2BCN

Solvent isotope effects on interfacial protein electron transfer between cytochrome c and cytochrome c peroxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 ?
  • R-Value Free: 0.230 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Solvent isotope effects on interfacial protein electron transfer in crystals and electrode films.

Kang, S.A.Hoke, K.R.Crane, B.R.

(2006) J Am Chem Soc 128: 2346-2355

  • DOI: https://doi.org/10.1021/ja0557482
  • Primary Citation of Related Structures:  
    2BCN

  • PubMed Abstract: 

    D(2)O-grown crystals of yeast zinc porphyrin substituted cytochrome c peroxidase (ZnCcP) in complex with yeast iso-1-cytochrome c (yCc) diffract to higher resolution (1.7 A) and pack differently than H(2)O-grown crystals (2.4-3.0 A). Two ZnCcP's bind the same yCc (porphyrin-to-porphyrin separations of 19 and 29 A), with one ZnCcP interacting through the same interface found in the H(2)O crystals. The triplet excited-state of at least one of the two unique ZnCcP's is quenched by electron transfer (ET) to Fe(III)yCc (k(e) = 220 s(-1)). Measurement of thermal recombination ET between Fe(II)yCc and ZnCcP+ in the D(2)O-treated crystals has both slow and fast components that differ by 2 orders of magnitude (k(eb)(1) = 2200 s(-1), k(eb)(2) = 30 s(-1)). Back ET in H(2)O-grown crystals is too fast for observation, but soaking H(2)O-grown crystals in D(2)O for hours generates slower back ET, with kinetics similar to those of the D(2)O-grown crystals (k(eb)(1) = 7000 s(-1), k(eb)(2) = 100 s(-1)). Protein-film voltammetry of yCc adsorbed to mixed alkanethiol monolayers on gold electrodes shows slower ET for D(2)O-grown yCc films than for H(2)O-grown films (k(H) = 800 s(-1); k(D) = 540 s(-1) at 20 degrees C). Soaking H(2)O- or D(2)O-grown films in the counter solvent produces an immediate inverse isotope effect that diminishes over hours until the ET rate reaches that found in the counter solvent. Thus, D(2)O substitution perturbs interactions and ET between yCc and either CcP or electrode films. The effects derive from slow exchanging protons or solvent molecules that in the crystal produce only small structural changes.


  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cytochrome c peroxidase
A, C
296Saccharomyces cerevisiaeMutation(s): 0 
EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00431
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c iso-1108Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: CYC1
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00044 
Go to UniProtKB:  P00044
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00044
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 ?
  • R-Value Free: 0.230 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 1
Unit Cell:
Length ( ? )Angle ( ? )
a = 44.533¦Á = 102.47
b = 47.089¦Â = 98.74
c = 84.289¦Ă = 102.16
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references
  • Version 2.2: 2024-12-25
    Changes: Advisory, Data collection, Derived calculations, Refinement description, Structure summary
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