5J6X | pdb_00005j6x

Crystal structure of the apo-Zalpha of Zebrafish PKZ

• PDB DOI: https://doi.org/10.2210/pdb5J6X/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Danio rerio
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-04-05 Released: 2016-09-07 
• Deposition Author(s): Subramani, V.K., Kim, D., Kim, K.K.
• Funding Organization(s): Samsung Science & Technology Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.269 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structural and functional studies of a large winged Z-DNA-binding domain of Danio rerio protein kinase PKZ

Subramani, V.K., Kim, D., Yun, K., Kim, K.K.

(2016) FEBS Lett 590: 2275-2285

• PubMed: 27265117 
• DOI: https://doi.org/10.1002/1873-3468.12238
• Primary Citation Related Structures: 
  5J6X


• PubMed Abstract: 
  

  The Z-DNA-binding domain of PKZ from zebrafish (Danio rerio; drZαPKZ ) contains the largest β-wing among known Z-DNA-binding domains. To elucidate the functional implication of the β-wing, we solved the crystal structure of apo-drZαPKZ . Structural comparison with its Z-DNA-bound form revealed a large conformational change within the β-wing during Z-DNA binding. Biochemical studies of protein mutants revealed that two basic residues in the β-wing are responsible for Z-DNA recognition as well as fast B-Z transition. Therefore, the extra basic residues in the β-wing of drZαPKZ are necessary for the fast B-Z transition activity.

---

Organizational Affiliation: 
• Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.08 kDa 
• Atom Count: 1,117 
• Modeled Residue Count: 131 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Z-DNA binding protein kinase	A, B	72	Danio rerio	Mutation(s): 0  Gene Names: pkz
UniProt
Find proteins for Q5NE12 (Danio rerio) Explore Q5NE12  Go to UniProtKB:  Q5NE12

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.269 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.304	α = 90
b = 44.304	β = 90
c = 71.369	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-09-07 
Deposition Author(s): Subramani, V.K., Kim, D., Kim, K.K.

---

Funding Organization	Location	Grant Number
Samsung Science & Technology Foundation	Korea, Republic Of	SSTF-BA1301-01

Revision History  

• Version 1.0: 2016-09-07
  Type: Initial release
  
• Version 1.1: 2021-09-15
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description