353D

CRYSTAL STRUCTURE OF DOMAIN A OF THERMUS FLAVUS 5S RRNA AND THE CONTRIBUTION OF WATER MOLECULES TO ITS STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb353D/pdb
• NAKB: 353D

• Classification: RNA
• Mutation(s): No 


• Deposited: 1997-09-29 Released: 1997-11-10 
• Deposition Author(s): Betzel, C., Lorenz, S., Furste, J.P., Bald, R., Zhang, M., Schneider, T.R., Wilson, K.S., Erdmann, V.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Observed: 0.180 

Literature

Crystal structure of domain A of Thermus flavus 5S rRNA and the contribution of water molecules to its structure.

Betzel, C., Lorenz, S., Furste, J.P., Bald, R., Zhang, M., Schneider, T.R., Wilson, K.S., Erdmann, V.A.

(1994) FEBS Lett 351: 159-164

• PubMed: 8082756 
• DOI: https://doi.org/10.1016/0014-5793(94)00834-5
• Primary Citation of Related Structures:  
  353D


• PubMed Abstract: 
  

  This is the first high resolution crystal structure of an RNA molecule made by solid phase chemical synthesis and representing a natural RNA. The structure of the domain A of Thermus flavus ribosomal 5S RNA is refined to R = 18% at 2.4 A including 159 solvent molecules. Most of the 2'-hydroxyl groups as well as the phosphate oxygens are involved either in specific hydrogen bonds in intermolecular contacts or to solvent molecules. The two U-G and G-U base-pairs are stabilized by H-bonds supplied via three water molecules to compensate for the lack of base-pair hydrogen bonds. The structure shows for the first time in detail the importance of highly ordered internal water in stabilizing an RNA structure.

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Organizational Affiliation: 

Institut für Biochemie, Freie Universität Berlin, Germany.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.69 kDa 
• Atom Count: 666 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*UP*CP*CP*CP*CP*CP*GP*UP*GP*CP*C)-3')	A	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*UP*GP*CP*GP*GP*GP*GP*GP*AP*U)-3')	B	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Observed: 0.180 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.1	α = 90
b = 30.1	β = 90
c = 86.8	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
NUCLSQ	refinement
XDS	data reduction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-11-10 
Deposition Author(s): Betzel, C., Lorenz, S., Furste, J.P., Bald, R., Zhang, M., Schneider, T.R., Wilson, K.S., Erdmann, V.A.

Revision History  

• Version 1.0: 1997-11-10
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-14
  Changes: Data collection, Experimental preparation
• Version 1.4: 2023-08-02
  Changes: Data collection, Database references, Refinement description