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- PDB-9uro: Response regulator RR468 binding with Mg2+ -

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Basic information

Entry
Database: PDB / ID: 9uro
TitleResponse regulator RR468 binding with Mg2+
ComponentsResponse regulator
KeywordsSIGNALING PROTEIN / Bacterial response regulator / Two-component system
Function / homology
Function and homology information


phosphorelay response regulator activity / phosphorelay signal transduction system / DNA binding / metal ion binding
Similarity search - Function
: / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsLiu, X.H. / Liu, Y.X. / Chen, J.W. / Jiang, L.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB0540000 China
National Natural Science Foundation of China (NSFC)22277123 China
National Natural Science Foundation of China (NSFC)22374156 China
CitationJournal: To Be Published
Title: Response regulator RR468 binding with Mg2+
Authors: Liu, X.H. / Liu, Y.X. / Chen, J.W. / Jiang, L.
History
DepositionApr 30, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8732
Polymers13,8481
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein Response regulator


Mass: 13848.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Gene: TM_0468
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9WYT9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D (H)CCH-TOCSY
141isotropic23D CBCA(CO)NH
151isotropic23D HN(CA)CB
161isotropic23D HNCA
171isotropic23D 1H-13C NOESY aliphatic
181isotropic23D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-100% 13C; U-100% 15N] RR468, 20 mM HEPES, 10 mM magnesium chloride, 50 mM potassium chloride, 90% H2O/10% D2O
Details: 20 mM HEPES, 10 mM MgCl2, 50 mM KCl / Label: 13C_15N_labeled / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMRR468[U-100% 13C; U-100% 15N]1
20 mMHEPESnatural abundance1
10 mMmagnesium chloridenatural abundance1
50 mMpotassium chloridenatural abundance1
Sample conditionsIonic strength: 120 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.9/v10 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
NMR software
NameDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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