1A2I

SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERROCYTOCHROME C3, NMR, 20 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 600 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

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This is version 1.2 of the entry. See complete history

Literature

Solution structure of Desulfovibrio vulgaris (Hildenborough) ferrocytochrome c3: structural basis for functional cooperativity.

Messias, A.C.Kastrau, D.H.Costa, H.S.LeGall, J.Turner, D.L.Santos, H.Xavier, A.V.

(1998) J.Mol.Biol. 281: 719-739

  • DOI: 10.1006/jmbi.1998.1974
  • Also Cited By: 2BPN

  • PubMed Abstract: 
  • Desulfovibrio vulgaris cytochrome c3 is a 14 kDa tetrahaem cytochrome that plays a central role in energy transduction. The three-dimensional structure of the ferrocytochrome at pH 8.5 was solved through two-dimensional 1H-NMR. The structures were ca ...

    Desulfovibrio vulgaris cytochrome c3 is a 14 kDa tetrahaem cytochrome that plays a central role in energy transduction. The three-dimensional structure of the ferrocytochrome at pH 8.5 was solved through two-dimensional 1H-NMR. The structures were calculated using a large amount of experimental information, which includes upper and lower distance limits as well as dihedral angle restraints. The analysis allows for fast-flipping aromatic residues and flexibility in the haem plane. The structure was determined using 2289 upper and 2390 lower distance limits, 63 restricted ranges for the phi torsion angle, 88 stereospecific assignments out of the 118 stereopairs with non-degenerate chemical shifts (74.6%), and 115 out of the 184 nuclear Overhauser effects to fast-flipping aromatic residues (62.5%), which were pseudo-stereospecifically assigned to one or the other side of the ring. The calculated NMR structures are very well defined, with an average root-mean-square deviation value relative to the mean coordinates of 0.35 A for the backbone atoms and 0.70 A for all heavy-atoms. Comparison of the NMR structures of the ferrocytochrome at pH 8.5 with the available X-ray structure of the ferricytochrome at pH 5.5 reveals that the general fold of the molecule is very similar, but that there are some distinct differences. Calculation of ring current shifts for the residues with significantly different conformations confirms that the NMR structures represent better its solution structure in the reduced form. Some of the localised differences, such as a reorientation of Thr24, are thought to be state-dependent changes that involve alterations in hydrogen bond networks. An important rearrangement in the vicinity of the propionate groups of haem I and involving the covalent linkage of haem II suggests that this is the critical region for the functional cooperativities of this protein.


    Related Citations: 
    • Redox-Bohr Effect in Electron/Proton Energy Transduction: Cytochrome C3 Coupled to Hydrogenase Works as a 'Proton Thruster' in Desulfovibrio Vulgaris
      Louro, R.O.,Catarino, T.,Legall, J.,Xavier, A.V.
      (1997) J.Biol.Inorg.Chem. 2: 488
    • Refinement of the Three-Dimensional Structures of Cytochromes C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 A Resolution and from Desulfovibrio Desulfuricans Atcc27774 at 1.6 A Resolution
      Simoes, P.,Matias, P.M.,Morais, J.,Wilson, K.,Dauter, Z.,Carrondo, M.A.
      () TO BE PUBLISHED --: --
    • NMR Studies of Cooperativity in the Tetrahaem Cytochrome C3 from Desulfovibrio Vulgaris
      Turner, D.L.,Salgueiro, C.A.,Catarino, T.,Legall, J.,Xavier, A.V.
      (1996) Eur.J.Biochem. 241: 723


    Organizational Affiliation

    Universidade Nova de Lisboa, Rua da Quinta Grande, 6 Apartado 127, Oeiras, 2780, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C3
A
107Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)N/A
Find proteins for P00131 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303))
Go to UniProtKB:  P00131
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download SDF File 
Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 600 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 
  • Olderado: 1A2I Olderado
Software Package:
Software NamePurpose
DYANAmodel building
DYANArefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance