3ESD

cut-2b; NCN-Pt-Pincer-Cutinase Hybrid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Solid-state structural characterization of cutinase-ECE-pincer-metal hybrids

Rutten, L.Wieczorek, B.Mannie, J.P.B.A.Kruithof, C.A.Dijkstra, H.P.Egmond, M.R.Lutz, M.Klein Gebbink, R.J.M.Gros, P.van Koten, G.

(2009) Chemistry 15: 4270-4280

  • DOI: 10.1002/chem.200801995
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The first crystal structures of lipases that have been covalently modified through site-selective inhibition by different organometallic phosphonate-pincer-metal complexes are described. Two ECE-pincer-type d(8)-metal complexes, that is, platinum (1) ...

    The first crystal structures of lipases that have been covalently modified through site-selective inhibition by different organometallic phosphonate-pincer-metal complexes are described. Two ECE-pincer-type d(8)-metal complexes, that is, platinum (1) or palladium (2) with phosphonate esters (ECE = [(EtO)-(O=)P(-O-C(6)H(4)-(NO(2))-4)(-C(3)H(6)-4-(C(6)H(2)-(CH(2)E)(2))](-); E = NMe(2) or SMe) were introduced prior to crystallization and have been shown to bind selectively to the Ser(120) residue in the active site of the lipase cutinase to give cut-1 (platinum) or cut-2 (palladium) hybrids. For all five presented crystal structures, the ECE-pincer-platinum or -palladium head group sticks out of the cutinase molecule and is exposed to the solvent. Depending on the nature of the ECE-pincer-metal head group, the ECE-pincer-platinum and -palladium guests occupy different pockets in the active site of cutinase, with concomitant different stereochemistries on the phosphorous atom for the cut-1 (S(P)) and cut-2 (R(P)) structures. When cut-1 was crystallized under halide-poor conditions, a novel metal-induced dimeric structure was formed between two cutinase-bound pincer-platinum head groups, which are interconnected through a single mu-Cl bridge. This halide-bridged metal dimer shows that coordination chemistry is possible with protein-modified pincer-metal complexes. Furthermore, we could use NCN-pincer-platinum complex 1 as site-selective tool for the phasing of raw protein diffraction data, which shows the potential use of pincer-platinum complex 1 as a heavy-atom derivative in protein crystallography.


    Organizational Affiliation

    Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cutinase 1
A
214Fusarium solani subsp. pisiMutation(s): 1 
Gene Names: CUT1 (CUTA)
EC: 3.1.1.74
Find proteins for P00590 (Fusarium solani subsp. pisi)
Go to UniProtKB:  P00590
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SXC
Query on SXC

Download SDF File 
Download CCD File 
A
bromo(4-{3-[(R)-ethoxy(4-nitrophenoxy)phosphoryl]propyl}-2,6-bis[(methylsulfanyl-kappaS)methyl]phenyl-kappaC~1~)palladium(2+)
ethyl 4-nitrophenyl P-[3-(4-(bromopallado)-1,3-bis[(methylthio)methyl]-phenyl)propyl]phosphonate
C21 H27 Br N O5 P Pd S2
UQJAYMPWLMSAFV-QDSLRZTOSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.199 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 72.360α = 90.00
b = 72.360β = 90.00
c = 110.770γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SHELXL-97refinement
XDSdata reduction
ADSCdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance