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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 2q4s | ||||||
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タイトル | Ensemble refinement of the protein crystal structure of cysteine dioxygenase type I from Mus musculus Mm.241056 | ||||||
![]() | Cysteine dioxygenase type 1 | ||||||
![]() | OXIDOREDUCTASE / Ensemble Refinement / Refinement Methodology Development / Mm.241056 / pfam05995.2 CDO_I / BC013638 / CUPIN FAMILY / Structural Genomics / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG | ||||||
機能・相同性 | ![]() L-cysteine catabolic process to taurine / Degradation of cysteine and homocysteine / taurine metabolic process / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / L-cysteine catabolic process / response to glucagon / nickel cation binding / response to amino acid ...L-cysteine catabolic process to taurine / Degradation of cysteine and homocysteine / taurine metabolic process / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / L-cysteine catabolic process / response to glucagon / nickel cation binding / response to amino acid / response to glucocorticoid / response to cAMP / : / lactation / ferrous iron binding / response to ethanol / zinc ion binding / plasma membrane / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() | ||||||
![]() | Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
![]() | ![]() タイトル: Ensemble refinement of protein crystal structures: validation and application. 著者: Levin, E.J. / Kondrashov, D.A. / Wesenberg, G.E. / Phillips, G.N. #1: ![]() タイトル: Structure and mechanism of mouse cysteine dioxygenase. 著者: McCoy, J.G. / Bailey, L.J. / Bitto, E. / Bingman, C.A. / Aceti, D.J. / Fox, B.G. / Phillips, G.N. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 627 KB | 表示 | ![]() |
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PDB形式 | ![]() | 538 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
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-検証レポート
文書・要旨 | ![]() | 536.7 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 554 KB | 表示 | |
XML形式データ | ![]() | 135.3 KB | 表示 | |
CIF形式データ | ![]() | 178.5 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 2q3mC ![]() 2q3oC ![]() 2q3pC ![]() 2q3qC ![]() 2q3rC ![]() 2q3sC ![]() 2q3tC ![]() 2q3uC ![]() 2q3vC ![]() 2q3wC ![]() 2q40C ![]() 2q41C ![]() 2q42C ![]() 2q43C ![]() 2q44C ![]() 2q45C ![]() 2q46C ![]() 2q47C ![]() 2q48C ![]() 2q49C ![]() 2q4aC ![]() 2q4bC ![]() 2q4cC ![]() 2q4dC ![]() 2q4eC ![]() 2q4fC ![]() 2q4hC ![]() 2q4iC ![]() 2q4jC ![]() 2q4kC ![]() 2q4lC ![]() 2q4mC ![]() 2q4nC ![]() 2q4oC ![]() 2q4pC ![]() 2q4qC ![]() 2q4rC ![]() 2q4tC ![]() 2q4uC ![]() 2q4vC ![]() 2q4xC ![]() 2q4yC ![]() 2q4zC ![]() 2q50C ![]() 2q51C ![]() 2q52C ![]() 2atfS S: 精密化の開始モデル C: 同じ文献を引用 ( |
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集合体
登録構造単位 | ![]()
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単位格子 |
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モデル数 | 16 |
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要素
#1: タンパク質 | 分子量: 23155.457 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
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#2: 化合物 | ChemComp-NI / |
#3: 化合物 | ChemComp-EDO / |
#4: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.2 Å3/Da / 溶媒含有率: 43.6 % / 解説: AUTHOR USED THE SF DATA FROM ENTRY 2ATF. |
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-データ収集
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
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放射波長 | 相対比: 1 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: Re-refinement using ensemble model 開始モデル: PDB entry 2ATF 解像度: 1.75→33.86 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1876902.375 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 立体化学のターゲット値: maximum likelihood using amplitudes 詳細: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2atf and the first data set in the deposited structure factor file for 2atf ...詳細: This PDB entry is a re-refinement using an ensemble model of the previously deposited single-conformer structure 2atf and the first data set in the deposited structure factor file for 2atf along with the R-free set defined therein. The coordinates were generated by an automated protocol from an initial model consisting of 16 identical copies of the protein and non-water hetero-atoms assigned fractional occupancies adding up to one, and a single copy of the solvent molecules. Refinement was carried out with all the conformers present simultaneously and with the potential energy terms corresponding to interactions between the different conformers excluded. The helix and sheet records were calculated using coordinates from the first conformer only. The structure visualization program PYMOL is well-suited for directly viewing the ensemble model presented in this PDB file.
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 43.205 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 17.1 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.75→33.86 Å
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拘束条件 |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Xplor file |
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