title: Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal.
abstract: The crystal structure of the 11.14 kDa orphan ORF 1382 from Archaeoglobus fulgidus (AF1382) has been determined by sulfur SAD phasing using a moderately diffracting crystal and 1.9 Å wavelength synchrotron X-rays. AF1382 was selected as a structural genomics target by the Southeast Collaboratory for Structural Genomics (SECSG) since sequence analyses showed that it did not belong to the Pfam-A database and thus could represent a novel fold. The structure was determined by exploiting longer wavelength X-rays and data redundancy to increase the anomalous signal in the data. AF1382 is a 95-residue protein containing five S atoms associated with four methionine residues and a single cysteine residue that yields a calculated Bijvoet ratio (ΔF(anom)/F) of 1.39% for 1.9 Å wavelength X-rays. Coupled with an average Bijvoet redundancy of 25 (two 360° data sets), this produced an excellent electron-density map that allowed 69 of the 95 residues to be automatically fitted. The S-SAD model was then manually completed and refined (R = 23.2%, R(free) = 26.8%) to 2.3 Å resolution (PDB entry 3o3k). High-resolution data were subsequently collected from a better diffracting crystal using 0.97 Å wavelength synchrotron X-rays and the S-SAD model was refined (R = 17.9%, R(free) = 21.4%) to 1.85 Å resolution (PDB entry 3ov8). AF1382 has a winged-helix-turn-helix structure common to many DNA-binding proteins and most closely resembles the N-terminal domain (residues 1-82) of the Rio2 kinase from A. fulgidus, which has been shown to bind DNA, and a number of MarR-family transcriptional regulators, suggesting a similar DNA-binding function for AF1382. The analysis also points out the advantage gained from carrying out data reduction and structure determination on-site while the crystal is still available for further data collection.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA.
authors.forename: Jin-Yi
authors.initials: JY
authors.lastname: Zhu
authors.forename: Zheng-Qing
authors.initials: ZQ
authors.lastname: Fu
authors.forename: Lirong
authors.initials: L
authors.lastname: Chen
authors.forename: Hao
authors.initials: H
authors.lastname: Xu
authors.forename: John
authors.initials: J
authors.lastname: Chrzas
authors.forename: John
authors.initials: J
authors.lastname: Rose
authors.forename: Bi-Cheng
authors.initials: BC
authors.lastname: Wang
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry*; D019611:Archaeoglobus fulgidus / Q000737:chemistry*; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D016366:Open Reading Frames; D017434:Protein Structure, Tertiary; D013455:Sulfur / Q000737:chemistry*
chemical_list: D019843:Archaeal Proteins; D013455:Sulfur