PDBsum entry 2q4d

Structural genomics, unknown function

PDB id: 2q4d

Contents

Protein chains

184 a.a. *

Ligands

NO3

EDO ×4

Waters ×319

* Residue conservation analysis

PDB id:

2q4d

Name:

Structural genomics, unknown function

Title:

Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene at5g11950

Structure:

Lysine decarboxylase-like protein at5g11950. Chain: a, b. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Strain: cv. Columbia. Gene: at5g11950, f14f18.120. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.15Å R-factor: 0.152 R-free: 0.207

Ensemble:

16 models

Authors:

E.J.Levin,D.A.Kondrashov,G.E.Wesenberg,G.N.Phillips Jr.,Center For Eukaryotic Structural Genomics (Cesg)

Key ref:

E.J.Levin et al. (2007). Ensemble refinement of protein crystal structures: validation and application. Structure, 15, 1040-1052. PubMed id: 17850744 DOI: 10.1016/j.str.2007.06.019

Date:

31-May-07 Release date: 19-Jun-07

Protein chains

Q84MC2  (LOG8_ARATH) -  Cytokinin riboside 5'-monophosphate phosphoribohydrolase LOG8 from Arabidopsis thaliana

Seq: 216 a.a.

Struc: 184 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.2.n1 - ?????

DOI no: 10.1016/j.str.2007.06.019

Structure 15:1040-1052 (2007)

PubMed id: 17850744

Ensemble refinement of protein crystal structures: validation and application.

E.J.Levin, D.A.Kondrashov, G.E.Wesenberg, G.N.Phillips.

ABSTRACT

X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.

Selected figure(s)

Figure 2.
Figure 2. Examples of Anharmonic Residue Probability Distributions for the Simulated Single- and Multiple-Conformer Models
The panels on the left show images of the electron density maps generated from the MD simulations of 1Q4R, along with a stick representation of the final 16-conformer model. The panels on the right show, for the red residues, the histograms of the projections of the simulation coordinates along the first principal components (shown in black), as well as the probability density functions calculated from the 1-conformer (red) and 16-conformer (blue) models along the same axis.

Figure 6.
Figure 6. Effect of Observation-to-Parameter Ratio on the Improvement in R[free] from Ensemble Refinement
The decrease in the R[free] value between the initial R[free] value and the R[free] value of the best-performing multiple-conformer model for the 50 experimental structures is plotted as a function of the ratio of the number of reflections used in the refinement to the number of atoms in the original one-conformer structure.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2007, 15, 1040-1052) copyright 2007.

Figures were selected by an automated process.