PDBsum entry: 1b1g

Metal binding protein

PDB id: 1b1g

Contents

Protein chain

75 a.a. *

Metals

_CA ×2

* Residue conservation analysis

PDB id:

1b1g

Name:

Metal binding protein

Title:

Solvated refinement of ca-loaded calbindin d9k

Structure:

Protein (calbindin d9k). Chain: a. Synonym: intestinal calcium-binding protein. Engineered: yes. Mutation: yes

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: bl21(de3)

NMR struc:

10 models

Authors:

J.Kordel,D.A.Pearlman,W.J.Chazin

Key ref:

J.Kördel et al. (1997). Protein solution structure calculations in solution: solvated molecular dynamics refinement of calbindin D9k. J Biomol Nmr, 10, 231-243. PubMed id: 9390401 DOI: 10.1023/A:1018383102870

Date:

20-Nov-98 Release date: 25-Nov-98

Protein chain

P02633  (S100G_BOVIN) -  Protein S100-G

Seq: 79 a.a.

Struc: 75 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: apical plasma membrane (2 terms)
• Biochemical function: vitamin D binding (2 terms)

DOI no: 10.1023/A:1018383102870

J Biomol Nmr 10:231-243 (1997)

PubMed id: 9390401

Protein solution structure calculations in solution: solvated molecular dynamics refinement of calbindin D9k.

J.Kördel, D.A.Pearlman, W.J.Chazin.

ABSTRACT

The three-dimensional solution structures of proteins determined with NMR-derived constraints are almost always calculated in vacuo. The solution structure of (Ca2+)2-calbindin D9k has been redetermined by new restrained molecular dynamics (MD) calculations that include Ca2+ ions and explicit solvent molecules. Four parallel sets of MD refinements were run to provide accurate comparisons of structures produced in vacuo, in vacuo with Ca2+ ions, and with two different protocols in a solvent bath with Ca2+ ions. The structural ensembles were analyzed in terms of structural definition, molecular energies, packing density, solvent-accessible surface, hydrogen bonds, and the coordination of calcium ions in the two binding loops. Refinement including Ca2+ ions and explicit solvent results in significant improvements in the precision and accuracy of the structure, particularly in the binding loops. These results are consistent with results previously obtained in free MD simulations of proteins in solution and show that the rMD refined NMR-derived solution structures of proteins, especially metalloproteins, can be significantly improved by these strategies.