4F3U | pdb_00004f3u

Crystal structure of 5-hydroxy-2'-deoxycytidine base paired with 2'-deoxyguanosine in Dickerson Drew Dodecamer

• PDB DOI: https://doi.org/10.2210/pdb4F3U/pdb
• NAKB: 4F3U

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2012-05-09 Released: 2013-06-05 
• Deposition Author(s): Szulik, M.W., Nocek, B., Joachimiak, A., Stone, M.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 5-hydroxy-2'-deoxycytidine base paired with 2'-deoxyguanosine in Dickerson Drew Dodecamer

Szulik, M.W., Nocek, B., Joachimiak, A., Stone, M.P.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 7.38 kDa 
• Atom Count: 583 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(5OC)P*GP*CP*G)-3')	A, B	12	synthetic construct

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: 1.40 Å
• R-Value Free:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.287	α = 90
b = 40.217	β = 90
c = 65.471	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-05 
Deposition Author(s): Szulik, M.W., Nocek, B., Joachimiak, A., Stone, M.P.

Revision History  

• Version 1.0: 2013-06-05
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description