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基本情報
| 登録情報 | データベース: PDB / ID: 1rxs | ||||||
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| タイトル | E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex | ||||||
 要素 | Uridine phosphorylase | ||||||
 キーワード | TRANSFERASE (転移酵素) / pentosyltransferase / uridine phosphorylase / 2'-deoxyuridine / induced fit (酵素反応) / specificity / potassium (カリウム) | ||||||
| 機能・相同性 |  機能・相同性情報uridine catabolic process / uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine phosphorylase activity / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / potassium ion binding / DNA damage response / protein-containing complex ...uridine catabolic process / uridine phosphorylase / nucleotide catabolic process / UMP salvage / uridine phosphorylase activity / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / potassium ion binding / DNA damage response / protein-containing complex / ATP binding / identical protein binding / 細胞質基質類似検索 - 分子機能 | ||||||
| 生物種 |   Escherichia coli (大腸菌) | ||||||
| 手法 | X線回折 / 分子置換 / 解像度: 2.8 Å | ||||||
 データ登録者 | Caradoc-Davies, T.T. / Cutfield, S.M. / Lamont, I.L. / Cutfield, J.F. | ||||||
 引用 | ジャーナル: J.Mol.Biol. / 年: 2004 タイトル: Crystal structures of escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium 著者: Caradoc-Davies, T.T. / Cutfield, S.M. / Lamont, I.L. / Cutfield, J.F. | ||||||
| 履歴 |
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構造の表示
| 構造ビューア | 分子: MolmilJmol/JSmol |
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ダウンロードとリンク
-ダウンロード
| PDBx/mmCIF形式 | 1rxs.cif.gz | 1.4 MB | 表示 | PDBx/mmCIF形式 |
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| PDB形式 | pdb1rxs.ent.gz | 1.1 MB | 表示 | PDB形式 |
| PDBx/mmJSON形式 | 1rxs.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
| その他 |  その他のダウンロード |
-検証レポート
| アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/rx/1rxsftp://data.pdbj.org/pub/pdb/validation_reports/rx/1rxs | HTTPS FTP |
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-関連構造データ
-リンク
PDBj-
集合体
| 登録構造単位 | 
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| 単位格子 |
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| 非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域: Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Label seq-ID: 4 - 253
NCSアンサンブル:
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-要素
-タンパク質 , 1種, 30分子 AaBbCcDdEeFRGPHhIiJjKkLlMmNQOo
| #1: タンパク質 | / UrdPase / UPase 分子量: 27189.055 Da / 分子数: 30 / 由来タイプ: 組換発現 詳細: This structure consists of thirty monomers, twelve of which are in the closed conformation, thirteen are in the intermediate (partially closed) conformation and five in the open conformation. ...詳細: This structure consists of thirty monomers, twelve of which are in the closed conformation, thirteen are in the intermediate (partially closed) conformation and five in the open conformation. The closed and intermediate monomers contain substrate (2'-deoxyuridine and phosphate). Due to the large size of the model it was refined using three template models, each of which was the best observed example of an individual conformation, and shell scripts were written to create the 30 monomer model from these input models and the ncs operators relating them. The vanadate component of this structure is an artifact of the crystal conditions with no functional significance. See "REMARK 3" for further details. 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: UDP / プラスミド: pPROEX::pvdS / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P12758, uridine phosphorylase |
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-非ポリマー , 5種, 1666分子 
| #2: 化合物 | ChemComp-K /  分子量: 39.098 Da / 分子数: 15 / 由来タイプ: 合成 / 式: K#3: 化合物 | ChemComp-V7O /  分子量: 660.579 Da / 分子数: 20 / 由来タイプ: 合成 / 式: O19V7#4: 化合物 | ChemComp-PO4 / リン酸塩 分子量: 94.971 Da / 分子数: 25 / 由来タイプ: 合成 / 式: PO4#5: 化合物 | ChemComp-DUR / デオキシウリジン 分子量: 228.202 Da / 分子数: 25 / 由来タイプ: 合成 / 式: C9H12N2O5 / コメント: 抗ウイルス剤*YM#6: 水 | ChemComp-HOH / | 水分子量: 18.015 Da / 分子数: 1581 / 由来タイプ: 天然 / 式: H2O |
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-実験情報
-実験
| 実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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試料調製
| 結晶 | マシュー密度: 2.25 Å3/Da / 溶媒含有率: 44.85 % |
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| 結晶化 | 温度: 289 K / 手法: batch method under oil / pH: 7.5 詳細: TRIS HCL, PEG4000, POTASSIUM ACETATE, 2'-DEOXYURIDINE, SODIUM ORTHOVANADATE, pH 7.50, BATCH METHOD UNDER OIL, temperature 289K |
-データ収集
| 回折 | 平均測定温度: 115 K |
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| 放射光源 | 由来: 回転陽極 / タイプ: RIGAKU RU200 / 波長: 1.5418 Å |
| 検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2002年8月5日 / 詳細: OSMIC |
| 放射 | モノクロメーター: NI FILTER / 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: 1.5418 Å / 相対比: 1 |
| 反射 | 解像度: 2.8→40.49 Å / Num. all: 173525 / Num. obs: 173525 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 3.1 % / Biso Wilson estimate: 46.18 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 5.4 |
| 反射 シェル | 解像度: 2.8→2.94 Å / 冗長度: 3.1 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.8 / Num. unique all: 19170 / % possible all: 95.3 |
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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: 分子置換 開始モデル: DETWINNED HEXAMERIC NATIVE UP 解像度: 2.8→26.75 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / SU B: 13.538 / SU ML: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC (TLS REFINEMENT) / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.367 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: TLS and restrained refinement was carried out using REFMAC5. Each conformation was restrained together using ncs restraints (tight positional (0.05a) and loose thermal (5.0a3) restraints). ...詳細: TLS and restrained refinement was carried out using REFMAC5. Each conformation was restrained together using ncs restraints (tight positional (0.05a) and loose thermal (5.0a3) restraints). Each monomer was split into two TLS domains, comprising the mobile and fixed regions of each monomer. This structure consists of thirty monomers, twelve of which are in the closed conformation, thirteen are in the intermediate (partially closed) conformation and five in the open conformation. Closed and intermediate conformation monomers contain substrate (2'-deoxyuridine and phosphate). Due to the large size of the model it was refined using three template models, each of which was the best observed example of an individual conformation, and shell scripts were written to create the 30 monomer model from these input models and the NCS operators relating them. The 30 monomer model was then refined using refmac5 and ncs restraints were applied as a tight positional (0.05a) and loose thermal (5.0a3) restraints. These restraints, along with tls restraints where the mobile and fixed regions of each monomer were treated as separate TLS domains, were applied to each conformation with each member of a conformation being restrained against the template model. The closed conformation monomers have 2000 added to each residue number, the intermediate monomers have 1000 added to each residue number and the open monomers have 3000 added to each reside number. Such renumbering was required for manipulation of the model and to allow the use of ncs restraints in refinement using refmac5. Each monomer has its associated water molecules added to the chain with a residue number starting at 300. Therefore a closed monomer has its first water molecule as residue 2301, an intermediate monomer has 1301 and an open monomer 3301. Residues 254 to 299 are not present in each chain. The twelve closed monomers are in chains: A, B, C, E, G, H, I, J, K, L, M, and P. The thirteen intermediate monomers are in chains B, C, D, E, F, H, I, J, K, N, O, Q, and R. The five open monomers are in chains: A, D, L, M, and O. Lower and upper case chain letters in the released model are equivalent. A large torus of electron density inside the central pore of each hexamer was modelled as a meta-vanavdate ion. Sodium orthovanadate was present in the crystallisation conditions, and therefore the trimeric head of the meta- vanadate ion from 1DKT (Human cyclin dependent kinase subunit type-A complex with meta vanadate) was used as a template model. The vanadate component of this structure is an artifact of the crystal conditions with no functional significance, as two other up substrate complexes have been solved in the absence of vanadate and no density corresponding to metavanadate is observed
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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: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 原子変位パラメータ | Biso mean: 17.286 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: 2.8→26.75 Å
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| 拘束条件 |
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| Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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