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- PDB-6j4e: Crystal structure of the AtWRKY1 domain -

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Basic information

Entry
Database: PDB / ID: 6j4e
TitleCrystal structure of the AtWRKY1 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')
  • WRKY transcription factor 1
KeywordsDNA BINDING PROTEIN/DNA / WRKY transcription factors N-terminal WRKY domain / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


salicylic acid mediated signaling pathway / response to salicylic acid / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / mitochondrion / DNA binding / zinc ion binding / nucleus
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
DNA / DNA (> 10) / WRKY transcription factor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.126 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 AtWRKY1 domain
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

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Assembly

Deposited unit
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')
B: WRKY transcription factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7994
Polymers18,7343
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-23 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.000, 99.000, 114.333
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: 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)
#2: 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)
#3: Protein WRKY transcription factor 1 / Transcription factor ZAP1 / WRKY DNA-binding protein 1 / Zinc-dependent activator protein 1


Mass: 9553.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WRKY1, ZAP1, At2g04880, F1O13.1, F28I8.34 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SI37
#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: 4.33 Å3/Da / Density % sol: 71.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate, 0.1M Sodium acetate trihydrate pH 4.6, 30% Polyethylene glycol monomethyl ether 2000

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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: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.126→28.58 Å / Num. obs: 6263 / % possible obs: 97.64 % / Redundancy: 36.8 % / CC1/2: 1 / Rmerge(I) obs: 0.1652 / Rrim(I) all: 0.1675 / Net I/σ(I): 16.02
Reflection shellResolution: 3.126→3.238 Å / Redundancy: 37.5 % / Rmerge(I) obs: 0.5812 / Num. unique obs: 599 / CC1/2: 0.996 / Rrim(I) all: 0.5892 / % possible all: 94.02

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ayd

2ayd


Resolution: 3.126→28.579 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.17
RfactorNum. reflection% reflection
Rfree0.2348 613 10 %
Rwork0.2029 --
obs-6130 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.126→28.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms503 609 1 0 1113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111199
X-RAY DIFFRACTIONf_angle_d1.1151743
X-RAY DIFFRACTIONf_dihedral_angle_d26.193598
X-RAY DIFFRACTIONf_chiral_restr0.059183
X-RAY DIFFRACTIONf_plane_restr0.007121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1262-3.44030.30191420.25071309X-RAY DIFFRACTION95
3.4403-3.93710.26481500.21781358X-RAY DIFFRACTION100
3.9371-4.95610.20631570.16871405X-RAY DIFFRACTION100
4.9561-28.580.20371640.16071444X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -46.8537 Å / Origin y: 14.9792 Å / Origin z: -15.7703 Å
111213212223313233
T0.595 Å2-0.0575 Å20.0182 Å2-0.4438 Å2-0.0144 Å2--0.4372 Å2
L3.9286 °2-1.5125 °20.4916 °2-2.2947 °20.7691 °2--5.4121 °2
S-0.0601 Å °-0.1289 Å °-0.3319 Å °0.0829 Å °0.0235 Å °-0.1367 Å °0.2476 Å °-0.0442 Å °0.0408 Å °
Refinement TLS groupSelection details: all

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