1XSO

THREE-DIMENSIONAL STRUCTURE OF XENOPUS LAEVIS CU,ZN SUPEROXIDE DISMUTASE B DETERMINED BY X-RAY CRYSTALLOGRAPHY AT 1.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.104 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 A resolution.

Djinovic Carugo, K.Battistoni, A.Carri, M.T.Polticelli, F.Desideri, A.Rotilio, G.Coda, A.Wilson, K.S.Bolognesi, M.

(1996) Acta Crystallogr D Biol Crystallogr 52: 176-188

  • DOI: 10.1107/S0907444995007608
  • Primary Citation of Related Structures:  
    1XSO

  • PubMed Abstract: 
  • Xenopus laevis Cu,Zn superoxide dismutase (recombinant isoenzyme b) has been crystallized and the structure determined at 1.49 A resolution. The crystals belong to space group P2(1)2(1)2(1), with cell constants a = 73.33, b = 68.86, c = 59.73 A, and contain one dimeric molecule of M(r) 32 000 per asymmetric unit ...

    Xenopus laevis Cu,Zn superoxide dismutase (recombinant isoenzyme b) has been crystallized and the structure determined at 1.49 A resolution. The crystals belong to space group P2(1)2(1)2(1), with cell constants a = 73.33, b = 68.86, c = 59.73 A, and contain one dimeric molecule of M(r) 32 000 per asymmetric unit. The structure was solved by molecular-replacement techniques using the semisynthetic Cu,Co bovine enzyme as search model, and refined by molecular dynamics with a crystallographic pseudo-energy term. During the final steps, positional and anisotropic thermal parameters of the atoms were refined. The R factor for the 49 209 unique reflections in the 10.0-1.49 A resolution range is 0.104, for a model comprising 2023 protein atoms, two Cu(2+), two Zn(2+), and 353 water molecules. The overall temperature factor for the model, including solvent, is 20.3 A(2), while the calculated r.m.s. coordinate error for the refined model is 0.036 A. As suggested by the primary structure homology to any other known intracellular eukaryotic superoxide dismutase (> 50%), the typical structural scaffolding of flattened antiparallel eight-stranded (beta-barrel is well conserved in X. laevis Cu,Zn superoxide dismutase b, together with the coordination geometry of the metal centers in the active site. The higher thermal stability of the bb X. laevis superoxide dismutase homodimer, with respect to dimers involving the a-type isoenzyme subunit(s), can be related, on the basis of the high-resolution structure, to side-chain and solvent interactions centered on residue Tyr149, in both b-type subunits. The analysis of the overall solvent structure reveals a number of equivalent water molecule sites in the two subunits, and in homologous superoxide dismutase models. Their locations are discussed in detail and classified on the basis of their structural role.


    Related Citations: 
    • Conserved Patterns in the Cu,Zn Superoxide Dismutase Family
      Bordo, D., Djinovic, K., Bolognesi, K.M.
      (1994) J Mol Biol 238: 366
    • Crystallographic Study of Azide-Inhibited Bovine Cu,Zn Superoxide Dismutase
      Djinovic Carugo, K., Polticelli, K.F., Desideri, A., Rotilio, G., Wilson, K.S., Bolognesi, M.
      (1994) J Mol Biol 240: 179
    • Crystal Structure of the Cyanide-Inhibited Xenopus Laevis Cu,Zn Superoxide Dismutase at 98 K
      Djinovic Carugo, K., Battistoni, K.A., Carri, M.T., Polticelli, F., Desideri, A., Rotilio, G., Coda, A., Bolognesi, M.
      (1994) FEBS Lett 349: 93
    • Crystallisation and Preliminary Crystallographic Analysis of Recombinant Xenopus Laevis Cu,Zn Superoxide Dismutase B
      Djinovic Carugo, K., Collyer, K.C., Coda, A., Carri, M.T., Battistoni, A., Botaro, G., Polticelli, F., Desideri, A., Bolognesi, M.
      (1993) Biochem Biophys Res Commun 194: 1008
    • Crystal Structure of Yeast Cu,Zn Superoxide Dismutase
      Djinovic, K., Gatti, G., Antolini, L., Pelosi, G., Desideri, A., Falconi, M., Marmocchi, F., Rotilio, G., Bolognesi, M.
      (1992) J Mol Biol 225: 791

    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
COPPER,ZINC SUPEROXIDE DISMUTASEA, B150Xenopus laevisMutation(s): 0 
Gene Names: sod1-b
EC: 1.15.1.1
UniProt
Find proteins for P15107 (Xenopus laevis)
Explore P15107 
Go to UniProtKB:  P15107
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15107
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.104 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.45α = 90
b = 68.94β = 90
c = 58.76γ = 90
Software Package:
Software NamePurpose
SHELXL-93refinement
PROLSQrefinement
X-PLORrefinement
X-PLORmodel building
MOSFLMdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-07-10
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Advisory, Data collection, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description