2E7Y | pdb_00002e7y

High resolution structure of T. maritima tRNase Z

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.249 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The structure of the flexible arm of Thermotoga maritima tRNase Z differs from those of homologous enzymes

Ishii, R., Minagawa, A., Takaku, H., Takagi, M., Nashimoto, M., Yokoyama, S.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 637-641

  • DOI: https://doi.org/10.1107/S1744309107033623
  • Primary Citation of Related Structures:  
    2E7Y

  • PubMed Abstract: 

    tRNA 3'-processing endoribonuclease (tRNase Z) is one of the enzymes involved in the 3'-end processing of precursor tRNAs and is a member of the metallo-beta-lactamase superfamily. tRNase Z crystal structures have revealed that the enzyme forms a dimer and has a characteristic domain, named a flexible arm or an exosite, which protrudes from the metallo-beta-lactamase core and is involved in tRNA binding. The refined structure of Thermotoga maritima tRNase Z has been determined at 1.97 A resolution, revealing the structure of the flexible arm and the zinc-bound active site. The structure of the flexible arm of T. maritima tRNase Z is distinct from those of the Bacillus subtilis and Escherichia coli tRNase Zs. A comparison of the three tRNase Z structures revealed differences in the dimer orientation, which may be related to the unique cleavage-site specificity of T. maritima tRNase Z.

    • Organizational Affiliation: 

    RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNase Z
A, B
280Thermotoga maritimaMutation(s): 0 
EC: 3.1.26.11
UniProt
Find proteins for Q9WZW8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WZW8 
Go to UniProtKB:  Q9WZW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WZW8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PGO
Query on PGO
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
K [auth B],
L [auth B]		S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B],
J [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.299α = 90
b = 172.694β = 90
c = 64.886γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description