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- PDB-1wj2: Solution Structure of the C-terminal WRKY Domain of AtWRKY4 -

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Basic information

Entry
Database: PDB / ID: 1wj2
TitleSolution Structure of the C-terminal WRKY Domain of AtWRKY4
ComponentsProbable WRKY transcription factor 4
KeywordsDNA BINDING PROTEIN / DNA-BINDING DOMAIN / ZINC-BINDING / STRUCTURAL GENOMICS / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of defense response to fungus / negative regulation of defense response to bacterium / response to ethylene / response to salicylic acid / response to jasmonic acid / defense response / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA binding ...regulation of defense response to fungus / negative regulation of defense response to bacterium / response to ethylene / response to salicylic acid / response to jasmonic acid / defense response / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA binding / nucleus / metal ion binding
Similarity search - Function
WRKY domain / WRKY transcription factor, plant / WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain / N-terminal domain of TfIIb / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Probable WRKY transcription factor 4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodSOLUTION NMR / simulated annealing
AuthorsYamasaki, K. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Plant Cell / Year: 2005
Title: Solution structure of an Arabidopsis WRKY DNA binding domain.
Authors: Yamasaki, K. / Kigawa, T. / Inoue, M. / Tateno, M. / Yamasaki, T. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Tomo, Y. / Hayami, N. / Terada, T. / Shirouzu, M. / Tanaka, A. / Seki, M. ...Authors: Yamasaki, K. / Kigawa, T. / Inoue, M. / Tateno, M. / Yamasaki, T. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Tomo, Y. / Hayami, N. / Terada, T. / Shirouzu, M. / Tanaka, A. / Seki, M. / Shinozaki, K. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 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: Probable WRKY transcription factor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6532
Polymers8,5881
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #15lowest energy

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Components

#1: Protein Probable WRKY transcription factor 4 / WRKY DNA-binding protein 4 / WRKY4


Mass: 8587.530 Da / Num. of mol.: 1 / Fragment: C-terminal WRKY domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: Cell-free synthesis / Gene: WRKY4 / Plasmid: pCR2.1 / References: UniProt: Q9XI90
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
151DQF-COSY
161HMQC-J

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Sample preparation

DetailsContents: 1mM WRKY domain; 20mM KPi; 300mM KCl; 0.02mM ZNCL2; 1mM DTT
Solvent system: 95% H2O; 10% D2O
Sample conditionsIonic strength: 0.3M / pH: 6 / Pressure: 1 atm / Temperature: 298 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000MSIdata analysis
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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