4JDG | pdb_00004jdg

Structure of Tomato Bifunctional Nuclease TBN1, variant N211D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 
    0.264 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4JDG

This is version 2.2 of the entry. See complete history

Literature

Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme

Stransky, J.Koval, T.Podzimek, T.Tycova, A.Lipovova, P.Matousek, J.Kolenko, P.Fejfarova, K.Duskova, J.Skalova, T.Hasek, J.Dohnalek, J.

(2015) Acta Crystallogr Sect F Struct Biol Cryst Commun 71: 1408-1415

  • DOI: https://doi.org/10.1107/S2053230X15018324
  • Primary Citation Related Structures: 
    4JDG

  • PubMed Abstract: 

    Tomato multifunctional nuclease TBN1 belongs to the type I nuclease family, which plays an important role in apoptotic processes and cell senescence in plants. The newly solved structure of the N211D mutant is reported. Although the main crystal-packing motif (the formation of superhelices) is conserved, the details differ among the known structures. A phosphate ion was localized in the active site of the enzyme. The binding of the surface loop to the active centre is stabilized by the phosphate ion, which correlates with the observed aggregation of TBN1 in phosphate buffer. The conserved binding of the surface loop to the active centre suggests biological relevance of the contact in a regulatory function or in the formation of oligomers.


  • Organizational Affiliation
    • Institute of Biotechnology CAS, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 33.27 kDa 
  • Atom Count: 2,277 
  • Modeled Residue Count: 266 
  • Deposited Residue Count: 277 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclease277Solanum lycopersicumMutation(s): 1 
Gene Names: tbn1
EC: 3.1.30 (PDB Primary Data), 3.1.30.1 (UniProt)
UniProt
Find proteins for Q0KFV0 (Solanum lycopersicum)
Explore Q0KFV0 
Go to UniProtKB:  Q0KFV0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0KFV0
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC
GlyCosmos: G22573RC
GlyGen: G22573RC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free:  0.264 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.944α = 90
b = 115.944β = 90
c = 74.713γ = 120
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary