3OV8

Crystal structure of AF1382 from Archaeoglobus fulgidus, High resolution

3OV8 の概要

• エントリーDOI: 10.2210/pdb3ov8/pdb
• 関連するPDBエントリー: 3O3K
• 分子名称: Protein AF_1382, ACETATE ION, CHLORIDE ION, ... (4 entities in total)
• 機能のキーワード: af1382, psi, structural genomics, southeast collaboratory for structural genomics, secsg, putative dns binding, unknown function
• 由来する生物種: Archaeoglobus fulgidus
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 11288.97

構造登録者

Zhu, J.-Y.,Zhao, M.,Fu, Z.-Q.,Yang, H.,Chang, J.,Hao, X.,Chen, L.,Rose, J.P.,Wang, B.C.,Southeast Collaboratory for Structural Genomics (SECSG) (登録日: 2010-09-16, 公開日: 2011-11-16, 最終更新日: 2023-09-06)

主引用文献

Zhu, J.Y.,Fu, Z.Q.,Chen, L.,Xu, H.,Chrzas, J.,Rose, J.,Wang, B.C.
Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal.
Acta Crystallogr.,Sect.D, 68:1242-1252, 2012

PubMed 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.

PubMed: 22948926
DOI: 10.1107/S0907444912026212

実験手法

X-RAY DIFFRACTION (1.8501 Å)