3EY1

A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution

• PDB DOI: https://doi.org/10.2210/pdb3EY1/pdb
• NAKB: 3EY1

• Classification: HYDROLASE/DNA
• Organism(s): Halalkalibacterium halodurans
• Mutation(s): Yes 


• Deposited: 2008-10-17 Released: 2009-04-28 
• Deposition Author(s): Egli, M., Pallan, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.261 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.

Pallan, P.S., Prakash, T.P., Li, F., Eoff, R.L., Manoharan, M., Egli, M.

(2009) Chem Commun (Camb) 15: 2017-2019

• PubMed: 19333476 
• DOI: https://doi.org/10.1039/b822781k
• Primary Citation of Related Structures:  
  3EY1, 3EY2, 3EY3


• PubMed Abstract: 
  

  Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.

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Organizational Affiliation: 

Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.92 kDa 
• Atom Count: 1,480 
• Modelled Residue Count: 149 
• Deposited Residue Count: 150 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease H	A	138	Halalkalibacterium halodurans	Mutation(s): 1  Gene Names: rnhA, BH0863 EC: 3.1.26.4
UniProt
Find proteins for Q9KEI9 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KEI9  Go to UniProtKB:  Q9KEI9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*CP*GP*AP*AP*(USM)P*(USM)P*CP*GP*CP*G)-3'	B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B], D [auth B], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.261 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.93	α = 90
b = 66.62	β = 103.3
c = 38.77	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-28 
Deposition Author(s): Egli, M., Pallan, P.S.

Revision History  

• Version 1.0: 2009-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description