2FK6 | pdb_00002fk6

Crystal Structure of RNAse Z/tRNA(Thr) complex

• PDB DOI: https://doi.org/10.2210/pdb2FK6/pdb
• NAKB: 2FK6

• Classification: HYDROLASE/RNA
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-01-04 Released: 2006-03-21 
• Deposition Author(s): Li de la Sierra-Gallay, I., Mathy, N., Pellegrini, O., Condon, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.299 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA.

Li de la Sierra-Gallay, I., Mathy, N., Pellegrini, O., Condon, C.

(2006) Nat Struct Mol Biol 13: 376-377

• PubMed: 16518398 
• DOI: https://doi.org/10.1038/nsmb1066
• Primary Citation Related Structures: 
  2FK6


• PubMed Abstract: 
  

  The highly conserved ribonuclease RNase Z catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Here we present the structure of the complex between Bacillus subtilis RNase Z and tRNA(Thr), the first structure of a ribonucleolytic processing enzyme bound to tRNA. Binding of tRNA to RNase Z causes conformational changes in both partners to promote reorganization of the catalytic site and tRNA cleavage.

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Organizational Affiliation: 
• Centre National de la Recherche (CNRS) FRC550, Institut de Biologie Physico-Chimique, Paris, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.44 kDa 
• Atom Count: 3,550 
• Modeled Residue Count: 360 
• Deposited Residue Count: 399 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE Z	B [auth A]	320	Bacillus subtilis	Mutation(s): 3  Gene Names: RNZ EC: 3.1.26.11
UniProt
Find proteins for P54548 (Bacillus subtilis (strain 168)) Explore P54548  Go to UniProtKB:  P54548

Entity ID: 1
Molecule	Chains	Length	Organism	Image
TRNA(THR)	A [auth R]	79	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.299 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.54	α = 90
b = 42.4	β = 121.42
c = 110.43	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-21 
Deposition Author(s): Li de la Sierra-Gallay, I., Mathy, N., Pellegrini, O., Condon, C.

Revision History  

• Version 1.0: 2006-03-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description