1GXW

the 2.2 A resolution structure of thermolysin crystallized in presence of potassium thiocyanate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The 2.2 A Resolution Structure of Thermolysin (Tln) Crystallized in the Presence of Potassium Thiocyanate.

Gaucher, J.Selkti, M.Prange, T.Tomas, A.

(2002) Acta Crystallogr.,Sect.D 58: 2198


  • PubMed Abstract: 
  • A new crystallization protocol for thermolysin (EC 3.4.24.27) from Bacillus thermoproteolyticus is presented. After dissolving the protein in the presence of KSCN, which avoids the use of DMSO and CsCl, crystals were obtained following the salting-in ...

    A new crystallization protocol for thermolysin (EC 3.4.24.27) from Bacillus thermoproteolyticus is presented. After dissolving the protein in the presence of KSCN, which avoids the use of DMSO and CsCl, crystals were obtained following the salting-in method. Crystal cell parameters are isomorphous with those previously reported from DMSO/CsCl mixtures. The new SCN(-) crystal structure has been analyzed. It shows the presence of one thiocyanate ion in the catalytic site and several rearrangements in the S(1) and S(2) subsites. These results are in agreement with the measurements of Inouye et al. [(1998), J. Biochem. (Tokyo), 123, 847-852], who observed in solution that the solubility of TLN, which is particularly poor in low ionic strength solutions, increases dramatically in the presence of several neutral salts. The results reported here suggest possible explanations for the solubility increase and for the inhibitory effects of high SCN(-) concentrations on thermolysin activity.


    Related Citations: 
    • Effect of Salts on the Solubility of Thermolysin: A Remarkable Increase in the Solubility as Well as the Activity by the Addition of Salts without Aggregation or Dispersion of Thermolysin
      Inouye, K.,Kuzuya, K.,Tonomura, B.
      (1998) J.Biochem. 123: 847
    • Structure of Thermolysin Refined at 1.6A Resolution
      Holmes, M.A.,Matthews, B.W.
      (1982) J.Mol.Biol. 160: 623


    Organizational Affiliation

    Laboratoire de Cristallographie et RMN Biologiques (UMR-8015, CNRS), Université Paris V, Faculté de Pharmacie, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France. gaucher@pharmacie.univ-paris5.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THERMOLYSIN
A
316Bacillus thermoproteolyticusGene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

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Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
LYS
Query on LYS

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Download CCD File 
A
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
VAL
Query on VAL

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Download CCD File 
A
VALINE
C5 H11 N O2
KZSNJWFQEVHDMF-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.163 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.170α = 90.00
b = 93.170β = 90.00
c = 130.630γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
CNSphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-05
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance