4GJP | pdb_00004gjp

Crystal structure of the TAL effector dHax3 bound to dsDNA containing repetitive methyl-CpG

• PDB DOI: https://doi.org/10.2210/pdb4GJP/pdb
• NAKB: 4GJP

• Classification: TRANSCRIPTION/DNA
• Organism(s): Xanthomonas campestris pv. armoraciae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-08-10 Released: 2012-10-03 
• Deposition Author(s): Yan, N., Deng, D., Yan, C.Y., Yin, P., Pan, X.J., Shi, Y.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a protein complex

Yan, N., Deng, D., Yan, C.Y., Yin, P., Pan, X.J., Shi, Y.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 124.45 kDa 
• Atom Count: 9,216 
• Modeled Residue Count: 1,051 
• Deposited Residue Count: 1,066 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hax3	A, D [auth B]	499	Xanthomonas campestris pv. armoraciae	Mutation(s): 17  Gene Names: hax3
UniProt
Find proteins for Q3ZD72 (Xanthomonas campestris pv. armoraciae) Explore Q3ZD72  Go to UniProtKB:  Q3ZD72

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*(5CM)P*GP*TP*CP*TP*CP*T)-3')	B [auth I], E [auth G]	17	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')	C [auth J], F [auth H]	17	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	G [auth J], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.203	α = 90
b = 87.114	β = 102.85
c = 88.147	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Yan, N., Deng, D., Yan, C.Y., Yin, P., Pan, X.J., Shi, Y.G.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description