+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1vwe | ||||||
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タイトル | STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 3.6 | ||||||
要素 |
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キーワード | COMPLEX (BIOTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) / CYCLIC PEPTIDE DISCOVERED BY PHAGE DISPLAY / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) complex | ||||||
機能・相同性 | 機能・相同性情報 | ||||||
生物種 | Streptomyces avidinii (バクテリア) | ||||||
手法 | X線回折 / 解像度: 1.5 Å | ||||||
データ登録者 | Katz, B.A. / Cass, R.T. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 1997 タイトル: In crystals of complexes of streptavidin with peptide ligands containing the HPQ sequence the pKa of the peptide histidine is less than 3.0. 著者: Katz, B.A. / Cass, R.T. #1: ジャーナル: J.Am.Chem.Soc. / 年: 1996 タイトル: Structure-Based Design Tools: Structural and Thermodynamic Comparison with Biotin of a Small Molecule that Binds Streptavidin with Micromolar Affinity 著者: Katz, B.A. / Liu, B. / Cass, R.T. #2: ジャーナル: J.Am.Chem.Soc. / 年: 1996 タイトル: Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design 著者: Katz, B.A. #3: ジャーナル: J.Biol.Chem. / 年: 1995 タイトル: Topochemical Catalysis Achieved by Structure-Based Ligand Design 著者: Katz, B.A. / Cass, R.T. / Liu, B. / Arze, R. / Collins, N. #4: ジャーナル: Chem.Biol. / 年: 1995 タイトル: Topochemistry for Preparing Ligands that Dimerize Receptors 著者: Katz, B.A. / Stroud, R.M. / Collins, N. / Liu, B. / Arze, R. #5: ジャーナル: Biochemistry / 年: 1995 タイトル: Binding to Protein Targets of Peptidic Leads Discovered by Phage Display: Crystal Structures of Streptavidin-Bound Linear and Cyclic Peptide Ligands Containing the Hpq Sequence 著者: Katz, B.A. #6: ジャーナル: J.Am.Chem.Soc. / 年: 1995 タイトル: Structure-Based Design of High Affinity Streptavidin Binding Cyclic Peptide Ligands Containing Thioether Cross-Links 著者: Katz, B.A. / Johnson, C.R. / Cass, R.T. | ||||||
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 | 1vwe.cif.gz | 60.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1vwe.ent.gz | 50.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1vwe.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/vw/1vwe ftp://data.pdbj.org/pub/pdb/validation_reports/vw/1vwe | HTTPS FTP |
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-関連構造データ
関連構造データ | 1vwaC 1vwbC 1vwcC 1vwdC 1vwfC 1vwgC 1vwhC 1vwiC 1vwjC 1vwkC 1vwlC 1vwmC 1vwnC 1vwoC 1vwpC 1vwqC 1vwrC C: 同じ文献を引用 (文献) |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 12965.025 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Streptomyces avidinii (バクテリア) 参照: UniProt: P22629 |
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#2: タンパク質・ペプチド | 分子量: 758.911 Da / 分子数: 1 / 由来タイプ: 組換発現 |
#3: 水 | ChemComp-HOH / |
-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: 2.79 Å3/Da / 溶媒含有率: 35.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 3.6 詳細: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M POTASSIUM ACETATE ADJUSTED TO PH 3.6. | |||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 20 ℃ / pH: 4.5 / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: Pahler, A., (1987) J. Biol. Chem., 262, 13933. | |||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 293 K |
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放射光源 | 波長: 1.5418 |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE |
放射 | 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 | Num. obs: 26406 / 冗長度: 4.8 % / Rmerge(I) obs: 0.081 |
反射 | *PLUS 最高解像度: 1.33 Å / Num. measured all: 126387 |
-解析
ソフトウェア |
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精密化 | 解像度: 1.5→7.5 Å / σ(F): 2.7 詳細: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, MAIN CHAIN OF GLN 24, SIDE CHAIN OF GLN 24, MAIN CHAIN OF LEU 25, SIDE CHAIN OF LEU 25, 26, 35, MAIN CHAIN AND ...詳細: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, MAIN CHAIN OF GLN 24, SIDE CHAIN OF GLN 24, MAIN CHAIN OF LEU 25, SIDE CHAIN OF LEU 25, 26, 35, MAIN CHAIN AND CB, HB1, HB2 OF ASP 36, CG, OD1, AND OD2 OF ASP 36, 46, 47, 48, 49, 50, 51 (EXCEPT C AND O), SIDE CHAIN OF SER 52, TERMINUS OF ARG 53, ARG 84 SIDE CHAIN FROM CB OUTWARD, 99, 100, SIDE CHAIN OF GLU 101 FROM CG OUTWARD, TERMINUS OF ARG 103, GLN 116 SIDE CHAIN, 117 MAIN CHAIN, 117 SIDE CHAIN, LYS 121 FROM CG OUTWARD, LYS 132 SIDE CHAIN. DISCRETELY DISORDERED ENTIRE RESIDUES WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, (ACE P 0 AND CYS P 1), (CYS P 6 AND NH2 P 7). DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: HIS 87, GLN 107. RESIDUES 60 - 69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF AS P61 AT LOW PH, ASP 61 UNDERGOES A LARGE SHIFT IN CONFORMATION AND CHANGE IN HYDROGEN BONDING. THE LOOP COMPRISING RESIDUES 61 - 69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. DISORDERED WATERS ARE HOH 142 WHICH OCCUPIES THE SPACE AVAILABLE WHEN ASP 61 IS IN CONFORMATION NO. 1; HOH 279, HOH 305, AND HOH 313 WHICH ARE CLOSE TO SYMMETRY-RELATED EQUIVALENTS OF THEMSELVES, RESPECTIVELY. NO ENERGY INTERACTIONS INVOLVING HOH 279, HOH 305 OR HOH 313 WERE TURNED ON DURING REFINEMENT. THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: 13, 14, 15, MAIN CHAIN OF GLN 24, SIDE CHAIN OF GLN 24, MAIN CHAIN OF LEU 25, SIDE CHAIN OF LEU 25, 26, 35, MAIN CHAIN AND CB, HB1, HB2 OF ASP 36, CG, OD1, AND OD2 OF ASP 36, 46, 47, 48, 49, 50, 51 (EXCEPT C AND O), SIDE CHAIN OF SER 52, TERMINUS OF ARG 53, ARG 84 SIDE CHAIN FROM CB OUTWARD, 99, 100, SIDE CHAIN OF GLU 101 FROM CG OUTWARD, TERMINUS OF ARG 103, GLN 116 SIDE CHAIN, 117 MAIN CHAIN, 117 SIDE CHAIN, LYS 121 FROM CG OUTWARD, LYS 132 SIDE CHAIN.
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精密化ステップ | サイクル: LAST / 解像度: 1.5→7.5 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.5→1.57 Å / % reflection obs: 32.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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ソフトウェア | *PLUS 名称: X-PLOR / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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