+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1vwq | |||||||||
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タイトル | STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 2.5, I4122 COMPLEX | |||||||||
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) Bothrops insularis (ヘビ) | |||||||||
手法 | X線回折 / 解像度: 1.7 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 | 1vwq.cif.gz | 67 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1vwq.ent.gz | 51.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1vwq.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 | 1vwq_validation.pdf.gz | 437.6 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1vwq_full_validation.pdf.gz | 443.4 KB | 表示 | |
XML形式データ | 1vwq_validation.xml.gz | 9.3 KB | 表示 | |
CIF形式データ | 1vwq_validation.cif.gz | 11.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/vw/1vwq ftp://data.pdbj.org/pub/pdb/validation_reports/vw/1vwq | HTTPS FTP |
-関連構造データ
関連構造データ | 1vwaC 1vwbC 1vwcC 1vwdC 1vweC 1vwfC 1vwgC 1vwhC 1vwiC 1vwjC 1vwkC 1vwlC 1vwmC 1vwnC 1vwoC 1vwpC 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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Components on special symmetry positions |
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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: 天然 / 由来: (天然) 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: 863.017 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bothrops insularis (ヘビ) |
#3: 化合物 | ChemComp-LEA / |
#4: 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: 2.66 Å3/Da / 溶媒含有率: 33.3 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 2.5 詳細: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M SODIUM FORMATE ADJUSTED TO PH 2.5. | |||||||||||||||||||||||||||||||||||||||||||||||||
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: 28160 / 冗長度: 4.5 % / Rmerge(I) obs: 0.107 |
反射 | *PLUS 最高解像度: 1.33 Å / Num. measured all: 127962 |
-解析
ソフトウェア |
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精密化 | 解像度: 1.7→7.5 Å / σ(F): 2.5 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), (N, HN, CA, HA1, HA2 OF GLY 26), (MAIN CHAIN OF ALA 35), (SIDE ...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), (N, HN, CA, HA1, HA2 OF GLY 26), (MAIN CHAIN OF ALA 35), (SIDE CHAIN OF ALA 35), (MAIN CHAIN AND CB, HB1, HB2 OF ASP 36), (CG, OD1, AND OD2 OF ASP 36), 46, 47, 48, 49, 50, (MAIN CHAIN AND CB, HB1, HB2 OF GLU 51), (CG, HG1, HG2, CD, OE1, OE2 OF GLU 51), (SIDE CHAIN OF SER 52), (TERMINUS OF ARG 53), 99, 100, (N AND HN OF GLU 101), (CG, HG1, HG2, CD, OE1, OE2 OF GLU 101), TERMINUS OF ARG 103, (N, HN, CA, HA OF GLU 116), (CB, HB1, HB2, CG, HG1, HG2 OF GLU 116), (CD, OE1, OE2 OF GLU 116), (N, HN, CA, HA OF ALA 117), (CB, HB1, HB2, HB3 OF ALA 117), LYS 121 FROM CG OUTWARD, LYS 132 SIDE CHAIN, (LYS P 9 AND NH2 P 10). DISCRETELY DISORDERED ENTIRE RESIDUES WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: 60, 61, 62, 63, 64, 65, 66, 67, 68, 69. DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: ARG 84, GLN 107. RESIDUES 60 - 69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP 61 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 166 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 354; HOH 148 WHICH OCCUPIES THE SPACE AVAILABLE WHEN ASP 61 IS IN CONFORMATION 2; HOH 279, HOH 305, HOH 313, HOH 516, HOH 526, HOH 532 WHICH ARE CLOSE TO SYMMETRY-RELATED EQUIVALENTS OF THEMSELVES; NO ENERGY INTERACTIONS INVOLVING HOH 279, HOH 305, HOH 313, HOH 516, HOH 526, HOH 532 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), (N, HN, CA, HA1, HA2 OF GLY 26), (MAIN CHAIN OF ALA 35), (SIDE CHAIN OF ALA 35), (MAIN CHAIN AND CB, HB1, HB2 OF ASP 36), (CG, OD1, AND OD2 OF ASP 36), 46, 47, 48, 49, 50, (MAIN CHAIN AND CB, HB1, HB2 OF GLU 51), (CG, HG1, HG2, CD, OE1, OE2 OF GLU 51), (SIDE CHAIN OF SER 52), (TERMINUS OF ARG 53), 99, 100, (N AND HN OF GLU 101), (CG, HG1, HG2, CD, OE1, OE2 OF GLU 101), TERMINUS OF ARG 103, (N, HN, CA, HA OF GLU 116), (CB, HB1, HB2, CG, HG1, HG2 OF GLU 116), (CD, OE1, OE2 OF GLU 116), (N, HN, CA, HA OF ALA 117), (CB, HB1, HB2, HB3 OF ALA 117), LYS 121 FROM CG OUTWARD, LYS 132 SIDE CHAIN, (LYS P 9 AND NH2 P 10). RESIDUES 60 - 69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP 61 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.
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精密化ステップ | サイクル: LAST / 解像度: 1.7→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: 1.7→1.78 Å / % reflection obs: 60.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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