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- PDB-1irz: Solution structure of ARR10-B belonging to the GARP family of pla... -

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Basic information

Entry
Database: PDB / ID: 1irz
TitleSolution structure of ARR10-B belonging to the GARP family of plant Myb-related DNA binding motifs of the Arabidopsis response regulators
ComponentsARR10-B
KeywordsDNA BINDING PROTEIN / Helix-turn-Helix
Function / homology
Function and homology information


cellular response to cytokinin stimulus / regulation of cytokinin-activated signaling pathway / regulation of seed growth / regulation of anthocyanin metabolic process / primary root development / maintenance of shoot apical meristem identity / regulation of root meristem growth / shoot system development / response to cytokinin / regulation of chlorophyll biosynthetic process ...cellular response to cytokinin stimulus / regulation of cytokinin-activated signaling pathway / regulation of seed growth / regulation of anthocyanin metabolic process / primary root development / maintenance of shoot apical meristem identity / regulation of root meristem growth / shoot system development / response to cytokinin / regulation of chlorophyll biosynthetic process / cytokinin-activated signaling pathway / root development / response to water deprivation / phosphorelay response regulator activity / DNA-binding transcription factor activity / DNA binding / nucleus
Similarity search - Function
Response regulator B-type, plant / Myb domain, plants / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT/Myb domain / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...Response regulator B-type, plant / Myb domain, plants / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT/Myb domain / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Two-component response regulator ARR10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsYamazaki, T. / Katoh, E. / Hosoda, K. / Mizuno, T.
CitationJournal: PLANT CELL / Year: 2003
Title: Molecular structure of the GARP family of plant Myb-related DNA binding motifs of the Arabidopsis response regulators
Authors: Hosoda, K. / Imamura, A. / Katoh, E. / Hatta, T. / Tachiki, M. / Yamada, H. / Mizuno, T. / Yamazaki, T.
History
DepositionOct 25, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2003Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: 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: ARR10-B


Theoretical massNumber of molelcules
Total (without water)7,3851
Polymers7,3851
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)15 / 50structures with lowest energies
Representative

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Components

#1: Protein ARR10-B / receiver-like protein 4 / ARP4


Mass: 7384.758 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O49397

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1224D 13C-separated NOESY
132(H)CCH-TOCSY
141CBCA(CO)NH
151HNCO
161HNCA
NMR detailsText: The structure was determined by multidimensional heteronuclear NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM ARR10-B[U-15N,13C]; 50mM sodium phosphate buffer 500mM NaCl90% H2O/10% D2O
21mM ARR10-B[U-15N,13C]; 50mM sodium phosphate buffer 500mM NaCl100% D2O
Sample conditionsIonic strength: 500mM NaCl / pH: 6.9 / Pressure: ambient / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8Frank Delaglioprocessing
X-PLOR3.1Brungerrefinement
PIPP/CAPP/STAPP4.3.2Dan Garrettdata analysis
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with lowest energies
Conformers calculated total number: 50 / Conformers submitted total number: 15

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