1I8O

RHODOPSEUDOMONAS PALUSTRIS CYT C2 AMMONIA COMPLEX AT 1.15 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.140 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Cleavage of the iron-methionine bond in c-type cytochromes: crystal structure of oxidized and reduced cytochrome c(2) from Rhodopseudomonas palustris and its ammonia complex.

Geremia, S.Garau, G.Vaccari, L.Sgarra, R.Viezzoli, M.S.Calligaris, M.Randaccio, L.

(2002) Protein Sci 11: 6-17

  • DOI: 10.1110/ps.ps.13102
  • Primary Citation of Related Structures:  
    1FJ0, 1I8O, 1I8P

  • PubMed Abstract: 
  • The three-dimensional structures of the native cytochrome c(2) from Rhodopseudomonas palustris and of its ammonia complex have been obtained at pH 4.4 and pH 8.5, respectively. The structure of the native form has been refined in the oxidized state at 1.70 A and in the reduced state at 1 ...

    The three-dimensional structures of the native cytochrome c(2) from Rhodopseudomonas palustris and of its ammonia complex have been obtained at pH 4.4 and pH 8.5, respectively. The structure of the native form has been refined in the oxidized state at 1.70 A and in the reduced state at 1.95 A resolution. These are the first high-resolution crystal structures in both oxidation states of a cytochrome c(2) with relatively high redox potential (+350 mV). The differences between the two oxidation states of the native form, including the position of internal water molecules, are small. The unusual six-residue insertion Gly82-Ala87, which precedes the heme binding Met93, forms an isolated 3(10)-helix secondary structural element not previously observed in other c-type cytochromes. Furthermore, this cytochrome shows an external methionine residue involved in a strained folding near the exposed edge of the heme. The structural comparison of the present cytochrome c(2) with other c-type cytochromes has revealed that the presence of such a residue, with torsion angles phi and psi of approximately -140 and -130 degrees, respectively, is a typical feature of this family of proteins. The refined crystal structure of the ammonia complex, obtained at 1.15 A resolution, shows that the sulphur atom of the Met93 axial ligand does not coordinate the heme iron atom, but is replaced by an exogenous ammonia molecule. This is the only example so far reported of an X-ray structure with the heme iron coordinated by an ammonia molecule. The detachment of Met93 is accompanied by a very localized change in backbone conformation, involving mainly the residues Lys92, Met93, and Thr94. Previous studies under typical denaturing conditions, including high-pH values and the presence of exogenous ligands, have shown that the detachment of the Met axial ligand is a basic step in the folding/unfolding process of c-type cytochromes. The ammonia adduct represents a structural model for this important step of the unfolding pathway. Factors proposed to be important for the methionine dissociation are the strength of the H-bond between the Met93 and Tyr66 residues that stabilizes the native form, and the presence in this bacterial cytochrome c(2) of the rare six-residue insertion in the helix 3(10) conformation that increases Met loop flexibility.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of Two Ph-Dependent Forms of Cytochrome C2 from Rhodopseudomonas Palustris
      Garau, G., Geremia, S., Randaccio, L., Vaccari, L., Viezzoli, M.S.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 1699
    • Crystal Structure of Oxidized and Reduced Cytochrome from Rhodopseudomonas Palustris: Relationship Between Hydrogen-Bonding Network of the Conservative Water Molecule and Reduction Potential
      Geremia, S., Calligaris, M., Garau, G., Vaccari, L., Viezzoli, M.S., Randaccio, L.
      () To be published --: --
    • Crystallization and X-Ray Structure Determination O Cytochrome C2 Fromrhodobacter Sphaeroides in Three Crystal Forms
      Axelrod, H., Feher, G., Allen, J.P., Chirino, A.J., Day, M.W., Hsu, B.T., Rees, D.C.
      (1994) Acta Crystallogr D Biol Crystallogr 50: 596
    • Cytochrome C2 Sequence Variation Among the Recognised Species of Purple Nonsulphur Photosynthetic Bacteria
      Ambler, R.P., Daniel, M., Hermoso, J., Meyer, T.E., Bartsch, R.G., Kamen, M.D.
      (1979) Nature 278: 659

    Organizational Affiliation

    Centro di Eccellenza di Biocristallografia, Dipartimento di Scienze Chimiche, Università di Trieste, I-34127 Trieste, Italy. geremia@univ.trieste.it



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C2A114Rhodopseudomonas palustrisMutation(s): 0 
UniProt
Find proteins for P00091 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009))
Explore P00091 
Go to UniProtKB:  P00091
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00091
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
D [auth A]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NH3
Query on NH3

Download Ideal Coordinates CCD File 
E [auth A]AMMONIA
H3 N
QGZKDVFQNNGYKY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.140 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.95α = 90
b = 64.95β = 90
c = 68.67γ = 120
Software Package:
Software NamePurpose
AMoREphasing
SHELXrefinement
MOSFLMdata reduction
CCP4data scaling
SHELXL-97refinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2001-03-15 
  • Released Date: 2001-04-04 
  • Deposition Author(s): Garau, G., Geremia, S.

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence