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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: 2izg | ||||||
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タイトル | STREPTAVIDIN-BIOTIN PH 2.0 I222 COMPLEX | ||||||
![]() | STREPTAVIDIN | ||||||
![]() | BIOTIN-BINDING PROTEIN / STREPTAVIDIN-BIOTIN | ||||||
機能・相同性 | ![]() | ||||||
生物種 | ![]() | ||||||
手法 | ![]() | ||||||
![]() | Katz, B.A. | ||||||
![]() | ![]() タイトル: Binding of biotin to streptavidin stabilizes intersubunit salt bridges between Asp61 and His87 at low pH. 著者: Katz, B.A. #1: ![]() タイトル: In Crystals of Complexes of Streptavidin with Thermodynamic Comparison with Biotin of a Small 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. #2: ![]() タイトル: Structure-Based Design Tools: Structural and Molecule that Binds Streptavidin with Micromolar Affinity 著者: Katz, B.A. / Liu, B. / Cass, R.T. #3: ![]() タイトル: Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design 著者: Katz, B.A. #4: ![]() 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. #5: ![]() 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: ![]() タイトル: Structure-Based Design of High Affinity Streptavidin Binding Ligands Containing Thioether Crosslinks 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: ![]() ![]() |
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ダウンロードとリンク
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PDBx/mmCIF形式 | ![]() | 118.2 KB | 表示 | ![]() |
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PDB形式 | ![]() | 95.2 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 455.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 465.5 KB | 表示 | |
XML形式データ | ![]() | 16.1 KB | 表示 | |
CIF形式データ | ![]() | 22 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 2izaC ![]() 2izbC ![]() 2izcC ![]() 2izdC ![]() 2izeC ![]() 2izfC ![]() 2izhC ![]() 2iziC ![]() 2izjC ![]() 2izkC ![]() 2izlC ![]() 2rtaC ![]() 2rtbC ![]() 2rtcC ![]() 2rtdC ![]() 2rteC ![]() 2rtfC ![]() 2rtgC ![]() 2rthC ![]() 2rtiC ![]() 2rtjC ![]() 2rtkC ![]() 2rtlC ![]() 2rtmC ![]() 2rtnC ![]() 2rtoC ![]() 2rtpC ![]() 2rtqC ![]() 2rtrC C: 同じ文献を引用 ( |
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類似構造データ |
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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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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: (-0.99975, -0.0213, -0.006845), ベクター: |
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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) ![]() #2: 化合物 | #3: 化合物 | ChemComp-SO4 / | #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: 2.33 Å3/Da / 溶媒含有率: 22 % 解説: REJECTION CRITERIA: (I(H)I - ) > [0.30 * () + 0.10*I(H)I], WHERE I(H)I IS THE ITH OBSERVATION OF THE INTENSITY OF REFLECTION H (M.G.ROSSMANN ET AL., J.APPL.CRYST. 12, 570-581). THIS REJECTION ...解説: REJECTION CRITERIA: (I(H)I - ) > [0.30 * ( | ||||||||||||||||||||
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結晶化 | pH: 2 詳細: SYNTHETIC MOTHER LIQUOR = 75 % SATURATED AMMONIUM SULFATE, 25 % 1.0 M SODIUM FORMATE ADJUSTED TO PH 2.0. | ||||||||||||||||||||
結晶 | *PLUS | ||||||||||||||||||||
結晶化 | *PLUS 温度: 20 ℃ / pH: 4 / 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 | Ambient temp details: ROOM |
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放射光源 | 由来: ![]() |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 詳細: MSC MIRRORS |
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: 43506 / 冗長度: 9.6 % / Rmerge(I) obs: 0.073 |
反射 | *PLUS 最高解像度: 1.33 Å / Num. measured all: 415631 |
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解析
ソフトウェア |
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精密化 | 解像度: 1.36→7.5 Å / 交差検証法: FREE R / σ(F): 1.3 詳細: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B13, B14, B15, B22, (CG, HG1, HG2, CD, OE1, OE2 OF GLU B51), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B53), (NE, ...詳細: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B13, B14, B15, B22, (CG, HG1, HG2, CD, OE1, OE2 OF GLU B51), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B53), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B84), (CG, HG1, HG2, CD, OE1, OE2 OF GLU B101), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG B103), (CG, HG1, HG2, CD, OE1, OE2 OF GLU B116), (CB, HB1, HB2, CG, HG1, HG2 OF LYS B134), (CD, HD1, HD2 OF LYS B134), (NZ, HZ1, HZ2, HZ3 OF LYS B134), PRO B135, (N, HT1, HT2, HT3, CA, HA, C, O OF D13), (CB, HB1, HB2, HB3 OF D13), D14, D15, (CG, OD1, OD2 OF ASP D36), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG D53), (CG, OD1, ND2, HD21, HD22 OF ASN D82), (CG AND OUTWARD OF TYR D83), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG D84), (CG, HG1, HG2, CD, OE1, OE2 OF GLU D101), (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22 OF ARG D103), (CG, HG1, HG2, CD, OE1, OE2 OF GLU D116). RESIDUES B60 - B69 AND D60 - D69 WERE REFINED IN 2 CONFORMATIONS BECAUSE UPON PROTONATION OF ASP61 AT LOW PH, ASP B61 AND ASP D61 UNDERGO LARGE SHIFTS IN CONFORMATION AND CHANGES IN HYDROGEN BONDING. THE LOOPS COMPRISING RESIDUES B61 - B69 AND D61 - D69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. B22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A 2 - FOLD RELATED B22. PROPER REFINEMENT WITH XPLOR 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 B22: HOH1637, HOH1777. NO HYDROGENS ARE INCLUDED FOR THESE "WATERS".
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精密化ステップ | サイクル: LAST / 解像度: 1.36→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: 1.36→1.42 Å / % reflection obs: 25.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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ソフトウェア | *PLUS 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor obs: 0.204 |