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基本情報
登録情報 | データベース: PDB / ID: 2rti | |||||||||
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タイトル | STREPTAVIDIN-GLYCOLURIL COMPLEX, PH 2.50, SPACE GROUP I222 | |||||||||
![]() | STREPTAVIDIN | |||||||||
![]() | BIOTIN-BINDING PROTEIN / STREPTAVIDIN-GLYCOLURIL / PH 2.50 | |||||||||
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 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 Thermodynamic Comparison with Biotin of a Small 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: Topochemistry for Preparing Ligands that Dimerize Receptors 著者: Katz, B.A. / Stroud, R.M. / Collins, N. / Liu, B. / Arze, R. #6: ![]() 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. #7: ![]() 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: ![]() ![]() |
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ダウンロードとリンク
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PDBx/mmCIF形式 | ![]() | 114.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 91.9 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 | ![]() | 450.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 463.2 KB | 表示 | |
XML形式データ | ![]() | 15 KB | 表示 | |
CIF形式データ | ![]() | 20.2 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 ![]() 2izgC ![]() 2izhC ![]() 2iziC ![]() 2izjC ![]() 2izkC ![]() 2izlC ![]() 2rtaC ![]() 2rtbC ![]() 2rtcC ![]() 2rtdC ![]() 2rteC ![]() 2rtfC ![]() 2rtgC ![]() 2rthC ![]() 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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2 | ![]()
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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: (-0.999852, -0.016006, -0.006257), ベクター: |
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要素
#1: タンパク質 | 分子量: 14181.324 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) ![]() #2: 化合物 | #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: 2.12 Å3/Da / 溶媒含有率: 23.9 % 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, A.G.W.LESLIE, S.S.ABDEL-MEGUID, T.TSUKIHARA, J. ...解説: REJECTION CRITERIA: (I(H)I - ) > [0.30 * ( | ||||||||||||||||||||||||||||||
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結晶化 | pH: 1.9 詳細: SYNTHETIC MOTHER LIQUOR, 75% SATURATED AMMONIUM SULFATE, 25% 1.0 M SODIUM FORMATE ADJUSTED TO PH 1.90. | ||||||||||||||||||||||||||||||
結晶 | *PLUS | ||||||||||||||||||||||||||||||
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
放射光源 | 波長: 1.5418 |
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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: 46071 / % possible obs: 66 % / 冗長度: 3.1 % / Rmerge(I) obs: 0.072 |
反射 シェル | 解像度: 1.4→1.46 Å / 冗長度: 3.1 % / % possible all: 31.9 |
反射 | *PLUS 最高解像度: 1.26 Å / Num. measured all: 142009 |
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解析
ソフトウェア |
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精密化 | 解像度: 1.4→7.5 Å / σ(F): 2.5 詳細: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B 13 GLU B 14 ALA B 15 GLU B 51 (CG, HG1, HG2, CD, OE1, OE2) ARG B 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ARG ...詳細: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA B 13 GLU B 14 ALA B 15 GLU B 51 (CG, HG1, HG2, CD, OE1, OE2) ARG B 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ARG B 84 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLY B 99 ALA B 100 GLU B 101 (CB, HB1, HB2, CG, HG1, HG2, CD, OE1, OE2) ARG B 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU B 116 (CG, HG1, HG2, CD, OE1, OE2) PRO B 135 ALA D 13 GLU D 14 ALA D 15 (EXCEPT C AND O) ASP D 36 (CG, OD1, OD2) GLU D 51 (CA, HA, CB, HB1, HB2, CG, HG1, HG2, CD, OE1, OE2) ARG D 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ASN D 82 (CG, OD1, ND2, HD21, HD22) TYR D 83 ARG D 84 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU D 101 (CB, HB1, HB2, CG, HG1, HG2, CD, OE1, OE2) ARG D 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU D 116 (CG, HG1, HG2, CD, OE1, OE2) 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. TYR B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A 2-FOLD RELATED B 22. 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 B 22: HOH 1468, HOH 1508, AND HOH 1539. 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: 1.4→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: 1.4→1.46 Å / % reflection obs: 31.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.209 |