249D | pdb_0000249d

STRUCTURAL COMPARISON BETWEEN THE D(CTAG) SEQUENCE IN OLIGONUCLEOTIDES AND TRP AND MET REPRESSOR-OPERATOR COMPLEXES

• PDB DOI: https://doi.org/10.2210/pdb249D/pdb
• NAKB: 249D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1996-02-22 Released: 1996-04-19 
• Deposition Author(s): Urpi, L., Tereshko, V., Malinina, L., Huynh-Dinh, T., Subirana, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Work: 
  0.197 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Structural comparison between the d(CTAG) sequence in oligonucleotides and trp and met repressor-operator complexes.

Urpi, L., Tereshko, V., Malinina, L., Huynh-Dinh, T., Subirana, J.A.

(1996) Nat Struct Biol 3: 325-328

• PubMed: 8599757 
• DOI: https://doi.org/10.1038/nsb0496-325
• Primary Citation Related Structures: 
  249D, 250D

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.69 kDa 
• Atom Count: 990 
• Modeled Residue Count: 47 
• Deposited Residue Count: 48 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*TP*CP*TP*AP*GP*AP*GP*CP*G)-3')	A, B, C, D	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Work:  0.197 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.05	α = 90
b = 68.91	β = 91.16
c = 26.15	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
ENRAF-NONIUS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-04-19 
Deposition Author(s): Urpi, L., Tereshko, V., Malinina, L., Huynh-Dinh, T., Subirana, J.A.

Revision History  

• Version 1.0: 1996-04-19
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-18
  Changes: Data collection
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations