4FKC

Recombinant prolidase from Thermococcus sibiricus

• PDB DOI: https://doi.org/10.2210/pdb4FKC/pdb

• Classification: HYDROLASE
• Organism(s): Thermococcus sibiricus MM 739
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-06-13 Released: 2012-11-07 
• Deposition Author(s): Trofimov, A.A., Slutskaya, E.S., Polyakov, K.M., Dorovatovskii, P.V., Gumerov, V.M., Popov, V.O.

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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 

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

• PubMed: 23143231 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russian Federation. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.95 kDa 
• Atom Count: 2,916 
• Modelled Residue Count: 370 
• Deposited Residue Count: 377 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xaa-Pro aminopeptidase	A	377	Thermococcus sibiricus MM 739	Mutation(s): 0  Gene Names: TSIB_0821
UniProt
Find proteins for C6A2N7 (Thermococcus sibiricus (strain DSM 12597 / MM 739)) Explore C6A2N7  Go to UniProtKB:  C6A2N7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	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]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

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 = 89.7	α = 90
b = 89.7	β = 90
c = 165.22	γ = 90

Software Package:

Software Name	Purpose
AUTOMAR	data collection
BALBES	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Trofimov, A.A., Slutskaya, E.S., Polyakov, K.M., Dorovatovskii, P.V., Gumerov, V.M., Popov, V.O.

Revision History  

• 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