2BC5

Crystal structure of E. coli cytochrome b562 with engineered c-type heme linkages


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Stability and Folding Kinetics of Structurally Characterized Cytochrome c-b(562).

Faraone-Mennella, J.Tezcan, F.A.Gray, H.B.Winkler, J.R.

(2006) Biochemistry 45: 10504-10511

  • DOI: https://doi.org/10.1021/bi060242x
  • Primary Citation of Related Structures:  
    2BC5

  • PubMed Abstract: 

    The four-helix-bundle protein fold can be constructed from a wide variety of primary amino acid sequences. Proteins with this structure are excellent candidates for investigations of the relationship between folding mechanism and topology. The folding of cytochrome b(562), a four-helix-bundle heme protein, is hampered by heme dissociation. To overcome this complication, we have engineered a variant of cytochrome b(562) (cyt c-b(562)) featuring a c-type linkage between the heme and the polypeptide chain. The replacement of the native cyt b(562) leader sequence in this protein with that of a c-type cytochrome (cyt c(556)) led to high yields of fully matured and correctly folded cyt c-b(562). We have determined the X-ray crystal structure of cyt c-b(562) at 2.25 A and characterized its physical, chemical, and folding properties. These measurements reveal that the c-type linkage does not perturb the protein fold or reduction potential of the heme group. The covalent attachment of the porphyrin to the polypeptide does, however, produce a substantial change in protein stability and folding kinetics.


  • Organizational Affiliation

    Beckman Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Soluble cytochrome b562
A, B, C, D
106Escherichia coliMutation(s): 3 
UniProt
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABE7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
O [auth C],
Q [auth D]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
G [auth B]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
G [auth B],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
M [auth C],
N [auth C],
P [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.861α = 90
b = 68.158β = 90
c = 90.44γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Advisory, Database references
  • Version 2.2: 2023-08-23
    Changes: Data collection, Refinement description