1K3G

NMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus pasteurii


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 30 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.

Banci, L.Bertini, I.Ciurli, S.Dikiy, A.Dittmer, J.Rosato, A.Sciara, G.Thompsett, A.R.

(2002) Chembiochem 3: 299-310

  • Primary Citation of Related Structures:  1K3H

  • PubMed Abstract: 
  • The solution structure of oxidized cytochrome c(553) (71 amino acid residues) from the Gram-positive bacterium Bacillus pasteurii is here reported and compared with the available crystal structure. The solution structure is obtained from 1609 meaning ...

    The solution structure of oxidized cytochrome c(553) (71 amino acid residues) from the Gram-positive bacterium Bacillus pasteurii is here reported and compared with the available crystal structure. The solution structure is obtained from 1609 meaningful NOE data (22.7 per residue), 76 dihedral angles, and 59 pseudocontact shifts. The root mean square deviations from the average structure are 0.25+/-0.07 and 0.59+/-0.13 A for the backbone and all heavy atoms, respectively, and the quality assessment of the structure is satisfactory. The solution structure closely reproduces the fold observed in the crystal structure. The backbone mobility was then investigated through amide (15)N relaxation rate and (15)N-(1)H NOE measurements. The protein is rigid in both the sub-nanosecond and millisecond time scales, probably due to the relatively large heme:number of amino acids ratio. Modeling of eight c-type cytochromes from other Gram-positive bacteria with a high sequence identity (>30 %) to the present cytochrome c(553) was performed. Analysis of consensus features accounts for the relatively low reduction potential as being due to extensive heme hydration and indicates residues 34-35, 44-46, 69-72, and 75 as a conserved hydrophobic patch for the interaction with a protein partner. At variance with mitochondrial c-type cytochrome, this protein does not experience pH-dependent coordination equilibria. The reasons for this difference are analyzed.


    Related Citations: 
    • Modulation of Bacillus pasteurii Cytochrome c553 Reduction Potential by Structural and Solution Parameters
      Benini, S.,Borsari, M.,Ciurli, S.,Dikiy, A.,Lamborghini, M.
      (1998) J.Biol.Inorg.Chem. 3: 371
    • Crystal Structure of Oxidized Bacillus pasteurii cytochrome c-553 at 0.97-A Resolution
      Benini, S.,Gonzalez, A.,Rypniewski, W.R.,Wilson, K.S.,Van Beeumen, J.J.,Ciurli, S.
      (2000) Biochemistry 39: 13115


    Organizational Affiliation

    Centro di Risonanze Magnetiche, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cytochrome c-553
A
71Sporosarcina pasteuriiN/A
Find proteins for P82599 (Sporosarcina pasteurii)
Go to UniProtKB:  P82599
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: 400 
  • Conformers Submitted: 30 
  • Selection Criteria: target function 
  • Olderado: 1K3G Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-10-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance