5LJ4 | pdb_00005lj4

Crystal structure of DNA duplex containing ZP base pair

• PDB DOI: https://doi.org/10.2210/pdb5LJ4/pdb
• NAKB: 5LJ4

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2016-07-17 Released: 2017-05-03 
• Deposition Author(s): Agnew, C.R.J., Brady, R.L.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structural Basis of the Mispairing of an Artificially Expanded Genetic Information System

Reichenbach, L.F., Sobri, A.A., Zaccai, N.R., Agnew, C.R.J., Burton, N., Eperon, L.P., de Ornellas, S., Eperon, I.C., Brady, R.L., Burley, G.A.

(2016) Chem 1: 946-958

• DOI: https://doi.org/10.1016/j.chempr.2016.11.009

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.58 kDa 
• Atom Count: 469 
• Modeled Residue Count: 22 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
ODN2	A, B	12	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.7	α = 90
b = 41.7	β = 90
c = 99.932	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
MOSFLM	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Agnew, C.R.J., Brady, R.L.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/J02080X/1

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-05-17
  Changes: Database references
• Version 1.2: 2017-08-30
  Changes: Author supporting evidence
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description