2GVR | pdb_00002gvr

Crystal structure of the berenil-D(CGCGAATTCGCG)2 complex at 1.65 A resolution.

• PDB DOI: https://doi.org/10.2210/pdb2GVR/pdb
• NAKB: 2GVR

• Classification: DNA
• Mutation(s): No 


• Deposited: 2006-05-03 Released: 2007-06-19 
• Deposition Author(s): Lee, M.P.H., Parkinson, G.N., Neidle, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.284 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the berenil-D(CGCGAATTCGCG)2 complex at 1.65 A resolution.

Neidle, S., Parkinson, G.N., Lee, M.P.H.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.63 kDa 
• Atom Count: 587 
• 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*CP*GP*CP*G)-3'	A, B	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BRN	C [auth A]	BERENIL C14 H15 N7 XNYZHCFCZNMTFY-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.284 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.124	α = 90
b = 39.633	β = 90
c = 65.728	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
CNS	refinement
DENZO	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Lee, M.P.H., Parkinson, G.N., Neidle, S.

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2007-10-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description