1P54

Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions

Structural Biology Knowledgebase: 1P54 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.215

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1P54

Classification: DNA

Total Structure Weight: 6282.87

Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*CP*AP*GP*TP*AP*CP*(BRU)P*GP*G)-3' A, B 10 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
BRU
Query on BRU
A, B DNA LINKING C9 H12 Br N2 O8 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.215
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 64.84 α = 90.00
b = 22.58 β = 106.78
c = 38.07 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2003-04-25
  • Released Date: 2003-09-02
  • Deposition author(s): Hays, F.A., Vargason, J.M., Ho, P.S.

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4