6FSM

Crystal structure of TCE-treated Thermolysin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 

Starting Model: experimental
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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
Thermolysin316Geobacillus stearothermophilusMutation(s): 0 
EC: 3.4.24.27
UniProt
Find proteins for P43133 (Geobacillus stearothermophilus)
Explore P43133 
Go to UniProtKB:  P43133
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43133
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LYS
Query on LYS

Download Ideal Coordinates CCD File 
L [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
VAL
Query on VAL

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K [auth A]VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
PO4
Query on PO4

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G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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H [auth A],
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

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C [auth A],
D [auth A],
E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.948α = 90
b = 92.948β = 90
c = 129.668γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-09
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description