6DY5 | pdb_00006dy5

Crystal structure of double-stranded DNA AGGGATCCCT in complex with Zn2+

• PDB DOI: https://doi.org/10.2210/pdb6DY5/pdb
• NAKB: 6DY5

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


• Deposited: 2018-07-01 Released: 2019-01-23 
• Deposition Author(s): Hou, C., Tsodikov, O.V.
• Funding Organization(s): Department of Defense (DOD, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Utilizing guanine coordinated Zn2+ to determine DNA crystal structures by single-wavelength anomalous diffraction

Hou, C., Tsodikov, O.V.

(2019) Acta Crystallogr D Biol Crystallogr 75: 32

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 6.43 kDa 
• Atom Count: 512 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*GP*AP*TP*CP*CP*CP*T)-3')	A, B	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPD	C [auth A]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN	D [auth A], E [auth B], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.567	α = 90
b = 42.451	β = 90
c = 49.212	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Hou, C., Tsodikov, O.V.

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Funding Organization	Location	Grant Number
Department of Defense (DOD, United States)	United States	PC150300P1

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations