4KA4

Crystal structure of a proteolytically defined Zbeta domain of human DAI (ZBP1, DLM-1)

• PDB DOI: https://doi.org/10.2210/pdb4KA4/pdb
• NAKB: 4KA4

• Classification: DNA Binding Protein/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-22 Released: 2013-05-15 
• Deposition Author(s): Athanasiadis, A., de Rosa, M., De Sanctis, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.302 
• R-Value Work: 0.248 
• R-Value Observed: 0.253 

Literature

Crystal structure of a proteolytically defined Zbeta domain of human DAI (ZBP1, DLM-1)

Athanasiadis, A., de Rosa, M., De Sanctis, D.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.46 kDa 
• Atom Count: 2,359 
• Modelled Residue Count: 264 
• Deposited Residue Count: 308 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Z-DNA-binding protein 1	A, B, C [auth D], D [auth E]	70	Homo sapiens	Mutation(s): 0  Gene Names: ZBP1, C20orf183, DLM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H171 (Homo sapiens) Explore Q9H171  Go to UniProtKB:  Q9H171
PHAROS:  Q9H171 GTEx:  ENSG00000124256

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')	E [auth C], F, G, H	7	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.302 
• R-Value Work: 0.248 
• R-Value Observed: 0.253 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.647	α = 90
b = 63.208	β = 90
c = 94.541	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Athanasiadis, A., de Rosa, M., De Sanctis, D.

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description