361D | pdb_0000361d

CRYSTAL STRUCTURE OF DOMAIN E OF THERMUS FLAVUS 5S RRNA: A HELICAL RNA-STRUCTURE INCLUDING A TETRALOOP

• PDB DOI: https://doi.org/10.2210/pdb361D/pdb
• NAKB: 361D

• Classification: RNA
• Mutation(s): No 


• Deposited: 1997-11-10 Released: 1998-07-01 
• Deposition Author(s): Perbandt, M., Nolte, A., Lorenz, S., Erdmann, V.A., Betzel, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.318 (Depositor) 
• R-Value Work: 
  0.241 (Depositor) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of domain E of Thermus flavus 5S rRNA: a helical RNA structure including a hairpin loop.

Perbandt, M., Nolte, A., Lorenz, S., Bald, R., Betzel, C., Erdmann, V.A.

(1998) FEBS Lett 429: 211-215

• PubMed: 9650592 
• DOI: https://doi.org/10.1016/s0014-5793(98)00436-0
• Primary Citation of Related Structures:  
  361D


• PubMed Abstract: 
  

  The synthetic RNA fragment 5'-CUGGGCGG(GCGA)CCGCCUGG (nucleotides in parentheses indicate the loop region) corresponds to the natural sequence of domain E from nucleotides 79-97 of the Thermus flavus 5S rRNA including a hairpin loop. The RNA structure determined at 3.0 A and refined to an R-value of 24.1% also represents the first X-ray structure GNRA tetraloop. The loop is in distinctly different conformation from other GNRA tetraloops analyzed by NMR. The conformation of the two molecules in the asymmetric unit is influenced and stabilized by specific intermolecular contacts. The structural features presented here give evidence for the ability of RNA molecules to adapt to specific environments.

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Organizational Affiliation: 

Institut für Biochemie, Freie Universität Berlin, Germany.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.97 kDa 
• Atom Count: 1,079 
• Modeled Residue Count: 40 
• Deposited Residue Count: 40 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*GP*GP*CP*GP*AP*CP*CP*GP*CP*C P*UP*GP*G)-3')	A, B	20	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.318 (Depositor) 
• R-Value Work:  0.241 (Depositor) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.68	α = 90
b = 42.68	β = 90
c = 161.2	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-07-01 
Deposition Author(s): Perbandt, M., Nolte, A., Lorenz, S., Erdmann, V.A., Betzel, C.

Revision History  

• Version 1.0: 1998-07-01
  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: 2024-02-21
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description