1H1O

Acidithiobacillus ferrooxidans cytochrome c4 structure supports a complex-induced tuning of electron transfer

PDB DOI: https://doi.org/10.2210/pdb1H1O/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Acidithiobacillus ferrooxidans
Mutation(s): No

Deposited: 2002-07-19 Released: 2003-07-17
Deposition Author(s): Abergel, C., Nitschke, W., Malarte, G., Bruschi, M., Claverie, J.-M., Guidici-Orticoni, M.-T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free:
0.284 (Depositor), 0.280 (DCC)
R-Value Work:
0.239 (Depositor), 0.240 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The Structure of Acidithiobacillus Ferrooxidans C(4)-Cytochrome. A Model for Complex-Induced Electron Transfer Tuning

Abergel, C., Nitschke, W., Malarte, G., Bruschi, M., Claverie, J.-M., Guidici-Orticoni, M.-T.

(2003) Structure 11: 547

PubMed: 12737820 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(03)00072-8
Primary Citation of Related Structures:
1H1O

PubMed Abstract:
The study of electron transfer between the copper protein rusticyanin (RCy) and the c(4)-cytochrome CYC(41) of the acidophilic bacterium Acidithiobacillus ferrooxidans has evidenced a remarkable decrease of RCy's redox potential upon complex formation. The structure of the CYC(41) obtained at 2.2 A resolution highlighted a specific glutamate residue (E121) involved in zinc binding as potentially playing a central role in this effect, required for the electron transfer to occur. EPR and stopped-flow experiments confirmed the strong inhibitory effect of divalent cations on CYC(41):RCy complex formation. A docking analysis of the CYC(41) and RCy structure allows us to propose a detailed model for the complex-induced tuning of electron transfer in agreement with our experimental data, which could be representative of other copper proteins involved in electron transfer.

Organizational Affiliation

Information Génomique et Structurale, UPR 2589, Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, 13402 20, Marseille cedex, France. chantal.abergel@igs.cnrs-mrs.fr

Macromolecule Content

Total Structure Weight: 43.02 kDa
Atom Count: 2,998
Modelled Residue Count: 342
Deposited Residue Count: 366
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C-552	A, B	183	Acidithiobacillus ferrooxidans	Mutation(s): 0
UniProt
Find proteins for P74917 (Acidithiobacillus ferridurans) Explore P74917 Go to UniProtKB: P74917
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P74917
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A], D [auth A], J [auth B], K [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	F [auth A] G [auth A] H [auth A] M [auth B] N [auth B] F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.284 (Depositor), 0.280 (DCC)
R-Value Work: 0.239 (Depositor), 0.240 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.049	α = 90
b = 100.049	β = 90
c = 149.668	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-07-17

Deposition Author(s):

Guidici-Orticoni, M.-T.

Revision History (Full details and data files)

Version 1.0: 2003-07-17
Type: Initial release
Version 1.1: 2011-10-12
Changes: Derived calculations, Non-polymer description, Other, Version format compliance
Version 1.2: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other