1LJX | pdb_00001ljx

THE STRUCTURE OF D(TPGPCPGPCPA)2 AT 293K: COMPARISON OF THE EFFECT OF SEQUENCE AND TEMPERATURE

• PDB DOI: https://doi.org/10.2210/pdb1LJX/pdb
• NAKB: 1LJX

• Classification: DNA
• Mutation(s): No 


• Deposited: 2002-04-23 Released: 2002-05-03 
• Deposition Author(s): Thiyagarajan, S., Satheesh Kumar, P., Rajan, S.S., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.267 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.213 (DCC) 

Starting Model: experimental

Literature

Structure of d(TGCGCA)2 at 293 K: comparison of the effects of sequence and temperature.

Thiyagarajan, S., Satheesh Kumar, P., Rajan, S.S., Gautham, N.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1381-1384

• PubMed: 12136163 
• DOI: https://doi.org/10.1107/s090744490200896x
• Primary Citation Related Structures: 
  1LJX


• PubMed Abstract: 
  

  The crystal structure of a hexameric DNA fragment with the sequence d(TGCGCA)(2) has been solved and refined at 293 K at a resolution of 1.64 A. The molecule adopts a left-handed Z-type helical conformation which is common in alternating pyrimidine-purine sequences. The presence of A.T base pairs at the two terminals does not perturb the structure to any great degree. However, several sequence-specific microstructural changes are noticeable. The structure of the identical sequence determined at 120 K involving somewhat different crystallization conditions has been reported previously [Harper et al. (1998), Acta Cryst. D54, 1273-1284]. A comparison of the present structure with that at low temperature and with that of d(CGCGCG)(2) shows that the effect of the change in sequence is greater than the combined effect of changes in temperature and environment.

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Organizational Affiliation: 
• Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, India.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.67 kDa 
• Atom Count: 300 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.267 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.213 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 21.182	α = 90
b = 28.363	β = 90
c = 44.44	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
MAR345	data collection
AUTOMAR	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-05-03 
Deposition Author(s): Thiyagarajan, S., Satheesh Kumar, P., Rajan, S.S., Gautham, N.

Revision History  

• Version 1.0: 2002-05-03
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description