4FKC

Recombinant prolidase from Thermococcus sibiricus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Influence of intermolecular contacts on the structure of recombinant prolidase from Thermococcus sibiricus.

Trofimov, A.A.Slutskaya, E.A.Polyakov, K.M.Dorovatovskii, P.V.Gumerov, V.M.Popov, V.O.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1275-1278

  • DOI: 10.1107/S174430911203761X
  • Primary Citation of Related Structures:  
    4FKC

  • PubMed Abstract: 
  • Prolidases are peptidases that are specific for dipeptides with proline as the second residue. The structure of recombinant prolidase from the hyperthermophilic archaeon Thermococcus sibiricus (Tsprol) was determined at 2.6 Å resolution. The homodimer of Tsprol is characterized by a complete lack of interactions between the N- and C-terminal domains of the two subunits and hence can be considered to be the most open structure when compared with previously structurally studied prolidases ...

    Prolidases are peptidases that are specific for dipeptides with proline as the second residue. The structure of recombinant prolidase from the hyperthermophilic archaeon Thermococcus sibiricus (Tsprol) was determined at 2.6 Å resolution. The homodimer of Tsprol is characterized by a complete lack of interactions between the N- and C-terminal domains of the two subunits and hence can be considered to be the most open structure when compared with previously structurally studied prolidases. This structure exists owing to intermolecular coordination bonds between cadmium ions derived from the crystallization solution and histidine residues of a His tag and aspartate and glutamate residues, which link the dimers to each other. This linking leads to the formation of a crystal with a loose packing of protein molecules and low resistance to mechanical influence and temperature increase.


    Organizational Affiliation

    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russian Federation. burayatina@gmail.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Xaa-Pro aminopeptidaseA377Thermococcus sibiricus MM 739Mutation(s): 0 
Gene Names: TSIB_0821
Find proteins for C6A2N7 (Thermococcus sibiricus (strain DSM 12597 / MM 739))
Explore C6A2N7 
Go to UniProtKB:  C6A2N7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.7α = 90
b = 89.7β = 90
c = 165.22γ = 90
Software Package:
Software NamePurpose
AUTOMARdata collection
BALBESphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Database references