1LU0

Atomic Resolution Structure of Squash Trypsin Inhibitor: Unexpected Metal Coordination


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.120 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Atomic resolution structure of squash trypsin inhibitor: unexpected metal coordination.

Thaimattam, R.Tykarska, E.Bierzynski, A.Sheldrick, G.M.Jaskolski, M.

(2002) Acta Crystallogr.,Sect.D 58: 1448-1461

  • DOI: 10.1107/S0907444902011769

  • PubMed Abstract: 
  • CMTI-I, a small-protein trypsin inhibitor, has been crystallized as a 4:1 protein-zinc complex. The metal is coordinated in a symmetric tetrahedral fashion by glutamate/glutamic acid side chains. The structure was solved by direct methods in the abse ...

    CMTI-I, a small-protein trypsin inhibitor, has been crystallized as a 4:1 protein-zinc complex. The metal is coordinated in a symmetric tetrahedral fashion by glutamate/glutamic acid side chains. The structure was solved by direct methods in the absence of prior knowledge of the special position metal centre and refined with anisotropic displacement parameters using diffraction data extending to 1.03 A. In the final calculations, the main-chain atoms of low B(eq) values were refined without restraint control. The two molecules in the asymmetric unit have a conformation that is very similar to that reported earlier for CMTI-I in complex with trypsin, despite the Met8Leu mutation of the present variant. The only significant differences are in the enzyme-binding epitope (including the Arg5 residue) and in a higher mobility loop around Glu24. The present crystal structure contains organic solvent molecules (glycerol, MPD) that interact with the inhibitor molecules in an area that is at the enzyme-inhibitor interface in the CMTI-I-trypsin complex. A perfectly ordered residue (Ala18) has an unusual Ramachandran conformation as a result of geometrical strain introduced by the three disulfide bridges that clamp the protein fold. The results confirm deficiencies of some stereochemical restraints, such as peptide planarity or the N-C(alpha)-C angle, and suggest a link between their violations and hydrogen bonding.


    Related Citations: 
    • Conservative mutation Met8 --> Leu Effects Folding and Stability of Squash Trypsin Inhibitor Cmti-I
      Zhukov, I.,Jaroszewski, L.,Bierzynski, A.
      (2000) Protein Sci. 9: 273
    • The refined 2.0 A X-ray crystal structure of the complex formed between bovine beta-trypsin and CMTI-I, a trypsin inhibitor from squash seeds (Cucurbita maxima). Topological similarity of the squash seed inhibitors with the carboxypeptidase A inhibitor from potatoes
      Bode, W.,Greyling, H.J.,Huber, R.,Otlewski, J.,Wilusz, T.
      (1989) FEBS Lett. 242: 285
    • High-Resolution Structures of Three New Trypsin-Squash-Inhibitor Complexes: A Detailed Comparison with Other Trypsins and Their Complexes
      Helland, R.,Berglund, G.I.,Otlewski, J.,Apostoluk, W.,Andersen, O.A.,Willassen, N.P.,Smalas, A.O.
      (1999) Acta Crystallogr.,Sect.D 55: 139
    • Relaxation matrix refinement of the solution structure of squash trypsin inhibitor
      Nilges, M.,Habazettl, J.,Brunger, A.T.,Holak, T.A.
      (1991) J.Mol.Biol. 219: 499


    Organizational Affiliation

    Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trypsin inhibitor I
A, B
29Cucurbita maximaMutations: M8L
Find proteins for P01074 (Cucurbita maxima)
Go to UniProtKB:  P01074
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD

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Download CCD File 
B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.120 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.280α = 90.00
b = 58.630β = 90.00
c = 19.320γ = 90.00
Software Package:
Software NamePurpose
SHELXDphasing
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-28
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2016-01-20
    Type: Derived calculations