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基本情報
登録情報 | データベース: PDB / ID: 1juj | ||||||
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タイトル | Human Thymidylate Synthase Bound to dUMP and LY231514, a Pyrrolo(2,3-d)pyrimidine-based Antifolate | ||||||
![]() | THYMIDYLATE SYNTHASE | ||||||
![]() | TRANSFERASE / cancer / dTMP synthesis / antifolate / drug resistance | ||||||
機能・相同性 | ![]() uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / developmental growth / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / liver regeneration / response to toxic substance / circadian rhythm / methylation / response to ethanol / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Sayre, P.H. / Finer-Moore, J.S. / Fritz, T.A. / Biermann, D. / Gates, S.B. / MacKellar, W.C. / Patel, V.F. / Stroud, R.M. | ||||||
![]() | ![]() タイトル: Multi-targeted antifolates aimed at avoiding drug resistance form covalent closed inhibitory complexes with human and Escherichia coli thymidylate synthases. 著者: Sayre, P.H. / Finer-Moore, J.S. / Fritz, T.A. / Biermann, D. / Gates, S.B. / MacKellar, W.C. / Patel, V.F. / Stroud, R.M. #1: ![]() タイトル: Crystal Structure of Human Thymidylate Synthase: A Structural Mechanism for Guiding Substrates into the Active Site 著者: Schiffer, C.A. / Clifton, I.J. / Davisson, V.J. / Santi, D.V. / Stroud, R.M. | ||||||
履歴 |
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Remark 295 | NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON- ...NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THIS ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS M 1 A 28 .. 313 B 28 .. 313 M 2 A 28 .. 313 C 28 .. 313 M 3 A 28 .. 313 D 28 .. 313 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK: THE AUTHORS RESTRAINED SUBUNIT B, C, AND D AGAINST SUBUNIT A, USING A WEIGHT OF 200 KCAL/MOL-A, AND SIGB OF 2 A2. |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 233.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 190.4 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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1 | ![]()
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2 | ![]()
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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper:
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詳細 | The biological dimer is generated from the coordinates with the following noncrystallographic symmetry rotation matrix and translation vector: {* real-space rotation matrix *} {===>} ncs_matrix_2=( -0.04364 0.52546 -0.84970 ) ( 0.53532 -0.70580 -0.46397 ) ( -0.84352 -0.47511 -0.25049 ); {* real-space translation vector *} {===>} ncs_vector_2=(-22.64756 -91.22199 -82.72397); A second dimer in the asymmetric unit is generated by the following NCS symmetry operations: {* real-space rotation matrix *} {===>} ncs_matrix_3=( -0.99996 0.00926 -0.00060 ) ( 0.00927 0.99993 -0.00771 ) ( 0.00053 -0.00771 -0.99997 ); {* real-space translation vector *} {===>} ncs_vector_3=(-48.72274 4.78975 -52.76192); and {* real-space rotation matrix *} {===>} ncs_matrix_4=( 0.04749 -0.53294 0.84482 ) ( 0.54116 -0.69717 -0.47021 ) ( 0.83958 0.47951 0.25530 ); {* real-space translation vector *} {===>} ncs_vector_4=(-27.02831 -85.96681 30.66597); |
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要素
#1: タンパク質 | 分子量: 35734.859 Da / 分子数: 4 / 変異: R46E / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: 化合物 | ChemComp-UMP / #3: 化合物 | ChemComp-LYA / |
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-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: 2.48 Å3/Da / 溶媒含有率: 50.47 % | ||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 296 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: PEG-monomethyl ether 5000, sodium cacodylate, ammonium sulfate, KCL, TRIS, EDTA, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 296 K |
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放射光源 | 由来: ![]() |
検出器 | タイプ: RIGAKU RAXIS II / 検出器: IMAGE PLATE / 日付: 1997年7月1日 |
放射 | モノクロメーター: graphite / 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: 1.54178 Å / 相対比: 1 |
反射 | 解像度: 3→40 Å / Num. all: 23396 / Num. obs: 23396 / % possible obs: 84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 2.1 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 5.8 |
反射 シェル | 解像度: 3→3.09 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 78 |
反射 | *PLUS 最高解像度: 3 Å / 最低解像度: 40 Å / % possible obs: 84 % / Num. measured all: 50715 |
反射 シェル | *PLUS % possible obs: 78 % |
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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: ![]() 開始モデル: thymidylate synthase from Leishmania major 解像度: 3→37.96 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 131081.01 / 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: Engh and Huber 詳細: The asymmetric unit contains four monomers and these were refined using strict noncrystallographic symmetry constraints. The strict noncrystallographic symmetry was broken at the interface ...詳細: The asymmetric unit contains four monomers and these were refined using strict noncrystallographic symmetry constraints. The strict noncrystallographic symmetry was broken at the interface between the two dimers and Arg42 at this interface in chains B and D had to be rebuilt at the end of refinement. Residues 1-27, as well as the sidechain of Arg147 are disordered in each monomer and are omitted from the structure.
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 30.2028 Å2 / ksol: 0.273945 e/Å3 | |||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 25.2 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: 3→37.96 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 3→3.19 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 1 / 分類: refinement | |||||||||||||||||||||||||
精密化 | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor all: 0.273 / Rfactor obs: 0.268 | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 25.2 Å2 | |||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.482 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.431 |