptor ArcB trans-membrane domain / : / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain ...Signal transduction histidine kinase, hybrid-type, aerobic respiration control ArcB / Aerobic respiration control sensor protein ArcB, transmembrane domain superfamily / Histidine kinase receptor ArcB, transmembrane domain / Histidine kinase receptor ArcB trans-membrane domain / : / HPT domain / Histidine Phosphotransfer domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / PAS fold / PAS fold / PAS domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Aerobic respiration control sensor protein ArcB / Aerobic respiration control sensor protein ArcB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsIkegami, T. / Okada, T. / Ohki, I. / Hirayama, J. / Mizuno, T. / Shirakawa, M.
CitationJournal: Biochemistry / Year: 2001
Title: Solution structure and dynamic character of the histidine-containing phosphotransfer domain of anaerobic sensor kinase ArcB from Escherichia coli.
Authors: Ikegami, T. / Okada, T. / Ohki, I. / Hirayama, J. / Mizuno, T. / Shirakawa, M.
History
DepositionSep 7, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 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: ARCB


Theoretical massNumber of molelcules
Total (without water)14,0141
Polymers14,0141
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)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ARCB


Mass: 14013.939 Da / Num. of mol.: 1
Fragment: THE HISTIDINE-CONTAINING PHOSPHOTRANSFER (HPT) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PSU2DH / Production host: Escherichia coli (E. coli)
References: UniProt: P22763, UniProt: P0AEC3*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D NOESY
1223D 13C-separated NOESY
1313D 15N-separated NOESY
1424D 13C-separated NOESY
151HMQC-J
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM HPtArcB, 50mM KH2PO4-K2HPO4 (pH6.5 at 37deg), 50mM KCl, and 1mM dithiothreitol (DTT) in 90% H2O/10% D2O90% H2O/10% D2O
21.5mM HPtArcB, 50mM KH2PO4-K2HPO4 (pH6.5 at 37deg), 50mM KCl, and 1mM dithiothreitol (DTT) in 99.8% D2O99.8% D2O
Sample conditionsIonic strength: 100mM / pH: 6.5 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851Bruengerrefinement
DYANA1.5Guentertstructure solution
XwinNMR2Brukercollection
NMRPipe1.7Delaglioprocessing
nmrPipp4.2.4Garrettdata analysis
MOLMOL2.3Koradidata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1348 restraints, 1188 are NOE-derived distance constraints, 83 dihedral angle restraints,77 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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