4FKC

Recombinant prolidase from Thermococcus sibiricus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.231 

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 68: 1275-1278

  • DOI: 10.1107/S174430911203761X

  • 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 homodime ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Xaa-Pro aminopeptidase
A
377Thermococcus sibiricus (strain MM 739 / DSM 12597)Mutation(s): 0 
Find proteins for C6A2N7 (Thermococcus sibiricus (strain MM 739 / DSM 12597))
Go to UniProtKB:  C6A2N7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.231 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 89.700α = 90.00
b = 89.700β = 90.00
c = 165.220γ = 90.00
Software Package:
Software NamePurpose
AUTOMARdata collection
XDSdata reduction
XSCALEdata scaling
BALBESphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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