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- PDB-2ayd: Crystal Structure of the C-terminal WRKY domainof AtWRKY1, an SA-... -

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Basic information

Entry
Database: PDB / ID: 2ayd
TitleCrystal Structure of the C-terminal WRKY domainof AtWRKY1, an SA-induced and partially NPR1-dependent transcription factor
ComponentsWRKY transcription factor 1
KeywordsTRANSCRIPTION / beta strands / zinc finger
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
SUCCINIC ACID / WRKY transcription factor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsDuan, M.R. / Nan, J. / Li, Y. / Su, X.D.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: DNA binding mechanism revealed by high resolution crystal structure of Arabidopsis thaliana WRKY1 protein.
Authors: Duan, M.R. / Nan, J. / Liang, Y.H. / Mao, P. / Lu, L. / Li, L. / Wei, C. / Lai, L. / Li, Y. / Su, X.D.
History
DepositionSep 7, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WRKY transcription factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9943
Polymers8,8111
Non-polymers1832
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.552, 45.552, 68.962
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein WRKY transcription factor 1 / WRKY DNA-binding protein 1 / Zinc-dependent activator protein 1 / Transcription factor ZAP1


Mass: 8810.977 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WRKY1 / Plasmid: pET21aDEST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9SI37
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: succinic acid, Tris HCl, PEG MME 2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.24 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionNumber: 14751 / Rmerge(I) obs: 0.081 / Χ2: 1.048 / D res high: 1.8 Å / D res low: 29 Å / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
3.882999.710.0611.579
3.083.8810010.0691.442
2.693.0810010.081.243
2.442.6910010.091.088
2.272.4410010.0981.005
2.132.2710010.1080.99
2.032.1310010.120.973
1.942.0310010.1340.833
1.861.9410010.1490.687
1.81.8610010.1770.583
ReflectionResolution: 1.6→29 Å / Num. obs: 11069 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 / Χ2: 1.433
Reflection shellResolution: 1.6→1.66 Å / % possible obs: 95.5 % / Rmerge(I) obs: 0.354 / Num. measured obs: 1043 / Χ2: 0.499 / % possible all: 95.5

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Phasing

PhasingMethod: SAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 8005
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
4.72-10069.60.619504
3.7-4.7262.50.67502
3.21-3.766.60.698507
2.9-3.2166.20.654501
2.68-2.9610.544512
2.52-2.6870.40.64506
2.39-2.52680.66505
2.28-2.3966.60.649511
2.19-2.2869.90.602507
2.11-2.1964.40.607506
2.04-2.1170.80.587510
1.98-2.0470.80.551513
1.93-1.9879.30.559501
1.88-1.9379.80.216504
1.8-1.8884.40.442916

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
MAR345data collection
OASISV. 2004phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.413 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.088 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 530 4.8 %RANDOM
Rwork0.179 ---
all0.18 11281 --
obs0.18 11062 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.297 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms619 0 9 99 727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021644
X-RAY DIFFRACTIONr_bond_other_d0.0020.02555
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.945868
X-RAY DIFFRACTIONr_angle_other_deg0.86531302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.738575
X-RAY DIFFRACTIONr_chiral_restr0.0950.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02700
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02137
X-RAY DIFFRACTIONr_nbd_refined0.2910.299
X-RAY DIFFRACTIONr_nbd_other0.280.2591
X-RAY DIFFRACTIONr_nbtor_other0.0840.2398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.280
X-RAY DIFFRACTIONr_metal_ion_refined0.0030.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5110.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3340.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.219
X-RAY DIFFRACTIONr_mcbond_it1.0511.5379
X-RAY DIFFRACTIONr_mcangle_it1.8872619
X-RAY DIFFRACTIONr_scbond_it2.4863265
X-RAY DIFFRACTIONr_scangle_it4.0144.5249
LS refinement shellResolution: 1.605→1.646 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.339 32
Rwork0.278 721
all-753
obs-721

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