Recombinant prolidase from Thermococcus sibiricus

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

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This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1107/S174430911203761X
  • Primary Citation of Related Structures:  

  • 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. 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Xaa-Pro aminopeptidase377Thermococcus 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6A2N7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CD

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
Experimental Data & Validation

Experimental Data

  • 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
XDSdata reduction
XSCALEdata scaling

Structure Validation

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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
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description