5HKG

Total chemical synthesis, refolding and crystallographic structure of a fully active immunophilin: calstabin 2 (FKBP12.6).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Total chemical synthesis, refolding, and crystallographic structure of fully active immunophilin calstabin 2 (FKBP12.6).

Bacchi, M.Jullian, M.Sirigu, S.Fould, B.Huet, T.Bruyand, L.Antoine, M.Vuillard, L.Ronga, L.Chavas, L.M.Nosjean, O.Ferry, G.Puget, K.Boutin, J.A.

(2016) Protein Sci. 25: 2225-2242

  • DOI: 10.1002/pro.3051

  • PubMed Abstract: 
  • Synthetic biology (or chemical biology) is a growing field to which the chemical synthesis of proteins, particularly enzymes, makes a fundamental contribution. However, the chemical synthesis of catalytically active proteins (enzymes) remains poorly ...

    Synthetic biology (or chemical biology) is a growing field to which the chemical synthesis of proteins, particularly enzymes, makes a fundamental contribution. However, the chemical synthesis of catalytically active proteins (enzymes) remains poorly documented because it is difficult to obtain enough material for biochemical experiments. We chose calstabin, a 107-amino-acid proline isomerase, as a model. We synthesized the enzyme using the native chemical ligation approach and obtained several tens of milligrams. The polypeptide was refolded properly, and we characterized its biophysical properties, measured its catalytic activity, and then crystallized it in order to obtain its tridimensional structure after X-ray diffraction. The refolded enzyme was compared to the recombinant, wild-type enzyme. In addition, as a first step of validating the whole process, we incorporated exotic amino acids into the N-terminus. Surprisingly, none of the changes altered the catalytic activities of the corresponding mutants. Using this body of techniques, avenues are now open to further obtain enzymes modified with exotic amino acids in a way that is only barely accessible by molecular biology, obtaining detailed information on the structure-function relationship of enzymes reachable by complete chemical synthesis.


    Organizational Affiliation

    Pôle d'Expertise Biotechnologie, Chimie and Biologie, Institut de Recherches Servier, 125 Chemin de Ronde, Croissy-sur-Seine, 78290, France.,Genepep, 12 Rue du Fer à Cheval, Saint-Jean-de-Védas, 34430, France.,PROXIMA-1, Division Expériences, Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin-BP48, Gif-sur-Yvette CEDEX, 91192, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase FKBP1B
A
107Homo sapiensMutation(s): 0 
Gene Names: FKBP1B (FKBP12.6, FKBP1L, FKBP9, OTK4)
EC: 5.2.1.8
Find proteins for P68106 (Homo sapiens)
Go to Gene View: FKBP1B
Go to UniProtKB:  P68106
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
RAP
Query on RAP

Download SDF File 
Download CCD File 
A
RAPAMYCIN IMMUNOSUPPRESSANT DRUG
C51 H79 N O13
QFJCIRLUMZQUOT-HPLJOQBZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RAPKd: 0.2 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.200α = 90.00
b = 48.610β = 90.00
c = 53.360γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-11-30
    Type: Database references