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- PDB-6ir8: Rice WRKY/DNA complex -

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Basic information

Entry
Database: PDB / ID: 6ir8
TitleRice WRKY/DNA complex
Components
  • DNA (5'-D(P*GP*AP*TP*AP*TP*TP*TP*GP*AP*CP*CP*GP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*CP*GP*GP*TP*CP*AP*AP*AP*TP*AP*TP*C)-3')
  • OsWRKY45
KeywordsTRANSCRIPTION/DNA / Transcription factor Complex Zinc finger Dimer / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / nucleus
Similarity search - Function
WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain
Similarity search - Domain/homology
DNA / DNA (> 10) / WRKY domain-containing protein
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiu, J. / Cheng, X. / Wang, D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFD0300700 China
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain.
Authors: Cheng, X. / Zhao, Y. / Jiang, Q. / Yang, J. / Zhao, W. / Taylor, I.A. / Peng, Y.L. / Wang, D. / Liu, J.
History
DepositionNov 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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
A: OsWRKY45
B: DNA (5'-D(P*GP*AP*TP*AP*TP*TP*TP*GP*AP*CP*CP*GP*GP*A)-3')
C: DNA (5'-D(P*TP*CP*CP*GP*GP*TP*CP*AP*AP*AP*TP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7894
Polymers16,7243
Non-polymers651
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-45 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.225, 87.831, 99.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

21A-361-

HOH

31A-365-

HOH

41B-113-

HOH

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Components

#1: Protein OsWRKY45


Mass: 8164.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: OsJ_18062 / Production host: Escherichia coli (E. coli) / References: UniProt: B9FNW2
#2: DNA chain DNA (5'-D(P*GP*AP*TP*AP*TP*TP*TP*GP*AP*CP*CP*GP*GP*A)-3')


Mass: 4319.828 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*CP*CP*GP*GP*TP*CP*AP*AP*AP*TP*AP*TP*C)-3')


Mass: 4239.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: 0.27 M calcium acetate hydrate, 21% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.3→49.85 Å / Num. obs: 9748 / % possible obs: 99.99 % / Redundancy: 12.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.024 / Net I/σ(I): 24.4
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.531 / CC1/2: 0.972 / Rpim(I) all: 0.1051

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUT

1aut


Resolution: 2.3→43.916 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.71
RfactorNum. reflection% reflection
Rfree0.2444 519 5.32 %
Rwork0.1929 --
obs0.1955 9748 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→43.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms571 574 1 111 1257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081225
X-RAY DIFFRACTIONf_angle_d0.9441771
X-RAY DIFFRACTIONf_dihedral_angle_d25.372628
X-RAY DIFFRACTIONf_chiral_restr0.05191
X-RAY DIFFRACTIONf_plane_restr0.005132
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.53160.30231220.23292278X-RAY DIFFRACTION100
2.5316-2.89780.24231510.22252237X-RAY DIFFRACTION100
2.8978-3.65070.25111180.18342309X-RAY DIFFRACTION100
3.6507-43.92370.22191280.17582405X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6548-0.1087-0.12814.3922-0.37644.42710.1044-0.05250.05570.14650.01280.0873-0.2093-0.1705-0.06010.06180.0010.01090.1423-00.14843.094711.2354-3.6926
20.47730.76941.67791.25722.68975.86610.1894-0.0458-0.07440.0389-0.1104-0.06150.57740.1350.08170.23-0.01230.00580.25150.02970.16763.5743.6972-24.7629
32.8832-0.24990.51475.8489-2.11845.26610.11560.24850.0841-0.3271-0.2478-0.2360.29850.64220.29880.10050.01480.00340.1443-0.0070.1759-1.03526.8836-47.4922
45.9534-0.6687-1.65395.20750.26723.66040.14321.3705-0.0728-0.4308-0.1108-0.5152-0.1668-0.2513-0.08370.2291-0.02320.0230.3517-0.08530.29544.049820.257-15.6352
56.28690.007-1.00124.40310.35285.1952-0.21391.0150.5288-0.26270.1112-0.343-0.31440.18870.11980.1905-0.0030.00670.29330.09560.3034.717421.9563-13.2372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 110 through 143 )
2X-RAY DIFFRACTION2chain 'A' and (resid 144 through 153 )
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 178 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 14 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 14 )

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