2NUK | pdb_00002nuk

Soluble Domain of the Rieske Iron-Sulfur Protein from Rhodobacter sphaeroides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.136 (Depositor), 0.136 (DCC) 
  • R-Value Work: 
    0.118 (Depositor), 0.119 (DCC) 
  • R-Value Observed: 
    0.120 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Atomic resolution structures of rieske iron-sulfur protein: role of hydrogen bonds in tuning the redox potential of iron-sulfur clusters.

Kolling, D.J.Brunzelle, J.S.Lhee, S.Crofts, A.R.Nair, S.K.

(2007) Structure 15: 29-38

  • DOI: https://doi.org/10.1016/j.str.2006.11.012
  • Primary Citation Related Structures: 
    2NUK, 2NUM, 2NVE, 2NVF, 2NVG, 2NWF

  • PubMed Abstract: 

    The Rieske [2Fe-2S] iron-sulfur protein of cytochrome bc(1) functions as the initial electron acceptor in the rate-limiting step of the catalytic reaction. Prior studies have established roles for a number of conserved residues that hydrogen bond to ligands of the [2Fe-2S] cluster. We have constructed site-specific variants at two of these residues, measured their thermodynamic and functional properties, and determined atomic resolution X-ray crystal structures for the native protein at 1.2 A resolution and for five variants (Ser-154-->Ala, Ser-154-->Thr, Ser-154-->Cys, Tyr-156-->Phe, and Tyr-156-->Trp) to resolutions between 1.5 A and 1.1 A. These structures and complementary biophysical data provide a molecular framework for understanding the role hydrogen bonds to the cluster play in tuning thermodynamic properties, and hence the rate of this bioenergetic reaction. These studies provide a detailed structure-function dissection of the role of hydrogen bonds in tuning the redox potentials of [2Fe-2S] clusters.


  • Organizational Affiliation
    • Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801, USA.

Macromolecule Content 

  • Total Structure Weight: 15.34 kDa 
  • Atom Count: 1,291 
  • Modeled Residue Count: 141 
  • Deposited Residue Count: 141 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunit141Cereibacter sphaeroidesMutation(s): 0 
Gene Names: petAfbcF
EC: 1.10.2.2 (PDB Primary Data), 7.1.1.8 (UniProt)
UniProt
Find proteins for Q02762 (Cereibacter sphaeroides)
Explore Q02762 
Go to UniProtKB:  Q02762
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02762
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES

Query on FES



Download:Ideal Coordinates CCD File
B [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.136 (Depositor), 0.136 (DCC) 
  • R-Value Work:  0.118 (Depositor), 0.119 (DCC) 
  • R-Value Observed: 0.120 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.568α = 90
b = 70.568β = 90
c = 54.769γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary