5ZT2 | pdb_00005zt2

Crystal structure of CCG DNA repeats at 1.66 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb5ZT2/pdb
• Entry: 5ZT2 supersedes: 4QNO
• NAKB: 5ZT2

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


• Deposited: 2018-05-01 Released: 2019-05-15 
• Deposition Author(s): Hou, M.H., Wu, P.C., Satange, R.B., Chen, Y.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

Crystallographic analysis of conformational change in CCG repeats into i-motif and unusual DNA duplex in presence and absence of CoII(Chro)2 complex

Hou, M.H.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.41 kDa 
• Atom Count: 279 
• Modeled Residue Count: 11 
• Deposited Residue Count: 11 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*CP*GP*CP*CP*GP*CP*CP*GP*A)-3')	A	11	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	B [auth A], C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.299	α = 90
b = 38.299	β = 90
c = 54.328	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Hou, M.H., Wu, P.C., Satange, R.B., Chen, Y.W.
• This entry supersedes: 4QNO

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2019-05-22
  Changes: Data collection, Derived calculations
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references, Derived calculations