6FF5 | pdb_00006ff5

X-ray structure of bovine heart cytochrome c at high ionic strength


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.203 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6FF5

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

X-ray structure of bovine heart cytochrome c at high ionic strength.

Merlino, A.

(2018) Biometals 31: 277-284

  • DOI: https://doi.org/10.1007/s10534-018-0090-x
  • Primary Citation Related Structures: 
    6FF5

  • PubMed Abstract: 

    Bovine heart cytochrome c (bCyt c) is an extensively studied hemoprotein of only 104 residues. Due to the existence of isoforms generated by non-enzymatic deaminidation, crystallization of bCyt c is difficult and involves extensive purification and the use of microseeding or the presence of an electric field. Taking advantage of the capacity of cytochrome c (cyt c) to bind anions on its protein surface, the commercially available bCyt c was crystallized without extra purifications, using ammonium sulfate as precipitant and nitrate ions as additives. The structure of the ferric bCyt c in a new crystal form is described and compared with that previously solved at low ionic strength and with those of human and horse cyt c. The overall structure of bCyt c is conserved, while the side chains of several residues that play a role in the interactions of cyt c with its partners have different rotamers in the two structures. The effect of the presence of nitrate ions on the structure of the protein is then evaluated and compared with that observed in the case of ferrous and ferric horse heart cyt c.


  • Organizational Affiliation
    • Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126, Naples, Italy. antonello.merlino@unina.it.

Macromolecule Content 

  • Total Structure Weight: 12.62 kDa 
  • Atom Count: 1,005 
  • Modeled Residue Count: 104 
  • Deposited Residue Count: 104 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c104Bos taurusMutation(s): 0 
UniProt
Find proteins for P62894 (Bos taurus)
Explore P62894 
Go to UniProtKB:  P62894
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62894
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC

Query on HEC



Download:Ideal Coordinates CCD File
B [auth A]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NO3

Query on NO3



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.203 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.35α = 90
b = 83.35β = 90
c = 92.49γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2018-03-21 
  • Deposition Author(s): Merlino, A.

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary