- PDB-5yh8: The crystal structure of Staphylococcus aureus CntA in complex wi... -
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基本情報
登録情報
データベース: PDB / ID: 5yh8
タイトル
The crystal structure of Staphylococcus aureus CntA in complex with staphylopine and nickel
要素
Nickel ABC transporter substrate-binding protein
キーワード
METAL BINDING PROTEIN / complex / receptor
機能・相同性
機能・相同性情報
nickel cation transport / zinc ion transport / cobalt ion transport / peptide transport / peptide transmembrane transporter activity / nickel cation binding / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / heme binding 類似検索 - 分子機能
Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta 類似検索 - ドメイン・相同性
Chem-8UX / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Nickel ABC transporter substrate-binding protein / Metal-staphylopine-binding protein CntA 類似検索 - 構成要素
プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長
波長: 0.9785 Å / 相対比: 1
反射
解像度: 2.12→70.88 Å / Num. obs: 30251 / % possible obs: 99.9 % / 冗長度: 12.7 % / Net I/σ(I): 16.1
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.8.0135
精密化
HKL-3000
データ削減
HKL-3000
データスケーリング
PHASER
位相決定
精密化
構造決定の手法: 分子置換 / 解像度: 2.12→70.88 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.733 / SU ML: 0.146 / 交差検証法: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.196 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Selection details
Rfree
0.22891
1588
5.2 %
RANDOM
Rwork
0.15547
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obs
0.15926
28663
99.77 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK