PDBsum entry 1bu3

Calcium binding

PDB id: 1bu3

Contents

Protein chain

109 a.a. *

Metals

_CA ×2

Waters ×114

* Residue conservation analysis

PDB id:

1bu3

Name:

Calcium binding

Title:

Refined crystal structure of calcium-bound silver hake (pi 4.2) parvalbumin at 1.65 a.

Structure:

Calcium-binding protein. Chain: a. Fragment: calcium-binding domain

Source:

Merluccius bilinearis. Silver hake. Organism_taxid: 79698. Tissue: muscle

Resolution:

1.65Å R-factor: 0.214 R-free: 0.251

Authors:

R.C.Richardson,D.J.Nelson,W.E.Royer,D.J.Harrington

Key ref:

R.C.Richardson et al. (2000). X-Ray crystal structure and molecular dynamics simulations of silver hake parvalbumin (Isoform B). Protein Sci, 9, 73-82. PubMed id: 10739249

Date:

30-Aug-98 Release date: 10-Aug-99

Protein chain

P56503  (PRVB_MERBI) -  Parvalbumin beta from Merluccius bilinearis

Seq: 108 a.a.

Struc: 108 a.a.

Protein Sci 9:73-82 (2000)

PubMed id: 10739249

X-Ray crystal structure and molecular dynamics simulations of silver hake parvalbumin (Isoform B).

R.C.Richardson, N.M.King, D.J.Harrington, H.Sun, W.E.Royer, D.J.Nelson.

ABSTRACT

Parvalbumins constitute a class of calcium-binding proteins characterized by the presence of several helix-loop-helix (EF-hand) motifs. In a previous study (Revett SP, King G, Shabanowitz J, Hunt DF, Hartman KL, Laue TM, Nelson DJ, 1997, Protein Sci 7:2397-2408), we presented the sequence of the major parvalbumin isoform from the silver hake (Merluccius bilinearis) and presented spectroscopic and structural information on the excised "EF-hand" portion of the protein. In this study, the X-ray crystal structure of the silver hake major parvalbumin has been determined to high resolution, in the frozen state, using the molecular replacement method with the carp parvalbumin structure as a starting model. The crystals are orthorhombic, space group C2221, with a = 75.7 A, b = 80.7 A, and c = 42.1 A. Data were collected from a single crystal grown in 15% glycerol, which served as a cryoprotectant for flash freezing at -188 degrees C. The structure refined to a conventional R-value of 21% (free R 25%) for observed reflections in the range 8 to 1.65 A [1 > 2sigma(I)]. The refined model includes an acetylated amino terminus, 108 residues (characteristic of a beta parvalbumin lineage), 2 calcium ions, and 114 water molecules per protein molecule. The resulting structure was used in molecular dynamics (MD) simulations focused primarily on the dynamics of the ligands coordinating the Ca2+ ions in the CD and EF sites. MD simulations were performed on both the fully Ca2+ loaded protein and on a Ca2+ deficient variant, with Ca2+ only in the CD site. There was substantial agreement between the MD and X-ray results in addressing the issue of mobility of key residues in the calcium-binding sites, especially with regard to the side chain of Ser55 in the CD site and Asp92 in the EF site.