3CYT

REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Redox conformation changes in refined tuna cytochrome c.

Dickerson, R.E., Takano, T.

(1980) Proc.Natl.Acad.Sci.USA 77: 6371-6375


  • PubMed Abstract: 

    • Tuna ferrocytochrome c and ferricytochrome c have been refined independently at high resolution (1.5 A and 1.8 A) to crystallographic residual errors of 17.3% and 20.8%, respectively. Small but significant conformational differences are seen surround ...

    Tuna ferrocytochrome c and ferricytochrome c have been refined independently at high resolution (1.5 A and 1.8 A) to crystallographic residual errors of 17.3% and 20.8%, respectively. Small but significant conformational differences are seen surrounding a buried water molecule that is hydrogen bonded to Asn-52, Tyr-67, and Thr-78. In the oxidized state, this water molecule is 1.0 A closer to the heme and the heme has moved 0.15 A out of its heme crevice; both changes lead to a more polar microenvironment for the heme. Chemical modification studies, patterns of evolutionary conservatism, structural differences in bacterial cytochromes, and x-ray studies all agree that the "active site" for cytochrome c is bounded by lysines 8, 13,27, 72, 79, 86, and 87 (thus containing the evolutionary conservative 72-87 loop) and has the buried water molecule just below its surface and the opening of the heme crevice slightly to one side.

    Related Citations: 
    • The Structure and History of an Ancient Protein
      Dickerson, R.E.
      (1972) Sci.Am. 226: 58
    • The Structure of Ferrocytochrome C at 2.45 Angstroms Resolution
      Takano, T.,Kallai, O.B.,Swanson, R.,Dickerson, R.E.
      (1973) J.Biol.Chem. 248: 5234
    • Conformation Change of Cytochrome C. II. Ferricytochrome C Refinement at 1.8 Angstroms and Comparison with the Ferrocytochrome Structure
      Takano, T.,Dickerson, R.E.
      (1981) J.Mol.Biol. 153: 95
    • Internal Mobility of Ferrocytochrome C
      Northrup, S.H.,Pear, M.R.,Mccammon, J.A.,Karplus, M.,Takano, T.
      (1980) Nature 287: 659
    • Conformation Change of Cytochrome C. I. Ferrocytochrome C Structure Refined at 1.5 Angstroms Resolution
      Takano, T.,Dickerson, R.E.
      (1981) J.Mol.Biol. 153: 79
    • Tuna Cytochrome C at 2.0 Angstroms Resolution. II. Ferrocytochrome Structure Analysis
      Takano, T.,Trus, B.L.,Mandel, N.,Mandel, G.,Kallai, O.B.,Swanson, R.,Dickerson, R.E.
      (1977) J.Biol.Chem. 252: 776
    • Cytochrome C and the Evolution of Energy Metabolism
      Dickerson, R.E.
      (1980) Sci.Am. 242: 136
    • Tuna Cytochrome C at 2.0 Angstroms Resolution. I. Ferricytochrome Structure Analysis
      Swanson, R.,Trus, B.L.,Mandel, N.,Mandel, G.,Kallai, O.B.,Dickerson, R.E.
      (1977) J.Biol.Chem. 252: 759



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME C
O, I
104Thunnus alalungaMutation(s): 0 
Gene Names: cyc
Find proteins for P81459 (Thunnus alalunga)
Go to UniProtKB:  P81459
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download SDF File 
Download CCD File 
I, O
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
I, O
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 74.420α = 90.00
b = 74.420β = 90.00
c = 36.300γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 1980-07-01 
  • Released Date: 1980-09-16 
  • Deposition Author(s): Takano, T.
  • This entry supersedes: 1CYT

Revision History 

  • Version 1.0: 1980-09-16
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other