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- PDB-2kx7: Solution structure of the E.coli RcsD-ABL domain (residues 688-795) -

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Basic information

Entry
Database: PDB / ID: 2kx7
TitleSolution structure of the E.coli RcsD-ABL domain (residues 688-795)
ComponentsSensor-like histidine kinase yojN
KeywordsPROTEIN BINDING / alpha-beta-loop (ABL) domain / phosphotransfer / rcs regulation / RcsD / two-component system
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 sensor kinase activity / phosphorelay signal transduction system / ATP binding / plasma membrane
Similarity search - Function
Phosphotransferase RcsD, RcsD-ABL domain / Phosphotransferase RcsD / Phosphotransferase RcsD, RcsD-ABL domain / Phosphotransferase RcsD, RcsD-ABL domain superfamily / RcsD-ABL domain / Hpt domain / Histidine-containing phosphotransfer (HPt) domain profile. / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Histidine kinase domain ...Phosphotransferase RcsD, RcsD-ABL domain / Phosphotransferase RcsD / Phosphotransferase RcsD, RcsD-ABL domain / Phosphotransferase RcsD, RcsD-ABL domain superfamily / RcsD-ABL 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. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphotransferase RcsD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsRogov, V.V. / Schmoee, K. / Rogova, N.Y. / Loehr, F. / Bernhard, F. / Doetsch, V.
CitationJournal: Structure / Year: 2011
Title: Structural Insights into Rcs Phosphotransfer: The Newly Identified RcsD-ABL Domain Enhances Interaction with the Response Regulator RcsB.
Authors: Schmoe, K. / Rogov, V.V. / Rogova, N.Y. / Lohr, F. / Guntert, P. / Bernhard, F. / Dotsch, V.
History
DepositionApr 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sensor-like histidine kinase yojN


Theoretical massNumber of molelcules
Total (without water)13,1691
Polymers13,1691
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)25 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Sensor-like histidine kinase yojN / Phosphotransfer intermediate yojN


Mass: 13168.624 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2216, JW2204, yojN, yojP, yojQ / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: P39838, histidine kinase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D HNCO
1423D HN(CO)CA
1523D (H)CCH-TOCSY
1613D 1H-15N TOCSY
1713D 1H-15N NOESY
1823D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
133 mM TRIS, 125 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O95% H2O/5% D2O
233 mM TRIS, 125 mM sodium chloride, 1 mM TCEP, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
33 mMTRIS1
125 mMsodium chloride1
1 mMTCEP1
33 mMTRIS2
125 mMsodium chloride2
1 mMTCEP2
Sample conditionsIonic strength: 0.125 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1-2Bruker Biospincollection
TopSpin1-2Bruker Biospinprocessing
TopSpin1-2Bruker Biospindata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Energy minimization in presence of H2O molecules in CNS/Aria
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: 25

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