2SCP

STRUCTURE OF A SARCOPLASMIC CALCIUM-BINDING PROTEIN FROM NEREIS DIVERSICOLOR REFINED AT 2.0 ANGSTROMS RESOLUTION

Replaces:  1SCP

Summary for 2SCP

• Entry DOI: 10.2210/pdb2scp/pdb
• Descriptor: SARCOPLASMIC CALCIUM-BINDING PROTEIN, CALCIUM ION (3 entities in total)
• Functional Keywords: binding protein
• Biological source: Neanthes diversicolor
• Total number of polymer chains: 2
• Total formula weight: 39248.30

Authors

Cook, W.J.,Vijay-Kumar, S. (deposition date: 1991-08-22, release date: 1993-10-31, Last modification date: 2024-02-21)

Primary citation

Vijay-Kumar, S.,Cook, W.J.
Structure of a sarcoplasmic calcium-binding protein from Nereis diversicolor refined at 2.0 A resolution.
J.Mol.Biol., 224:413-426, 1992

PubMed Abstract: The crystal structure of a sarcoplasmic Ca(2+)-binding protein (SCP) from the sandworm Nereis diversicolor has been determined and refined at 2.0 A resolution using restrained least-squares techniques. The two molecules in the crystallographic asymmetric unit, which are related by a non-crystallographic 2-fold axis, were refined independently. The refined model includes all 174 residues and three calcium ions for each molecule, as well as 213 water molecules. The root-mean-square difference in co-ordinates for backbone atoms and calcium ions of the two molecules is 0.51 A. The final crystallographic R-factor, based on 18,959 reflections in the range 2.0 A less than or equal to d less than or equal to 7.0 A, with intensities exceeding 2.0 sigma, is 0.182. Bond lengths and bond angles in the molecules have root-mean-square deviations from ideal values of 0.013 A and 2.2 degrees, respectively. SCP has four distinct domains with the typical helix-loop-helix (EF-hand) Ca(2+)-binding motif, although the second Ca(2+)-binding domain is not functional due to amino acid changes in the loop. The structure shows several unique features compared to other Ca(2+)-binding proteins with four EF-hand domains. The overall structure is highly compact and globular with a predominant hydrophobic core, unlike the extended dumbbell-shaped structure of calmodulin or troponin C. A hydrophobic tail at the COOH terminus adds to the structural stability by packing against a hydrophobic pocket created by the folding of the NH2 and COOH-terminal Ca(2+)-binding domain pairs. The first and second domains show different helix-packing arrangements from any previously described for Ca(2+)-binding proteins.

PubMed: 1560459
DOI: 10.1016/0022-2836(92)91004-9

Experimental method

X-RAY DIFFRACTION (2 Å)