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- PDB-6j4f: Crystal structure of the AtWRKY2 domain -

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Basic information

Entry
Database: PDB / ID: 6j4f
TitleCrystal structure of the AtWRKY2 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 2
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


longitudinal axis specification / pollen development / establishment of cell polarity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / metal ion binding / nucleus
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 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 AtWRKY2 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
B: Probable WRKY transcription factor 2
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')
F: Probable WRKY transcription factor 2
G: DNA (5'-D(*AP*GP*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*G)-3')
H: 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)37,7548
Polymers37,6246
Non-polymers1312
Water1448
1
F: Probable WRKY transcription factor 2
G: DNA (5'-D(*AP*GP*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*G)-3')
H: 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)18,8774
Polymers18,8123
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-21 kcal/mol
Surface area8780 Å2
MethodPISA
2
B: Probable WRKY transcription factor 2
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)18,8774
Polymers18,8123
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-22 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.100, 48.300, 69.100
Angle α, β, γ (deg.)93.70, 87.30, 97.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Probable WRKY transcription factor 2 / WRKY DNA-binding protein 2


Mass: 9631.860 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WRKY2, At5g56270, K24C1.9, MXK23.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FG77
#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.: 2 / 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.: 2 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 3.53 Å3/Da / Density % sol: 65.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium sulfate, 0.1M MES pH 6.0, 20% PEG 4000

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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: Jan 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→29.58 Å / Num. obs: 17894 / % possible obs: 93.47 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.044 / Rrim(I) all: 0.084 / Net I/σ(I): 9.59
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 1813 / CC1/2: 0.926 / Rpim(I) all: 0.29 / Rrim(I) all: 0.55 / % possible all: 96.37

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Processing

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

2ayd


Resolution: 2.4→29.58 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.88
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1787 10.05 %0.1
Rwork0.188 ---
obs0.1919 17785 93.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 1218 2 8 2265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092431
X-RAY DIFFRACTIONf_angle_d0.9873532
X-RAY DIFFRACTIONf_dihedral_angle_d25.0411232
X-RAY DIFFRACTIONf_chiral_restr0.048374
X-RAY DIFFRACTIONf_plane_restr0.007245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.46490.34951420.29131247X-RAY DIFFRACTION96
2.4649-2.53740.30061310.28311292X-RAY DIFFRACTION96
2.5374-2.61930.35841540.27111239X-RAY DIFFRACTION97
2.6193-2.71280.34551310.28371228X-RAY DIFFRACTION92
2.7128-2.82140.32741360.26671178X-RAY DIFFRACTION91
2.8214-2.94970.30111390.2431291X-RAY DIFFRACTION96
2.9497-3.1050.30121360.24741264X-RAY DIFFRACTION96
3.105-3.29930.28091390.22841213X-RAY DIFFRACTION93
3.2993-3.55370.24111270.19541199X-RAY DIFFRACTION90
3.5537-3.91060.25241340.19121156X-RAY DIFFRACTION88
3.9106-4.47480.1811410.1541244X-RAY DIFFRACTION95
4.4748-5.63130.15571420.14071207X-RAY DIFFRACTION91
5.6313-29.58710.15031350.13431234X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 54.5719 Å / Origin y: 1.9362 Å / Origin z: -27.3918 Å
111213212223313233
T0.3588 Å2-0.0451 Å2-0.0639 Å2-0.3928 Å20.1007 Å2--0.4087 Å2
L2.5759 °2-1.3593 °2-0.6698 °2-2.0192 °20.873 °2--2.3544 °2
S0.2768 Å °0.2667 Å °-0.0502 Å °-0.3098 Å °-0.2174 Å °0.0644 Å °-0.0291 Å °-0.0102 Å °-0.0475 Å °
Refinement TLS groupSelection details: all

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