6J4E | pdb_00006j4e

Crystal structure of the AtWRKY1 domain

• PDB DOI: https://doi.org/10.2210/pdb6J4E/pdb
• NAKB: 6J4E

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-08 Released: 2020-01-15 
• Deposition Author(s): Xu, Y.P., Xu, H., Wang, B., Su, X.D.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Crystal structure of the AtWRKY1 domain

Xu, Y.P., Xu, H., Wang, B., Su, X.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 18.8 kDa 
• Atom Count: 1,113 
• Modeled Residue Count: 91 
• Deposited Residue Count: 110 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
WRKY transcription factor 1	C [auth B]	80	Arabidopsis thaliana	Mutation(s): 0  Gene Names: WRKY1, ZAP1, At2g04880, F1O13.1, F28I8.34
UniProt
Find proteins for Q9SI37 (Arabidopsis thaliana) Explore Q9SI37  Go to UniProtKB:  Q9SI37

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*CP*CP*TP*TP*TP*GP*AP*CP*CP*AP*GP*CP*G)-3')	A [auth C]	15	Arabidopsis thaliana

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*GP*CP*TP*GP*GP*TP*CP*AP*AP*AP*GP*GP*C)-3')	B [auth D]	15	Arabidopsis thaliana

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.13 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99	α = 90
b = 99	β = 90
c = 114.333	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Xu, Y.P., Xu, H., Wang, B., Su, X.D.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31670740

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description