+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2rta | |||||||||
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タイトル | APOSTREPTAVIDIN, PH 2.97, SPACE GROUP I4122 | |||||||||
要素 | STREPTAVIDINストレプトアビジン | |||||||||
キーワード | BIOTIN-BINDING PROTEIN / I4122 APOSTREPTAVIDIN / PH 2.97 | |||||||||
機能・相同性 | 機能・相同性情報 | |||||||||
生物種 | Streptomyces avidinii (バクテリア) | |||||||||
手法 | X線回折 / 解像度: 1.39 Å | |||||||||
データ登録者 | Katz, B.A. | |||||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 1997 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: 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. #2: 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. #3: 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. #4: 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. #5: 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. #6: 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. #7: 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 | 2rta.cif.gz | 63.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2rta.ent.gz | 49.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2rta.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/rt/2rta ftp://data.pdbj.org/pub/pdb/validation_reports/rt/2rta | HTTPS FTP |
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-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 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 (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: 14181.324 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: 化合物 | #3: 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: 2.89 Å3/Da / 溶媒含有率: 37.1 % 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: 2.97 詳細: SYNTHETIC MOTHER LIQUOR OF 75% SATURATED AMMONIUM SULFATE, 25% 1.0 M SODIUM FORMATE ADJUSTED TO PH 2.97. | ||||||||||||||||||||||||||||||
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
回折 | 平均測定温度: 273 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: 30482 / 冗長度: 4.1 % / Rmerge(I) obs: 0.066 |
反射 | *PLUS 最高解像度: 1.32 Å / Num. measured all: 123910 |
-解析
ソフトウェア |
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精密化 | 解像度: 1.39→7.5 Å / σ(F): 1.8 詳細: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA 13, GLU 14, ALA 15 (EXCEPT FOR C AND O), GLN 24, LEU 25, GLY 26 ALA 35 (SIDE CHAIN), ASP 36 (N, HN, CA, HA, C, O, CB, ...詳細: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA 13, GLU 14, ALA 15 (EXCEPT FOR C AND O), GLN 24, LEU 25, GLY 26 ALA 35 (SIDE CHAIN), ASP 36 (N, HN, CA, HA, C, O, CB, HB1, HB2, CG, OD1,OD2), GLU 44 (CG, HG1, HG2, CD, OE1, OE2) SER 45 (MAIN CHAIN), ALA 46 (CA, HA, C, O, CB, HB1, HB2, HB3), VAL 47, GLY 48 ASN 49, ALA 50, GLU 51, SER 52 (SIDE CHAIN), ARG 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ARG 84 (CG, HG1, HG2, CD, HD1, HD2, NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLY 99, ALA 100 (MAIN CHAIN), ALA 100 (SIDE CHAIN), GLU 101 (N, HN, CA, HA, CB, HB1, HB2, C, O, CG, HG1, HG2, CD, OE1, OE2) ARG 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22), GLU 116 (N, HN, CA, HA, CB, HB1, HB2, CG, HG1, HG2, C, O, CD, OE1, OE2) ALA 117, ASN 118 (SIDE CHAIN), LYS 121 (CG, HG1, HG2, CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1,HZ2, HZ3) RESIDUES TYR 60 TO SER 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 ASP 61 TO SER 69 ALSO UNDERGO CORRESPONDING CONFORMATIONAL CHANGES. HOWEVER SOME OF THESE RESIDUES ARE DISORDERED AND NOT VISIBLE IN EITHER CONFORMATION. DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED ARE: SER 45, LEU 73, HIS 87, GLN 107, LEU 110, LYS 132. DISORDERED SOLVENTS ARE: HOH 134 WHICH OCCUPIES THE SPACE AVAILABLE WHEN ASP 61 IS IN CONFORMATION NUMBER 2 HOH 142 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF HOH 150 WHICH IS CLOSE TO HOH 151 SO4 153 WHICH IS CLOSE TO HOH 545 HOH 152 WHICH IS CLOSE TO SO4 154 HOH 207 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 354 HOH 305 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF HOH 546 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF HOH 550 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF HOH 635 WHICH IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF ITSELF THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: ALA 13 GLU 14 ALA 15 (EXCEPT FOR C AND O) GLN 24 LEU 25 GLY 26 ALA 35 (SIDE CHAIN) ASP 36 (N, HN, CA, HA, C, O, CB, HB1, HB2, CG, OD1,OD2) GLU 44 (CG, HG1, HG2, CD, OE1, OE2) SER 45 (MAIN CHAIN) ALA 46 (CA, HA, C, O, CB, HB1, HB2, HB3) VAL 47 GLY 48 ASN 49 ALA 50 GLU 51 SER 52 (SIDE CHAIN) ARG 53 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) ARG 84 (CG, HG1, HG2, CD, HD1, HD2, NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLY 99 ALA 100 (MAIN CHAIN) ALA 100 (SIDE CHAIN) GLU 101 (N, HN, CA, HA, CB, HB1, HB2, C, O, CG, HG1, HG2, CD, OE1, OE2) ARG 103 (NE, HE, CZ, NH1, HH11, HH12, NH2, HH21, HH22) GLU 116 (N, HN, CA, HA, CB, HB1, HB2, CG, HG1, HG2, C, O, CD, OE1, OE2) ALA 117 ASN 118 (SIDE CHAIN) LYS 121 (CG, HG1, HG2, CD, HD1, HD2, CE, HE1, HE2, NZ, HZ1, HZ2, HZ3) RESIDUES TYR 60 TO SER 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 ASP 61 TO SER 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: 1.39→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: 1.39→1.45 Å / % reflection obs: 30.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: X-PLOR / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor obs: 0.206 |