1DD5 | pdb_00001dd5

CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA RIBOSOME RECYCLING FACTOR, RRF

• PDB DOI: https://doi.org/10.2210/pdb1DD5/pdb

• Classification: RIBOSOME
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-11-08 Released: 1999-12-22 
• Deposition Author(s): Selmer, M., Al-Karadaghi, S., Hirokawa, G., Kaji, A., Liljas, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.277 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic.

Selmer, M., Al-Karadaghi, S., Hirokawa, G., Kaji, A., Liljas, A.

(1999) Science 286: 2349-2352

• PubMed: 10600747 
• DOI: https://doi.org/10.1126/science.286.5448.2349
• Primary Citation Related Structures: 
  1DD5


• PubMed Abstract: 
  

  Ribosome recycling factor (RRF), together with elongation factor G (EF-G), catalyzes recycling of ribosomes after one round of protein synthesis. The crystal structure of RRF was determined at 2.55 angstrom resolution. The protein has an unusual fold where domain I is a long three-helix bundle and domain II is a three-layer beta/alpha/beta sandwich. The molecule superimposes almost perfectly with a transfer RNA (tRNA) except that the amino acid-binding 3' end is missing. The mimicry suggests that RRF interacts with the posttermination ribosomal complex in a similar manner to a tRNA, leading to disassembly of the complex. The structural arrangement of this mimicry is entirely different from that of other cases of less pronounced mimicry of tRNA so far described.

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Organizational Affiliation: 
• Molecular Biophysics, Center for Chemistry and Chemical Engineering, Lund University, Post Office Box 124, SE-22100 Lund, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.67 kDa 
• Atom Count: 1,577 
• Modeled Residue Count: 184 
• Deposited Residue Count: 185 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOME RECYCLING FACTOR	A	185	Thermotoga maritima	Mutation(s): 0
UniProt
Find proteins for Q9X1B9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1B9  Go to UniProtKB:  Q9X1B9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	B [auth A], C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.277 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.25	α = 90
b = 47.25	β = 90
c = 297.55	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MLPHARE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-12-22 
Deposition Author(s): Selmer, M., Al-Karadaghi, S., Hirokawa, G., Kaji, A., Liljas, A.

Revision History  

• Version 1.0: 1999-12-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations