3EF4

Crystal structure of native pseudoazurin from Hyphomicrobium denitrificans

Summary for 3EF4

• Entry DOI: 10.2210/pdb3ef4/pdb
• Descriptor: Blue copper protein, COPPER (II) ION, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: copper, electron transfer, blue copper protein, electron transport
• Biological source: Hyphomicrobium denitrificans
• Total number of polymer chains: 3
• Total formula weight: 42387.20

Authors

Hira, D.,Nojiri, M.,Suzuki, S. (deposition date: 2008-09-08, release date: 2008-12-30, Last modification date: 2023-11-01)

Primary citation

Hira, D.,Nojiri, M.,Suzuki, S.
Atomic resolution structure of pseudoazurin from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans: structural insights into its spectroscopic properties
Acta Crystallogr.,Sect.D, 65:85-92, 2009

PubMed Abstract: The crystal structure of native pseudoazurin (HdPAz) from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans has been determined at a resolution of 1.18 A. After refinement with SHELX employing anisotropic displacement parameters and riding H atoms, R(work) and R(free) were 0.135 and 0.169, respectively. Visualization of the anisotropic displacement parameters as thermal ellipsoids provided insight into the atomic motion within the perturbed type 1 Cu site. The asymmetric unit includes three HdPAz molecules which are tightly packed by head-to-head cupredoxin dimer formation. The shape of the Cu-atom ellipsoid implies significant vibrational motion diagonal to the equatorial xy plane defined by the three ligands (two His and one Cys). The geometric parameters of the type 1 Cu site in the HdPAz structure differ unambiguously from those of other pseudoazurins. It is demonstrated that their structural aspects are consistent with the unique visible absorption spectrum.

PubMed: 19153470
DOI: 10.1107/S0907444908040195

Experimental method

X-RAY DIFFRACTION (1.18 Å)