1COB

CRYSTAL STRUCTURE SOLUTION AND REFINEMENT OF THE SEMISYNTHETIC COBALT SUBSTITUTED BOVINE ERYTHROCYTE ENZYME SUPEROXIDE DISMUTASE AT 2.0 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure solution and refinement of the semisynthetic cobalt-substituted bovine erythrocyte superoxide dismutase at 2.0 A resolution.

Djinovic, K.Coda, A.Antolini, L.Pelosi, G.Desideri, A.Falconi, M.Rotilio, G.Bolognesi, M.

(1992) J Mol Biol 226: 227-238

  • DOI: 10.1016/0022-2836(92)90135-7
  • Primary Citation of Related Structures:  
    1COB

  • PubMed Abstract: 
  • The semisynthetic Co-substituted bovine erythrocyte superoxide dismutase (SOD) has been crystallized in a new crystalline form and the structure determined at 2.0 A (1 A = 0.1 nm) resolution. The crystals belong to space group P2(1)2(1)2(1) with cell constants: a = 51 ...

    The semisynthetic Co-substituted bovine erythrocyte superoxide dismutase (SOD) has been crystallized in a new crystalline form and the structure determined at 2.0 A (1 A = 0.1 nm) resolution. The crystals belong to space group P2(1)2(1)2(1) with cell constants: a = 51.0, b = 147.6, c = 47.5 A, and contain one dimeric molecule of 32,000 M(r) per asymmetric unit. The structure has been solved by molecular replacement techniques using the Cu,Zn bovine enzyme as a search model, and refined by molecular dynamics with the crystallographic pseudo-energy term, followed by conventional crystallographic refinement. The R-factor for the 18,964 unique reflections in the resolution range from 10.0 to 2.0 A is 0.176 for a model comprising 2188 protein atoms and 200 solvent molecules; the root-mean-square deviation from the ideal bond lengths is 0.010 A, and the average atomic temperature factor is 26.5 A2. The dimeric molecule of the enzyme is composed of two identical subunits related by a non-crystallographic 2-fold axis. The subunit has as its structural scaffolding the conventional SOD-flattened antiparallel eight-stranded beta-barrel, with three external loops. The co-ordination geometry of the metal center in the active site is fairly well preserved when compared with the native Cu,Zn bovine enzyme. Co2+ is in tetrahedral co-ordination, while the Cu2+ ligands show an uneven distortion from the square planar geometry. The least-squares superposition of the metals ligands and the catalytically important Arg141 of the native and Co-substituted enzyme yields a root-mean-square value of 0.401 A, the largest deviation occurring at the Co2+ ligand Asp81. An additional copper ligand, compatible with a water molecule, is observed at 2.38 A from Cu2+ in the active-site channel, at the supposed binding site of the O2- anion substrate. Several ordered water molecules have been observed on the protein surface and in the active-site channel; their structural locations coincide remarkably with those of related water molecules found in the crystal structure of the phylogenetically distant superoxide dismutase from yeast.


    Related Citations: 
    • Crystal Structure of Yeast Cu,Zn Superoxide Dismutase. Crystallographic Refinement at 2.5 Angstroms Resolution
      Djinovic, K., Gatti, G., Coda, A., Antolini, L., Pelosi, G., Desideri, A., Falconi, M., Marmocchi, F., Rotilio, G., Bolognesi, M.
      (1992) J Mol Biol 225: 791
    • Structure Solution and Molecular Dynamics Refinement of the Yeast Cu,Zn Enzyme Superoxide Dismutase
      Djinovic, K., Gatti, G., Coda, A.
      (1991) Acta Crystallogr B 47: 918
    • Three-Dimensional Structure of Cu,Zn Superoxide Dismutase from Spinach at 2.0 Angstroms Resolution
      Kitagawa, Y., Tanaka, N., Hata, Y., Kusonoki, M., Lee, G., Katsube, Y., Asada, K., Aibara, S., Morita, Y.
      (1991) J Biochem 109: 447
    • Evolution of Cu,Zn Superoxide Dismutase and the Greek-Key B-Barrel Structural Motif
      Getzoff, E.D., Tainer, J.A., Stempien, M.M., Bell, G.I., Hallewell, R.A.
      (1989) Proteins 5: 322
    • Determination and Analysis of the 2 Angstroms Structure of Copper, Zinc Superoxide Dismutase
      Tainer, J.A., Getzoff, E.D., Beem, K.M., Richardson, J.S., Richardson, D.C.
      (1982) J Mol Biol 160: 181

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUPEROXIDE DISMUTASEA, B151Bos taurusMutation(s): 0 
Gene Names: SOD1
EC: 1.15.1.1
UniProt
Find proteins for P00442 (Bos taurus)
Explore P00442 
Go to UniProtKB:  P00442
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00442
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.99α = 90
b = 147.63β = 90
c = 47.53γ = 90
Software Package:
Software NamePurpose
TNTrefinement
FRODOmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance