1NGT | pdb_00001ngt

The Role of Minor Groove Functional Groups in DNA Hydration

• PDB DOI: https://doi.org/10.2210/pdb1NGT/pdb
• NAKB: 1NGT

• Classification: DNA
• Mutation(s): No 


• Deposited: 2002-12-17 Released: 2003-03-04 
• Deposition Author(s): Woods, K.K., Lan, T., McLaughlin, L.W., Williams, L.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.281 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

The Role of Minor Groove Functional Groups in DNA Hydration

Woods, K.K., Lan, T., McLaughlin, L.W., Williams, L.D.

(2003) Nucleic Acids Res 31: 1536-1540

• PubMed: 12595562 
• DOI: https://doi.org/10.1093/nar/gkg240
• Primary Citation Related Structures: 
  1NGT


• PubMed Abstract: 
  

  Here we describe the crystal structure of modified [d(CGCGAATTCGCG)]2 refined to 2.04 A. The modification, which affects only the two thymines at the central ApT step, involves isosteric removal of the 2-keto oxygen atoms and substitution of the N1 nitrogen with carbon. The crystal structure reveals the ability of this modified thymine to effectively base pair with adenine in [d(CGCGAAtTCGCG)]2. The structure also suggests that the minor groove 'spine of hydration' is destabilized but essentially intact.

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Organizational Affiliation: 
• School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.32 kDa 
• Atom Count: 567 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.281 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.17	α = 90
b = 41.05	β = 90
c = 65.72	γ = 90

Software Package:

Software Name	Purpose
SAINT	data reduction
CNS	refinement
SAINT	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-04 
Deposition Author(s): Woods, K.K., Lan, T., McLaughlin, L.W., Williams, L.D.

Revision History  

• Version 1.0: 2003-03-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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: 2018-03-07
  Changes: Data collection
• Version 1.5: 2024-02-14
  Changes: Data collection, Database references, Derived calculations