9G3A | pdb_00009g3a

Crystal Structure of the artificial protein METP in complex with cadmium ion at different temperature, 160 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 
    0.160 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into temperature-dependent dynamics of METPsc1, a miniaturized electron-transfer protein.

Di Costanzo, L.F.Sgueglia, G.Orlando, C.Polentarutti, M.Leone, L.La Gatta, S.De Fenza, M.De Gioia, L.Lombardi, A.Arrigoni, F.Chino, M.

(2025) J Inorg Biochem 264: 112810-112810

  • DOI: https://doi.org/10.1016/j.jinorgbio.2024.112810
  • Primary Citation of Related Structures:  
    9G39, 9G3A, 9G3B, 9G3C, 9G3U

  • PubMed Abstract: 

    The design of protein-metal complexes is rapidly advancing, with applications spanning catalysis, sensing, and bioremediation. We report a comprehensive investigation of METPsc1, a Miniaturized Electron Transfer Protein, in complex with cadmium. This study elucidates the impact of metal coordination on protein folding and structural dynamics across temperatures from 100 K to 300 K. Our findings reveal that METPsc1, composed of two similar halves stabilized by intramolecular hydrogen bonds, exhibits a unique "clothespin-like" recoil mechanism. This allows it to adapt to metal ions of varying radii, mirroring the flexibility observed in natural rubredoxins. High-resolution crystallography and molecular dynamics simulations unveil concerted backbone motions and subtle temperature-dependent shifts in side-chain conformations, particularly for residues involved in crystal packing. Notably, CdS bond lengths increase with temperature, correlating with anisotropic motions of the sulfur atoms involved in second-shell hydrogen bonding. This suggests a dynamic role of protein matrix upon redox cycling. These insights into METPsc1 highlight its potential for catalysis and contribute to the designing of artificial metalloproteins with functional plasticity.


  • Organizational Affiliation

    Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, NA, Italy. Electronic address: luigi.dicostanzo4@unina.it.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
METP ARTIFICIAL PROTEINA [auth C]30synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
AIB
Query on AIB
A [auth C]L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.384α = 90
b = 56.338β = 90
c = 19.191γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XPREPdata reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)ItalyCUP H53D23007950001

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Database references