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 
  • R-Value Observed: 0.164 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1107/S2053230X18005253
  • Primary Citation of Related Structures:  
    5N12, 6FSJ, 6FSM

  • 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 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, Zülpicher Strasse 47, 50674 Cologne, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pro-Pro endopeptidase
A, B
197Clostridioides difficile 630Mutation(s): 0 
Gene Names: zmp1CD630_28300
EC: 3.4.24.89
UniProt
Find proteins for Q183R7 (Clostridioides difficile (strain 630))
Explore Q183R7 
Go to UniProtKB:  Q183R7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ183R7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8FH
Query on 8FH

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth B]
2,2,2-tris-chloroethanol
C2 H3 Cl3 O
KPWDGTGXUYRARH-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.169α = 90
b = 71.769β = 90
c = 117.798γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description