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 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1C52

  • 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 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 ...

    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: 
    • 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
    • Reversible Thermal Unfolding of Thermostable Cytochrome C-552
      Nojima, H., Hon-Nami, K., Oshima, T., Noda, H.
      (1978) J Mol Biol 122: 33
    • Purification and Some Properties of Cytochrome C-552 from an Extreme Thermophile, Thermus Thermophilus Hb8
      Hon-Nami, K., Oshima, T.
      (1977) J Biochem 82: 769

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME-C552A131Thermus thermophilusMutation(s): 0 
Gene Names: cycA
Find proteins for P04164 (Thermus thermophilus)
Explore P04164 
Go to UniProtKB:  P04164
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
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 
  • R-Value Observed: 0.191 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.1α = 90
b = 47.1β = 90
c = 68.82γ = 90
Software Package:
Software NamePurpose
MADPRBmodel building
MADSYSphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
MOSFLMdata reduction
SCALEPACKdata scaling
CCP4data scaling
ROTAVATAdata scaling
TRUNCATE)data scaling
MADPRBphasing
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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