5N12

Crystal structure of TCE treated rPPEP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Improved protein-crystal identification by using 2,2,2-trichloroethanol as a fluorescence enhancer.

Pichlo, C.Toelzer, C.Chojnacki, K.Ocal, S.Uthoff, M.Ruegenberg, S.Hermanns, T.Schacherl, M.Denzel, M.S.Hofmann, K.Niefind, K.Baumann, U.

(2018) Acta Crystallogr F Struct Biol Commun 74: 307-314

  • DOI: 10.1107/S2053230X18005253
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The identification of initial lead conditions for successful protein crystallization is crucial for structural studies using X-ray crystallography. In order to reduce the number of false-negative conditions, an emerging number of fluorescence-based m ...

    The identification of initial lead conditions for successful protein crystallization is crucial for structural studies using X-ray crystallography. In order to reduce the number of false-negative conditions, an emerging number of fluorescence-based methods have been developed which allow more efficient identification of protein crystals and help to distinguish them from salt crystals. Detection of the native tryptophan fluorescence of protein crystals is one of the most widely used methods. However, this method can fail owing to the properties of the crystallized protein or the chemical composition of the crystallization trials. Here, a simple, fast and cost-efficient method employing 2,2,2-trichloroethanol (TCE) has been developed. It can be performed with a standard UV-light microscope and can be applied to cases in which detection of native tryptophan fluorescence fails. In four test cases this method had no effect on the diffraction properties of the crystals and no structural changes were observed. Further evidence is provided that TCE can be added to crystallization trials during their preparation, making this method compatible with high-throughput approaches.


    Organizational Affiliation

    Institute of Biochemistry, University of Cologne, Z├╝lpicher Strasse 47, 50674 Cologne, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pro-Pro endopeptidase
A, B
197Peptoclostridium difficile (strain 630)Mutation(s): 0 
Gene Names: zmp1 (ppep-1)
EC: 3.4.24.89
Find proteins for Q183R7 (Peptoclostridium difficile (strain 630))
Go to UniProtKB:  Q183R7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
8FH
Query on 8FH

Download SDF File 
Download CCD File 
A, B
2,2,2-tris-chloroethanol
C2 H3 Cl3 O
KPWDGTGXUYRARH-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.169α = 90.00
b = 71.769β = 90.00
c = 117.798γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release