418D | pdb_0000418d

5'-R(*GP*UP*GP*CP*AP*CP*A)-D(P*C)-3'

• PDB DOI: https://doi.org/10.2210/pdb418D/pdb
• NAKB: 418D

• Classification: DNA-RNA HYBRID
• Mutation(s): No 


• Deposited: 1998-08-12 Released: 2003-06-10 
• Deposition Author(s): Mitra, S.N., Biswas, R., Shi, K., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.259 (Depositor) 
• R-Value Work: 
  0.208 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an RNA duplex [r(gugcaca)dC]2 with 3'-dinucleoside overhangs forming a superhelix.

Mitra, S.N., Biswas, R., Shi, K., Sundaralingam, M.

(2000) J Biomol Struct Dyn 11: 189-194

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.02 kDa 
• Atom Count: 360 
• Modeled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*UP*GP*CP*AP*CP*AP*C)-3')	A, B	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.259 (Depositor) 
• R-Value Work:  0.208 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.29	α = 90
b = 45.25	β = 90
c = 73.68	γ = 90

Software Package:

Software Name	Purpose
X-GEN	data scaling
X-GEN	data reduction
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-10 
Deposition Author(s): Mitra, S.N., Biswas, R., Shi, K., Sundaralingam, M.

Revision History  

• Version 1.0: 2003-06-10
  Type: Initial release
  
• Version 1.1: 2008-04-02
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description
• Version 1.4: 2023-12-27
  Changes: Advisory, Data collection, Database references
• Version 1.5: 2024-04-03
  Changes: Refinement description