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- PDB-1sr2: Solution structure of the Escherichia coli YojN Histidine-Phospho... -

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Basic information

Entry
Database: PDB / ID: 1sr2
TitleSolution structure of the Escherichia coli YojN Histidine-Phosphotransferase (HPt) domain
ComponentsPutative sensor-like histidine kinase yojN
KeywordsTRANSFERASE / Four-helical bundle
Function / homology
Function and homology information


phosphotransferase activity, carboxyl group as acceptor / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a carboxy group as acceptor / histidine phosphotransfer kinase activity / phosphorelay signal transduction system / phosphorelay sensor kinase activity / ATP binding / plasma membrane
Similarity search - Function
Phosphotransferase RcsD / Phosphotransferase RcsD, RcsD-ABL domain / Phosphotransferase RcsD, RcsD-ABL domain superfamily / RcsD-ABL domain / HPT domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Histidine kinase domain ...Phosphotransferase RcsD / Phosphotransferase RcsD, RcsD-ABL domain / Phosphotransferase RcsD, RcsD-ABL domain superfamily / RcsD-ABL domain / HPT domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphotransferase RcsD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / Energy minimization
AuthorsRogov, V.V. / Bernhard, F. / Loehr, F. / Doetsch, V.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Solution Structure of the Escherichia coli YojN Histidine-phosphotransferase Domain and its Interaction with Cognate Phosphoryl Receiver Domains
Authors: Rogov, V.V. / Bernhard, F. / Loehr, F. / Doetsch, V.
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 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: Putative sensor-like histidine kinase yojN


Theoretical massNumber of molelcules
Total (without water)12,8491
Polymers12,8491
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)25 / 50structures with the lowest energy
Representative

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Components

#1: Protein Putative sensor-like histidine kinase yojN


Mass: 12848.516 Da / Num. of mol.: 1 / Fragment: C-terminal domain (residues 775-890)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: XL1 Blue / Gene: YOJN, B2216 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: P39838, 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
1113D 15N-separated NOESY
1223D 13C-separated NOESY
NMR detailsText: The 3D_13C-Separated_NOESY was recorded in three modifications

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM YojN-HPt U-15N, 15 mM Bis-Tris, 15 mM NaCl, 95% H2O, 5% D2O95% H2O/5% D2O
21 mM YojN-HPt U-15N,13C, 15 mM Bis-Tris, 15 mM NaCl, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 15 mM Bis-Tris, 15 mM NaCl / pH: 7 / Pressure: 1 atm / Temperature: 295 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionClassification
XwinNMR2.6collection
XwinNMR2.6processing
AURELIA2.7.5data analysis
DYANA1.5structure solution
CNS1.1refinement
RefinementMethod: Energy minimization / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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