3HQE | pdb_00003hqe

Crystal Structure of the decamer CGGGCGCCCG forming a Holliday junction

• PDB DOI: https://doi.org/10.2210/pdb3HQE/pdb
• NAKB: 3HQE

• Classification: DNA
• Mutation(s): No 


• Deposited: 2009-06-06 Released: 2010-06-09 
• Deposition Author(s): Venkadesh, S., Mandal, P.K., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.239 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Sequence dependent structural variation of Holliday junction - crystal structure of d(CGGGCGCCCG)4

Venkadesh, S., Mandal, P.K., Gautham, N.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 6.09 kDa 
• Atom Count: 414 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.239 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.004	α = 90
b = 22.813	β = 116.75
c = 40.708	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-09 
Deposition Author(s): Venkadesh, S., Mandal, P.K., Gautham, N.

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description