7YVX | pdb_00007yvx

Left-handed DNA duplex containing consecutive G-G base pairs

• PDB DOI: https://doi.org/10.2210/pdb7YVX/pdb
• NAKB: 7YVX

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


• Deposited: 2022-08-19 Released: 2022-10-12 
• Deposition Author(s): Kondo, J.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 
  0.255 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Left-handed DNA duplex containing consecutive G-G base pairs

Kondo, J.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 3.34 kDa 
• Atom Count: 209 
• Modeled Residue Count: 10 
• Deposited Residue Count: 10 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*(CBR)P*GP*GP*GP*CP*GP*CP*G)-3')	A	10	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free:  0.255 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.375	α = 90
b = 43.375	β = 90
c = 71.998	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Kondo, J.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21H01956

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection