+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1vwk | ||||||
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タイトル | STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2 | ||||||
要素 |
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キーワード | COMPLEX (BIOTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) / LINEAR THIOETHER-CONTAINING PEPTIDE ENGINEERED / 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: 1.45 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 | 1vwk.cif.gz | 119.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1vwk.ent.gz | 102.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1vwk.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/1vwk ftp://data.pdbj.org/pub/pdb/validation_reports/vw/1vwk | HTTPS FTP |
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-関連構造データ
関連構造データ | 1vwaC 1vwbC 1vwcC 1vwdC 1vweC 1vwfC 1vwgC 1vwhC 1vwiC 1vwjC 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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Components on special symmetry positions |
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非結晶学的対称性 (NCS) | NCS oper: (Code: given Matrix: (-0.999869, -0.01571, 0.003906), ベクター: |
-要素
#1: タンパク質 | 分子量: 12965.025 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Streptomyces avidinii (バクテリア) / 参照: UniProt: P22629 #2: タンパク質・ペプチド | 分子量: 863.017 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bothrops insularis (ヘビ) #3: 化合物 | #4: 水 | ChemComp-HOH / | 構成要素の詳細 | DISULFIDE BOND OF PHAGE-DISCOVERED | |
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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: 2.17 Å3/Da / 溶媒含有率: 18.5 % | ||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 3 詳細: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M SODIUM FORMATE ADJUSTED TO PH 3.0. | ||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 20 ℃ / 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. / pH: 4 | ||||||||||||||||||||||||||||||||||||
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: 41763 / 冗長度: 2 % / Rmerge(I) obs: 0.079 |
反射 | *PLUS 最高解像度: 1.33 Å / Num. measured all: 82155 |
-解析
ソフトウェア |
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精密化 | 解像度: 1.45→7.5 Å / σ(F): 1.6 詳細: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 22, B 46, B 47, B 48, B 49, B 50, (TERMINUS OF ARG B 53), (TERMINUS OF ARG B 59), (TERMINUS OF ARG B 84) ...詳細: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 22, B 46, B 47, B 48, B 49, B 50, (TERMINUS OF ARG B 53), (TERMINUS OF ARG B 59), (TERMINUS OF ARG B 84), (SIDE CHAIN OF GLU B 101), (TERMINUS OF ARG B 103), (CG, HG1, HG2, CD, OE1, OE2 OF GLU B 116), B 135, D 13, D 14, D 15, D 46, D 47, D 48, D 49, D 50, (TERMINUS OF ARG D 53), (TERMINUS OF ARG D 59), (TERMINUS OF ARG D 84), (TERMINUS OF ARG D 103), (M 9 AND M 10), (P 9 AND P 10). DISCRETELY DISORDERED ENTIRE RESIDUES WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: B 60, B 61, B 62, B 63, B 64, B 65, B 66, B 67, B 68, B 69, D 61, D 62, D 63, D 64, D 65, D 66, D 67, D 68, D 69, (ACE P 0 AND CYS P 1), (CYS P 6 AND NH2 P 7). RESIDUES B 60 - B 69 AND D 60 - D 69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP 61 AT LOW PH, ASP B 61 AND ASP D 61 UNDERGO LARGE SHIFTS IN CONFORMATION AND CHANGES IN HYDROGEN BONDING. THE LOOPS COMPRISING RESIDUES B 61 - B 69 AND D 61 - D 69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. ISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND TRUCTURES WERE SIMULTANEOUSLY REFINED WERE B 40, B 42, B 73, B 87, B 110, D 32, D 87, D 107, D 110, M 3. B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A TWO-FOLD RELATED B 22. PROPER REFINEMENT WITH X-PLOR IS NOT POSSIBLE BECAUSE OF THE OVERLAP OF ONE CONFORMER WITH THE SYMMETRY-RELATED COUNTERPART. THE FOLLOWING WATERS WERE USED TO ACCOUNT FOR DENSITY DUE TO THIS CONFORMER OF TYR B 22: HOH 516, HOH 519, HOH 1249. DISORDERED WATERS ARE HOH 852 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENTS OF ITSELF; HOH 1284 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENTS OF ITSELF AND OCCUPIES THE SPACE AVAILABLE WHEN ASN D 107 IS IN ONE OF ITS DISCRETE CONFORMATIONS; HOH 624 WHICH IS CLOSE TO HOH 1182; HOH 1026 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 1253; HOH 1139 THAT OCCUPIES THE REGION OF SPACE AVAILABLE WHEN ASP B 61 IS IN CONFORMATION NO. 2; HOH 1167 THAT OCCUPIES THE REGION OF SPACE AVAILABLE WHEN ASP D 61 IS IN CONFORMATION NO. 2; HOH 513 WHICH IS CLOSE TO MAIN CHAIN CARBONYL OF B 49 AND MAIN CHAIN AMIDE OF B 50; HOH 514 WHICH IS CLOSE TO B 51; HOH 1287 WHICH IS CLOSE TO O OF B 14 FOR WHICH THERE IS LITTLE DENSITY; HOH 1251 WHICH IS CLOSE TO O OF B 51; HOH 1209 WHICH IS CLOSE TO CA OF B 48. IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS INVOLVING HOH 513, HOH 852, HOH 516, HOH 519, HOH 1249, HOH 1209, HOH 1251, HOH 1284, HOH 1287. DISULFIDE BOND OF PHAGE-DISCOVERED PEPTIDE IS REPLACED WITH THIOETHER. THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 22, B 46, B 47, B 48, B 49, B 50, (TERMINUS OF ARG B 53), (TERMINUS OF ARG B 59), (TERMINUS OF ARG B 84), (SIDE CHAIN OF GLU B 101), (TERMINUS OF ARG B 103), (CG, HG1, HG2, CD, OE1, OE2 OF GLU B 116), B 135, D 13, D 14, D 15, D 46, D 47, D 48, D 49, D 50, (TERMINUS OF ARG D 53), (TERMINUS OF ARG D 59), (TERMINUS OF ARG D 84), (TERMINUS OF ARG D 103), (M 9 AND M 10), (P 9 AND P 10). B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A TWO-FOLD RELATED B 22. PROPER REFINEMENT WITH X-PLOR IS NOT POSSIBLE BECAUSE OF THE OVERLAP OF ONE CONFORMER WITH THE SYMMETRY-RELATED COUNTERPART. THE FOLLOWING WATERS WERE USED TO ACCOUNT FOR DENSITY DUE TO THIS CONFORMER OF TYR B 22: HOH 516, HOH 519, HOH 1249.
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精密化ステップ | サイクル: LAST / 解像度: 1.45→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: 1.45→1.52 Å / % reflection obs: 33.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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ソフトウェア | *PLUS 名称: X-PLOR / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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