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- PDB-8iex: Solution structure of AtWRKY11-DBD -

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Basic information

Entry
Database: PDB / ID: 8iex
TitleSolution structure of AtWRKY11-DBD
ComponentsProbable WRKY transcription factor 11
KeywordsDNA BINDING PROTEIN / transcriptional factor
Function / homology
Function and homology information


regulation of jasmonic acid mediated signaling pathway / induced systemic resistance / response to bacterium / calmodulin binding / transcription cis-regulatory region binding / defense response to bacterium / DNA-binding transcription factor activity / nucleus
Similarity search - Function
Zn-cluster domain / Plant zinc cluster domain / WRKY transcription factor, plant / WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain
Similarity search - Domain/homology
Probable WRKY transcription factor 11
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
AuthorsDong, X. / Hu, Y.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)21991083 China
CitationJournal: To Be Published
Title: Solution structure of AtWRKY11-DBD
Authors: Hu, Y.F. / Dong, X.
History
DepositionFeb 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable WRKY transcription factor 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0902
Polymers11,0251
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 216structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Probable WRKY transcription factor 11 / WRKY DNA-binding protein 11


Mass: 11024.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WRKY11, At4g31550, F3L17.120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SV15
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

DetailsType: solution
Contents: 30 mM MES, 150 mM sodium chloride, 20 uM ZnSO4, 90% H2O/10% D2O
Label: double label / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
30 mMMESnatural abundance1
150 mMsodium chloridenatural abundance1
20 uMZnSO4natural abundance1
Sample conditionsIonic strength: 150 mM / Label: condition-1 / pH: 6 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 216 / Conformers submitted total number: 20

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