+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2ux8 | ||||||
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タイトル | Crystal Structure of Sphingomonas elodea ATCC 31461 Glucose-1- phosphate uridylyltransferase in Complex with glucose-1-phosphate. | ||||||
要素 | GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE | ||||||
キーワード | TRANSFERASE / UGPG / GALU PYROPHOSPHORYLASE / GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE / NUCLEOTIDYLTRANSFERASE | ||||||
機能・相同性 | 機能・相同性情報 UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / biosynthetic process 類似検索 - 分子機能 | ||||||
生物種 | SPHINGOMONAS ELODEA (バクテリア) | ||||||
手法 | X線回折 / シンクロトロン / 多重同系置換・異常分散 / 解像度: 2.65 Å | ||||||
データ登録者 | Aragao, D. / Fialho, A.M. / Marques, A.R. / Frazao, C. / Sa-Correia, I. / Mitchell, E.P. | ||||||
引用 | ジャーナル: J.Bacteriol. / 年: 2007 タイトル: The Complex of Sphingomonas Elodea Atcc 31461 Glucose-1-Phosphate Uridylyltransferase with Glucose-1-Phosphate Reveals a Novel Quaternary Structure, Unique Among Nucleoside Diphosphate- ...タイトル: The Complex of Sphingomonas Elodea Atcc 31461 Glucose-1-Phosphate Uridylyltransferase with Glucose-1-Phosphate Reveals a Novel Quaternary Structure, Unique Among Nucleoside Diphosphate-Sugar Pyrophosphorylase Members. 著者: Aragao, D. / Fialho, A.M. / Marques, A.R. / Mitchell, E.P. / Sa-Correia, I. / Frazao, C. #1: ジャーナル: Acta Crystallogr.,Sect.F / 年: 2006 タイトル: Cloning, Expression, Purification, Crystallisation and Preliminary Structure Determination of Glucose- 1-Phosphate Uridylyltransferase (Ugpg) Bound to Glucose-1-Phosphate from Sphingomonas Elodea Atcc31461 著者: Aragao, D. / Marques, A.R. / Frazao, C. / Enguita, F.J. / Carrondo, M.A. / Fialho, A.M. / Sa-Correia, I. / Mitchell, E.P. | ||||||
履歴 |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 17-STRANDED BARREL THIS IS REPRESENTED BY A 18-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-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 | 2ux8.cif.gz | 416.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2ux8.ent.gz | 345.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2ux8.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
文書・要旨 | 2ux8_validation.pdf.gz | 2.6 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 2ux8_full_validation.pdf.gz | 2.7 MB | 表示 | |
XML形式データ | 2ux8_validation.xml.gz | 87.1 KB | 表示 | |
CIF形式データ | 2ux8_validation.cif.gz | 114.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ux/2ux8 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/2ux8 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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2 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 32213.961 Da / 分子数: 8 / 由来タイプ: 組換発現 / 詳細: CO-CRYSTALLISED WITH GLUCOSE-1-PHOSPHATE 由来: (組換発現) SPHINGOMONAS ELODEA (バクテリア) プラスミド: PUGPG2 BASED ON PWH844 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 参照: UniProt: Q5FYV5, UTP-glucose-1-phosphate uridylyltransferase #2: 糖 | ChemComp-G1P / #3: 水 | ChemComp-HOH / | 配列の詳細 | THIS RECOMBINANT PLASMID CARRIES THE UGPG GENE PRECEDED BY A SEQUENCE CODING FOR SIX HISTIDINE ...THIS RECOMBINAN | |
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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: 2.55 Å3/Da / 溶媒含有率: 51.7 % |
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結晶化 | pH: 4.6 詳細: 0.1M AMMONIUM ACETATE, 0.1M SODIUM CITRATE PH=4.6, 15% PEGMME, 5MM G1P, pH 4.60 |
-データ収集
回折 | 平均測定温度: 100 K | |||||||||
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放射光源 | 由来: シンクロトロン / サイト: ESRF / ビームライン: ID29 / 波長: 0.97564, 1.13980 | |||||||||
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2005年9月12日 / 詳細: TOROIDAL MIRROR | |||||||||
放射 | モノクロメーター: SI(111) / 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 |
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反射 | 解像度: 2.65→102 Å / Num. obs: 85566 / % possible obs: 100 % / Observed criterion σ(I): 2 / 冗長度: 5.7 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.1 | |||||||||
反射 シェル | 解像度: 2.65→2.67 Å / 冗長度: 3.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 多重同系置換・異常分散 / 解像度: 2.65→74.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 884457.43 / Isotropic thermal model: B-GROUP / 交差検証法: THROUGHOUT / σ(F): 0 立体化学のターゲット値: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES 詳細: DIFFERENT NCS RESTRAINS USED FOR MAIN-CHAINS AND FOR SIDE-CHAINS. GROUP B-FACTOR REFINEMENT DOES NOT ALLOW NCS RESTRAINS. DISORDERED REGIONS WERE NOT INCLUDED IN THE REFINEMENT.
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溶媒の処理 | 溶媒モデル: CNS BULK SOLVENT MODEL USED / Bsol: 45.5985 Å2 / ksol: 0.351613 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 54.23 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: 2.65→74.9 Å
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拘束条件 |
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Refine LS restraints NCS | NCS model details: RESTRAINS / Rms dev position: 2 Å / Weight position: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.75→2.77 Å / Total num. of bins used: 39
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM |