1SDY

STRUCTURE SOLUTION AND MOLECULAR DYNAMICS REFINEMENT OF THE YEAST CU,ZN ENZYME SUPEROXIDE DISMUTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure solution and molecular dynamics refinement of the yeast Cu,Zn enzyme superoxide dismutase.

Djinovic, K.Gatti, G.Coda, A.Antolini, L.Pelosi, G.Desideri, A.Falconi, M.Marmocchi, F.Rolilio, G.Bolognesi, M.

(1991) Acta Crystallogr.,Sect.B 47: 918-927


  • PubMed Abstract: 
  • Cu,Zn yeast superoxide dismutase was crystallized from polyethylene glycol solutions. The crystals belong to the P2(1)2(1)2 space group, with cell dimensions a = 105.3, b = 143.0, c = 62.1 A; two dimers of Mr = 32,000 each are contained in the asymme ...

    Cu,Zn yeast superoxide dismutase was crystallized from polyethylene glycol solutions. The crystals belong to the P2(1)2(1)2 space group, with cell dimensions a = 105.3, b = 143.0, c = 62.1 A; two dimers of Mr = 32,000 each are contained in the asymmetric unit. Diffraction data at 2.5 A resolution were collected with the image-plate system at the EMBL synchrotron radiation facility in Hamburg. The structure was determined by molecular replacement using as a search model the 'blue-green' dimer of the bovine Cu,Zn superoxide dismutase. The crystallographic refinement of the molecular replacement solution was performed by means of molecular dynamics techniques and resulted in an R factor of 0.268 for the data between 6.0 and 2.5 A. The model was subsequently subjected to conventional restrained crystallographic refinement of the coordinates and temperature factors. The current R value for the data between 6.0 and 2.5 A is 0.220. Owing to the large radius of convergence of the molecular dynamics-crystallographic refinement, the convergence of the refinement process was reached after 18.1 ps of simulation time. The geometry of the active site of the enzyme appears essentially preserved compared with the bovine superoxide dismutase. The beta-barrel structure in the yeast enzyme is closed at the upper part by an efficient hydrogen-bonding scheme.


    Related Citations: 
    • Evolution of Cuzn Superoxide Dismutase and the Greek Key Beta-Barrel Structural Motif
      Getzoff, E.D.,Tainer, J.A.,Stempien, M.M.,Bell, G.I.,Hallewell, R.A.
      (1989) Proteins 5: 322
    • Crystallographic Characterization and Three-Dimensional Model of Yeast Cu,Zn Superoxide Dismutase
      Frigerio, F.,Falconi, M.,Gatti, G.,Bolognesi, M.,Desideri, A.,Marmocchi, F.,Rotilio, G.
      (1989) Biochem.Biophys.Res.Commun. 160: 677
    • Conservation of Local Electric Fields in the Evolution of Cu,Zn Superoxide Dismutase
      Desideri, A.,Falconi, M.,Parisi, V.,Rotilio, G.
      (1989) FEBS Lett. 250: 45


    Organizational Affiliation

    Dipartimento di Genetica e Microbiologia, Università di Pavia, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COPPER,ZINC SUPEROXIDE DISMUTASE
A, B, C, D
153Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SOD1
EC: 1.15.1.1
Find proteins for P00445 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: SOD1
Go to UniProtKB:  P00445
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C, D
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.300α = 90.00
b = 143.000β = 90.00
c = 62.100γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-01-31
    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: Advisory, Derived calculations, Other