8XPA

Crystal structure of d(ACGmCCGT/ACGGCGT)

• PDB DOI: https://doi.org/10.2210/pdb8XPA/pdb
• NAKB: 8XPA

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2024-01-03 Released: 2024-05-29 
• Deposition Author(s): Hou, M.H., Lin, S.M., Neidle, S.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.252 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 

Literature

Crystal structure of d(ACGmCCGT/ACGGCGT)

Hou, M.H., Lin, S.M.

To be published.

Biological Assembly 1  

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

Biological Assembly 2  

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

Biological Assembly 3  

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17.19 kDa 
• Atom Count: 1,318 
• Modelled Residue Count: 56 
• Deposited Residue Count: 56 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*GP*GP*CP*GP*T)-3')	A, D, E [auth F], H	7	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*GP*(5CM)P*CP*GP*T)-3')	B, C, F [auth E], G	7	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	I [auth A], J [auth A], K [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.252 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.432	α = 90
b = 46.243	β = 110.92
c = 47.061	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Hou, M.H., Lin, S.M., Neidle, S.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release