3FYS

Crystal Structure of DegV, a fatty acid binding protein from Bacillus subtilis

Summary for 3FYS

• Entry DOI: 10.2210/pdb3fys/pdb
• Descriptor: Protein degV, PALMITIC ACID, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: fatty acid-binding, edd fold, fatty acid-binding protein
• Biological source: Bacillus subtilis
• Total number of polymer chains: 1
• Total formula weight: 36050.89

Authors

Nan, J.,Zhou, Y.F.,Yang, C. (deposition date: 2009-01-23, release date: 2009-05-12, Last modification date: 2024-03-20)

Primary citation

Nan, J.,Zhou, Y.F.,Yang, C.,Brostromer, E.,Kristensen, O.,Su, X.-D.
Structure of a fatty acid-binding protein from Bacillus subtilis determined by sulfur-SAD phasing using in-house chromium radiation
Acta Crystallogr.,Sect.D, 65:440-448, 2009

PubMed Abstract: Sulfur single-wavelength anomalous dispersion (S-SAD) and halide-soaking methods are increasingly being used for ab initio phasing. With the introduction of in-house Cr X-ray sources, these methods benefit from the enhanced anomalous scattering of S and halide atoms, respectively. Here, these methods were combined to determine the crystal structure of BsDegV, a DegV protein-family member from Bacillus subtilis. The protein was cocrystallized with bromide and low-redundancy data were collected to 2.5 A resolution using Cr Kalpha radiation. 17 heavy-atom sites (ten sulfurs and seven bromides) were located using standard methods. The anomalous scattering of some of the BsDegV S atoms and Br atoms was weak, thus neither sulfurs nor bromides could be used alone for structure determination using the collected data. When all 17 heavy-atom sites were used for SAD phasing, an easily interpretable electron-density map was obtained after density modification. The model of BsDegV was built automatically and a palmitate was found tightly bound in the active site. Sequence alignment and comparisons with other known DegV structures provided further insight into the specificity of fatty-acid selection and recognition within this protein family.

PubMed: 19390149
DOI: 10.1107/S0907444909007756

Experimental method

X-RAY DIFFRACTION (2.5 Å)