4C63 | pdb_00004c63

ULTRA HIGH RESOLUTION DICKERSON-DREW DODECAMER B-DNA WITH 5- METHYLCYSTOSINE MODIFICATION

• PDB DOI: https://doi.org/10.2210/pdb4C63/pdb
• NAKB: 4C63

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


• Deposited: 2013-09-17 Released: 2013-10-02 
• Deposition Author(s): Mcdonough, M., El-Sagheer, A.H., Brown, T., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.185 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Structural insights into how 5-hydroxymethylation influences transcription factor binding.

Lercher, L., McDonough, M.A., El-Sagheer, A.H., Thalhammer, A., Kriaucionis, S., Brown, T., Schofield, C.J.

(2014) Chem Commun (Camb) 50: 1794-1796

• PubMed: 24287551 
• DOI: https://doi.org/10.1039/c3cc48151d
• Primary Citation Related Structures: 
  4C5X, 4C63, 4C64


• PubMed Abstract: 
  

  Transcription factor binding and high resolution crystallographic studies (1.3 Å) of Dickerson-Drew duplexes with cytosine, methylcytosine and hydroxymethylcytosine bases provide evidence that C-5 cytosine modifications could regulate transcription by context dependent effects on DNA transcription factor interactions.

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Organizational Affiliation: 
• Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, Oxford, UK. [e-mail].

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
5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*5CMP*GP*CP*GP)-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: 1.32 Å
• R-Value Free:  0.185 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.456	α = 90
b = 40.06	β = 90
c = 65.414	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Mcdonough, M., El-Sagheer, A.H., Brown, T., Schofield, C.J.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2013-12-11
  Changes: Database references
• Version 1.2: 2014-02-12
  Changes: Database references
• Version 1.3: 2014-05-07
  Changes: Structure summary
• Version 1.4: 2018-02-21
  Changes: Database references
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description