3P4J | pdb_00003p4j

Ultra-high resolution structure of d(CGCGCG)2 Z-DNA

• PDB DOI: https://doi.org/10.2210/pdb3P4J/pdb
• NAKB: 3P4J

• Classification: DNA
• Mutation(s): No 


• Deposited: 2010-10-06 Released: 2011-08-24 
• Deposition Author(s): Brzezinski, K., Brzuszkiewicz, A., Dauter, M., Kubicki, M., Jaskolski, M., Dauter, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.55 Å
• R-Value Free: 
  0.085 (Depositor), 0.077 (DCC) 
• R-Value Work: 
  0.078 (Depositor), 0.082 (DCC) 
• R-Value Observed: 
  0.078 (Depositor) 

Starting Model: experimental

Literature

High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A.

Brzezinski, K., Brzuszkiewicz, A., Dauter, M., Kubicki, M., Jaskolski, M., Dauter, Z.

(2011) Nucleic Acids Res 39: 6238-6248

• PubMed: 21459852 
• DOI: https://doi.org/10.1093/nar/gkr202
• Primary Citation Related Structures: 
  3P4J


• PubMed Abstract: 
  

  The crystal structure of a Z-DNA hexamer duplex d(CGCGCG)(2) determined at ultra high resolution of 0.55 Å and refined without restraints, displays a high degree of regularity and rigidity in its stereochemistry, in contrast to the more flexible B-DNA duplexes. The estimations of standard uncertainties of all individually refined parameters, obtained by full-matrix least-squares optimization, are comparable with values that are typical for small-molecule crystallography. The Z-DNA model generated with ultra high-resolution diffraction data can be used to revise the stereochemical restraints applied in lower resolution refinements. Detailed comparisons of the stereochemical library values with the present accurate Z-DNA parameters, shows in general a good agreement, but also reveals significant discrepancies in the description of guanine-sugar valence angles and in the geometry of the phosphate groups.

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Organizational Affiliation: 
• Synchrotron Radiation Research Section, MCL, National Cancer Institute, Argonne National Laboratory, Argonne, IL 60439, USA.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 3.82 kDa 
• Atom Count: 403 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')	A, B	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	C [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.55 Å
• R-Value Free:  0.085 (Depositor), 0.077 (DCC) 
• R-Value Work:  0.078 (Depositor), 0.082 (DCC) 
• R-Value Observed: 0.078 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33p4j

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.88	α = 90
b = 31.42	β = 90
c = 43.9	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SHELX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SHELXL	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-24 
Deposition Author(s): Brzezinski, K., Brzuszkiewicz, A., Dauter, M., Kubicki, M., Jaskolski, M., Dauter, Z.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2014-04-16
  Changes: Refinement description
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description