5CH0 | pdb_00005ch0

Crystal structure of an A-form DNA duplex containing 5-hydroxylmethylcytidine

• PDB DOI: https://doi.org/10.2210/pdb5CH0/pdb
• NAKB: 5CH0

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


• Deposited: 2015-07-10 Released: 2016-07-20 
• Deposition Author(s): Sheng, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an A-form DNA duplex containing 5-hydroxylmethylcytidine

Sheng, J.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 2.54 kDa 
• Atom Count: 201 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-R(*G)-D(P*(UMS))-R(P*G)-D(P*T)-R(P*A)-D(P*(5HC))-R(P*AP*C)-3')	A	8	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.05	α = 90
b = 43.05	β = 90
c = 23.764	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Sheng, J.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 2.0: 2021-01-20
  Changes: Data collection, Derived calculations, Polymer sequence
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description