1C52

THERMUS THERMOPHILUS CYTOCHROME-C552: A NEW HIGHLY THERMOSTABLE CYTOCHROME-C STRUCTURE OBTAINED BY MAD PHASING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Thermus thermophilus cytochrome-c552: A new highly thermostable cytochrome-c structure obtained by MAD phasing.

Than, M.E.Hof, P.Huber, R.Bourenkov, G.P.Bartunik, H.D.Buse, G.Soulimane, T.

(1997) J.Mol.Biol. 271: 629-644

  • DOI: 10.1006/jmbi.1997.1181

  • PubMed Abstract: 
  • The three-dimensional structure of cytochrome-c552 from Thermus thermophilus has been determined by the multiple anomalous dispersion technique using synchrotron radiation and refined to a resolution of 1.28 A. Data collection at 90 K and the recordi ...

    The three-dimensional structure of cytochrome-c552 from Thermus thermophilus has been determined by the multiple anomalous dispersion technique using synchrotron radiation and refined to a resolution of 1.28 A. Data collection at 90 K and the recording of three data sets (f'-minimum: 7125 eV, f"-maximum: 7138 eV and reference for scaling: 10,077 eV) resulted in an initial electron density of very high quality at 2.1 A, which was readily interpretable for model building. The model was refined to an R value of 19.1% (Rfree=22.4%) at 1.28 A resolution using a fourth data set collected at a photon energy of 11,810 eV. Comparison of this thermophilic cytochrome with its mesophilic mitochondrial or bacterial counterparts reveals significant structural differences which are discussed with respect to their importance for thermostability and binding between this cytochrome and its corresponding ba3-oxidase. Amino acid sequence similarities to other class I cytochromes are very weak and entirely limited to the region around the CXXCH motif close to the N terminus. The N-terminal two-thirds of cytochrome-c552 cover spatial regions around the heme prosthetic group that are similar to those observed for other cytochromes. The actual secondary structural elements that are responsible for that shielding do not, however, correlate well to other structures. Only the N-terminal helix (containing the heme binding cysteine residues) aligns reasonably well with other class I cytochromes. The most striking differences that distinguish the present structure from all other class I cytochromes is the C-terminal one-third of the molecule that wraps around the remainder of the structure as a stabilizing clamp, the existence of an extended beta-sheet covering one edge of the heme and the lack of any internal water molecule.


    Related Citations: 
    • Purification and Some Properties of Cytochrome C-552 from an Extreme Thermophile, Thermus Thermophilus Hb8
      Hon-Nami, K.,Oshima, T.
      (1977) J.Biochem.(Tokyo) 82: 769
    • Reversible Thermal Unfolding of Thermostable Cytochrome C-552
      Nojima, H.,Hon-Nami, K.,Oshima, T.,Noda, H.
      (1978) J.Mol.Biol. 122: 33
    • Amino Acid Sequence of Cytochrome C-552 from Thermus Thermophilus Hb8
      Titani, K.,Ericsson, L.H.,Hon-Nami, K.,Miyazawa, T.
      (1985) Biochem.Biophys.Res.Commun. 128: 781


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Am Klopferspitz 18 A, Martinsried, 82152, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME-C552
A
131Thermus thermophilusGene Names: cycA
Find proteins for P04164 (Thermus thermophilus)
Go to UniProtKB:  P04164
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.28 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 47.100α = 90.00
b = 47.100β = 90.00
c = 68.820γ = 90.00
Software Package:
Software NamePurpose
ROTAVATAdata scaling
MADPRBphasing
MADPRBmodel building
X-PLORmodel building
X-PLORphasing
CCP4data scaling
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
TRUNCATE)data scaling
X-PLORrefinement
MADSYSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-24
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance