PDBsum entry 1aiz

Electron transport(cadmium binding)

PDB id: 1aiz

Contents

Protein chains

129 a.a. *

Ligands

SO4 ×4

Metals

_CD ×2

Waters ×239

* Residue conservation analysis

PDB id:

1aiz

Name:

Electron transport(cadmium binding)

Title:

Structure of apo-azurin from alcaligenes denitrificans at 1.8 angstroms resolution

Structure:

Azurin. Chain: a, b. Engineered: yes

Source:

Achromobacter denitrificans. Organism_taxid: 32002

Resolution:

1.80Å R-factor: 0.168

Authors:

E.N.Baker,B.F.Anderson,K.A.Blackwell

Key ref:

W.E.Shepard et al. (1993). Structure of apo-azurin from Alcaligenes denitrificans at 1.8 A resolution. Acta Crystallogr D Biol Crystallogr, 49, 331-343. PubMed id: 15299522 DOI: 10.1107/S0907444992013544

Date:

11-Nov-93 Release date: 31-Jan-94

Protein chains

P00280  (AZUR_ACHDE) -  Azurin from Achromobacter denitrificans

Seq: 149 a.a.

Struc: 129 a.a.

DOI no: 10.1107/S0907444992013544

Acta Crystallogr D Biol Crystallogr 49:331-343 (1993)

PubMed id: 15299522

Structure of apo-azurin from Alcaligenes denitrificans at 1.8 A resolution.

W.E.Shepard, R.L.Kingston, B.F.Anderson, E.N.Baker.

ABSTRACT

The structure of apo-azurin from Alcaligenes denitrificans has been determined at high resolution by X-ray crystallography. Two separate structure analyses have been carried out, (i) on crystals obtained from solutions of apo-azurin and (ii) on crystals obtained by removal of copper from previously formed crystals of holo-azurin. Data to 1.8 A resolution were collected from the apo-azurin crystals, by Weissenberg photography (with image plates) using synchrotron radiation and by diffractometry, and the structure was refined by restrained least-squares methods to a final R value of 0.160 for all data in the range 10.0-1.8 A. The final model of 1954 protein atoms, 246 water molecules (66 half-weighted), four SO(4)(2-) ions, and two low-occupancy (0.13 and 0.15) Cu atoms has r.m.s. deviations of 0.012, 0.045 and 0.013 A from standard bond lengths, angle distances and planar groups. For copper-removed azurin, data to 2.2 A were collected by diffractometry and the structure refined by restrained least squares to a final R value of 0.158 for all data in the range 10.0-2.2 A. The final model of 1954 protein atoms, 264 water molecules, two SO(4)(2-) ions, two low occupancy (0.18 and 0.22) metal atoms and one unidentified atom (modelled as S) has r.m.s. deviations of 0.013, 0.047 and 0.012 A from standard bond lengths, angle distances and planar groups. The two structures are essentially identical to each other and show no significant differences from the oxidized and reduced holo-azurin structures. The ligand side chains move slightly closer together following the removal of copper, with the radius of the cavity between the three strongly binding ligands, His 46, His 117 and Cys 112, shrinking from 1.31 A in reduced azurin to 1.24 A in oxidized azurin and 1.16 A in apo-azurin. There is a suggestion of increased flexibility in one of the copper-binding loops but the structure supports the view that the copper site found in holo-azurin is a stable structure, defined by the constraints of the polypeptide structure even in the absence of a bound metal ion.

Selected figure(s)

Figure 2.
Fig. 2. Electron density for the two sulfate ions bound o olecule A o apo-azurin, taken from an omit map in which these ions di not contribute to the phasing. (a) The sulfate ion, which is also found in the oxidized and reduced holo-azurin structures, bound to His 83N e2 and Gly 76NH. (b) The sulfate ion bound betwen Lys 56 and Lys 122, with a thrd Lys side chain (from Lys 38 of a neighbouring molecule) and a water olecule completing the ite.

Figure 9.
Fig. 9. Superposition of the copper binding sites of apo-azurin (yellow), copper-removed aurin (green), oxidized azuin (blue) and reduced azurin (purple). Th copper position in oxidized azurin is shown with a cross.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 331-343) copyright 1993.

Figures were selected by an automated process.