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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 3al1 | |||||||||
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タイトル | DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM | |||||||||
![]() | PROTEIN (D, L-ALPHA-1) | |||||||||
![]() | STRUCTURAL PROTEIN / HELICAL BILAYER / BIOMATERIAL / CENTRIC / RACEMIC | |||||||||
機能・相同性 | ETHANOLAMINE![]() | |||||||||
手法 | ![]() ![]() | |||||||||
![]() | Patterson, W.R. / Anderson, D.H. / Degrado, W.F. / Cascio, D. / Eisenberg, D. | |||||||||
![]() | ![]() タイトル: Centrosymmetric bilayers in the 0.75 A resolution structure of a designed alpha-helical peptide, D,L-Alpha-1. 著者: Patterson, W.R. / Anderson, D.H. / DeGrado, W.F. / Cascio, D. / Eisenberg, D. #1: ![]() タイトル: Packed Protein Bilayers in the 0.90A Resolution Structure of a Designed Alpha Helical Bundle 著者: Prive, G.G. / Anderson, D.H. / Wesson, L. / Cascio, D. / Eisenberg, D. #2: ![]() タイトル: Crystal Structure of Alpha-1: Implications for Protein Design 著者: Hill, C.P. / Anderson, D.H. / Wesson, L. / Degrado, W.F. / Eisenberg, D. #3: ![]() タイトル: The Design, Synthesis, and Crystallization of an Alpha-Helical Peptide 著者: Eisenberg, D. / Wilcox, W. / Eshita, S.M. / Pryciak, P.M. / Ho, S.P. | |||||||||
履歴 |
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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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PDBx/mmCIF形式 | ![]() | 36.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 27.5 KB | 表示 | ![]() |
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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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単位格子 |
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要素
#1: タンパク質・ペプチド | 分子量: 1441.775 Da / 分子数: 2 / 由来タイプ: 合成 詳細: PEPTIDE WAS SYNTHESIZED VIA SOLID PHASE SYNTHESIS AND DESIGNED TO BE AN AMPHIPHILIC HELIX #2: 化合物 | ChemComp-MPD / ( | #3: 化合物 | #4: 水 | ChemComp-HOH / | |
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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: 1.61 Å3/Da / 溶媒含有率: 14.8 % 解説: THERE IS NO REDUNDANCY IN THE DATA SET BEYOND 1.28A RESOLUTION; RSYM CAN BE EVALUATED ONLY FOR 18-1.28A. DATA REDUNDANCY IN 18-1.28A SHELL IS 2.51 | ||||||||||||||||||||||||||||||
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結晶化 | 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 詳細: EQUAL VOLUMES OF 10 MG/ML D-ALPHA-1 AND 10 MG/ML L-ALPHA-1 WERE MIXED IMMEDIATELY BEFORE CRYSTALLIZATION. THE RESERVOIR SOLUTION CONTAINED 90-93% 2-METHYL-2,4-PENTANEDIOL, 0.075 M ...詳細: EQUAL VOLUMES OF 10 MG/ML D-ALPHA-1 AND 10 MG/ML L-ALPHA-1 WERE MIXED IMMEDIATELY BEFORE CRYSTALLIZATION. THE RESERVOIR SOLUTION CONTAINED 90-93% 2-METHYL-2,4-PENTANEDIOL, 0.075 M ETHANOLAMINE HCL PH 9.75, 0.05 M TRIETHANOLAMINE HCL PH 8. THE HANGING DROP CONTAINED EQUAL VOLUMES OF RESERVOIR AND 10 MG/ML D,L MIX ALPHA-1. THE ACIDIC PEPTIDE PARTWAY TITRATES THE BASIC BUFFERS TO REACH THE UNKNOWN RESULTANT PH., vapor diffusion - hanging drop PH範囲: 8-9.75 | ||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 | ||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 115 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 1996年6月1日 |
放射 | モノクロメーター: SI / 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: 0.9 Å / 相対比: 1 |
反射 | 解像度: 0.75→18 Å / Num. obs: 33573 / % possible obs: 71.5 % / Observed criterion σ(I): 1 / 冗長度: 1.4 % / Rsym value: 10 / Net I/σ(I): 10.6 |
反射 シェル | 解像度: 0.75→0.78 Å / 冗長度: 1 % / Mean I/σ(I) obs: 2 / % possible all: 24.9 |
反射 | *PLUS Rmerge(I) obs: 0.1 |
反射 シェル | *PLUS % possible obs: 24.9 % / Num. unique obs: 1172 |
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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: DIRECT METHODS / 解像度: 0.75→18 Å / Num. parameters: 2939 / Num. restraintsaints: 4291 / 交差検証法: FREE R / σ(F): 0 StereochEM target val spec case: GLU 108 CONFORMATION C CARBOXYLATE HAS A STIFF PLANARITY RESTRAINT. ETHANOLAMINE AND MPD RESTRAINTS WERE DERIVED BY ANALOGY TO OTHER SIMILAR GROUPS. 立体化学のターゲット値: ENGH AND HUBER 詳細: STRUCTURE WAS REDETERMINED WITH SHAKE AND BAKE BECAUSE THE REFINEMENT WAS STUCK AT R ABOUT 21%. THE SNB RESULT CONFIRMED THE SHELXS STRUCTURE. SAME TEST SET WAS USED FOR SHELXL-93 AND -97. ...詳細: STRUCTURE WAS REDETERMINED WITH SHAKE AND BAKE BECAUSE THE REFINEMENT WAS STUCK AT R ABOUT 21%. THE SNB RESULT CONFIRMED THE SHELXS STRUCTURE. SAME TEST SET WAS USED FOR SHELXL-93 AND -97. SAME RESTRAINTS WERE CARRIED ALONG INTO SHELXL-97; THERE WAS NO DFIX/DANG DISTINCTION. INTRODUCTION OF ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ONLY 1%. IN THIS REFINEMENT, THE ALTERNATE CONFORMATIONS EVENTUALLY REDUCED FREE R FROM 22.6 - 14.5%
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溶媒の処理 | 溶媒モデル: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 250.04 / Occupancy sum non hydrogen: 237.88 | |||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 0.75→18 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: SHELXL-97 / 分類: refinement | |||||||||||||||||||||||||||||||||
精密化 | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.13 / Rfactor Rwork: 0.13 | |||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS |