1DPL | pdb_00001dpl

A-DNA DECAMER GCGTA(T23)TACGC WITH INCORPORATED 2'-METHOXY-3'-METHYLENEPHOSPHATE-THYMIDINE

• PDB DOI: https://doi.org/10.2210/pdb1DPL/pdb
• NAKB: 1DPL

• Classification: DNA
• Mutation(s): No 


• Deposited: 1999-12-27 Released: 2000-04-04 
• Deposition Author(s): Egli, M., Tereshko, V., Teplova, M., Minasov, G., Joachimiak, A., Sanishvili, R., Weeks, C.M., Miller, R., Maier, M.A., An, H., Dan Cook, P., Manoharan, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.83 Å
• R-Value Free: 
  0.121 (Depositor), 0.139 (DCC) 
• R-Value Work: 
  0.115 (Depositor), 0.125 (DCC) 
• R-Value Observed: 
  0.117 (Depositor) 

Literature

X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution.

Egli, M., Tereshko, V., Teplova, M., Minasov, G., Joachimiak, A., Sanishvili, R., Weeks, C.M., Miller, R., Maier, M.A., An, H., Dan Cook, P., Manoharan, M.

(1998) Biopolymers 48: 234-252

• PubMed: 10699842 
• DOI: https://doi.org/10.1002/(SICI)1097-0282(1998)48:4<234::AID-BIP4>3.0.CO;2-H
• Primary Citation Related Structures: 
  1DPL, 1DPN


• PubMed Abstract: 
  

  We have determined single crystal structures of an A-DNA decamer and a B-DNA dodecamer at 0.83 and 0.95 A, respectively. The resolution of the former is the highest reported thus far for any right-handed nucleic acid duplex and the quality of the diffraction data allowed determination of the structure with direct methods. The structures reveal unprecedented details of DNA fine structure and hydration; in particular, we have reexamined the overall hydration of A- and B-form DNA, the distribution of water around phosphate groups, and features of the water structure that may underlie the B to A transition.

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Organizational Affiliation: 
• Department of Molecular Pharmacology and Biological Chemistry and The Drug Discovery Program, Northwestern University Medical School, Chicago, IL 60611, USA. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.6 kDa 
• Atom Count: 650 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'	A, B	10	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	D [auth B], E [auth B]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.83 Å
• R-Value Free:  0.121 (Depositor), 0.139 (DCC) 
• R-Value Work:  0.115 (Depositor), 0.125 (DCC) 
• R-Value Observed: 0.117 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.627	α = 90
b = 42.717	β = 90
c = 46.906	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELXS	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-04-04 
Deposition Author(s): Egli, M., Tereshko, V., Teplova, M., Minasov, G., Joachimiak, A., Sanishvili, R., Weeks, C.M., Miller, R., Maier, M.A., An, H., Dan Cook, P., Manoharan, M.

Revision History  

• Version 1.0: 2000-04-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2022-06-22
  Changes: Data collection, Database references, Derived calculations, Polymer sequence
• Version 2.1: 2024-02-07
  Changes: Data collection