5TGP | pdb_00005tgp

DNA 8mer containing two 2SeT modifications

• PDB DOI: https://doi.org/10.2210/pdb5TGP/pdb
• NAKB: 5TGP

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


• Deposited: 2016-09-28 Released: 2017-10-18 
• Deposition Author(s): Zhang, W., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.208 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

DNA 8mer containing two 2SeT modifications

Zhang, W., Huang, Z.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 5.3 kDa 
• Atom Count: 347 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(*G)-D(P*(2ST))-R(P*G)-D(P*(2ST))-R(P*AP*CP*AP*C)-3')	A, B [auth C]	8	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.208 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.861	α = 90
b = 44.861	β = 90
c = 41.736	γ = 120

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: 2017-10-18 
Deposition Author(s): Zhang, W., Huang, Z.

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description