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- PDB-6j4g: Crystal structure of the AtWRKY33 domain -

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Basic information

Entry
Database: PDB / ID: 6j4g
TitleCrystal structure of the AtWRKY33 domain
Components
  • DNA (5'-D(*AP*GP*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*G)-3')
  • DNA (5'-D(*TP*CP*GP*CP*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*C)-3')
  • Probable WRKY transcription factor 33
KeywordsDNA BINDING PROTEIN / WRKY transcription factors N-terminal WRKY domain
Function / homology
Function and homology information


camalexin biosynthetic process / response to chitin / systemic acquired resistance / cellular heat acclimation / response to water deprivation / response to osmotic stress / defense response to fungus / positive regulation of autophagy / response to salt stress / response to cold ...camalexin biosynthetic process / response to chitin / systemic acquired resistance / cellular heat acclimation / response to water deprivation / response to osmotic stress / defense response to fungus / positive regulation of autophagy / response to salt stress / response to cold / cellular response to heat / response to heat / transcription cis-regulatory region binding / defense response to bacterium / DNA-binding transcription factor activity / nucleus / metal ion binding
Similarity search - Function
WRKY domain / 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
DNA / DNA (> 10) / Probable WRKY transcription factor 33
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsXu, Y.P. / Xu, H. / Wang, B. / Su, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670740 China
CitationJournal: To Be Published
Title: Crystal structure of the N-terminal DNA binding domain of AtWRKY33
Authors: Xu, Y.P. / Xu, H. / Wang, B. / Su, X.D.
History
DepositionJan 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Probable WRKY transcription factor 33
C: DNA (5'-D(*AP*GP*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*G)-3')
D: DNA (5'-D(*TP*CP*GP*CP*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1504
Polymers18,0853
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-23 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.900, 97.900, 94.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Probable WRKY transcription factor 33 / WRKY DNA-binding protein 33


Mass: 8905.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WRKY33, At2g38470, T19C21.4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8S8P5
#2: DNA chain DNA (5'-D(*AP*GP*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*G)-3')


Mass: 4569.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#3: DNA chain DNA (5'-D(*TP*CP*GP*CP*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*C)-3')


Mass: 4609.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#4: 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 8% v/v Ethylene glycol, 0.1M HEPES/Sodium hydroxide pH 7.5, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→29.474 Å / Num. obs: 5684 / % possible obs: 98.83 % / Redundancy: 24.4 % / Biso Wilson estimate: 82.13 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.035 / Rrim(I) all: 0.179 / Net I/σ(I): 13
Reflection shellResolution: 3→3.11 Å / Redundancy: 24.1 % / Rmerge(I) obs: 0.8 / Num. unique obs: 550 / Rpim(I) all: 0.47 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ayd

2ayd


Resolution: 3→29.473 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.65
RfactorNum. reflection% reflection
Rfree0.2461 567 10 %
Rwork0.2036 --
obs0.2079 5670 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→29.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms479 609 1 0 1089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011175
X-RAY DIFFRACTIONf_angle_d1.1681711
X-RAY DIFFRACTIONf_dihedral_angle_d24.339593
X-RAY DIFFRACTIONf_chiral_restr0.058180
X-RAY DIFFRACTIONf_plane_restr0.01116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.30170.33171350.26381207X-RAY DIFFRACTION97
3.3017-3.77860.23721390.2161258X-RAY DIFFRACTION100
3.7786-4.75740.25581400.19781267X-RAY DIFFRACTION100
4.7574-29.47440.22891530.19111371X-RAY DIFFRACTION100

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