5N12 | pdb_00005n12

Crystal structure of TCE treated rPPEP-1

• PDB DOI: https://doi.org/10.2210/pdb5N12/pdb

• Classification: HYDROLASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-04 Released: 2018-05-30 
• Deposition Author(s): Pichlo, C., Schacherl, M., Baumann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

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

• PubMed: 29717999 
• DOI: https://doi.org/10.1107/S2053230X18005253
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany.
Max Planck Institute for Biology of Ageing, Research Institute, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany.
Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674 Cologne, Germany.
Structural Dynamics of Proteins, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.68 kDa 
• Atom Count: 3,615 
• Modeled Residue Count: 391 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pro-Pro endopeptidase	A, B	197	Clostridioides difficile 630	Mutation(s): 0  Gene Names: zmp1, CD630_28300 EC: 3.4.24.89
UniProt
Find proteins for Q183R7 (Clostridioides difficile (strain 630)) Explore Q183R7  Go to UniProtKB:  Q183R7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8FH	D [auth A], G [auth B], H [auth B]	2,2,2-tris-chloroethanol C2 H3 Cl3 O KPWDGTGXUYRARH-UHFFFAOYSA-N
TRS	E [auth A], I [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN	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 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.169	α = 90
b = 71.769	β = 90
c = 117.798	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Pichlo, C., Schacherl, M., Baumann, U.

Revision History  

• 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