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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: 2pcd | ||||||||||||
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タイトル | STRUCTURE OF PROTOCATECHUATE 3,4-DIOXYGENASE FROM PSEUDOMONAS AERUGINOSA AT 2.15 ANGSTROMS RESOLUTION | ||||||||||||
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![]() | DIOXYGENASE | ||||||||||||
機能・相同性 | ![]() protocatechuate 3,4-dioxygenase / protocatechuate 3,4-dioxygenase activity / 3,4-dihydroxybenzoate catabolic process / beta-ketoadipate pathway / ferric iron binding 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | ![]() | ||||||||||||
![]() | Ohlendorf, D.H. / Orville, A.M. / Lipscomb, J.D. | ||||||||||||
![]() | ![]() タイトル: Structure of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa at 2.15 A resolution. 著者: Ohlendorf, D.H. / Orville, A.M. / Lipscomb, J.D. #1: ![]() タイトル: Structure and Assembly of Protocatechuate 3,4-Dioxygenase 著者: Ohlendorf, D.H. / Lipscomb, J.D. / Weber, P.C. #2: ![]() タイトル: Determination of the Quaternary Structure of Protocatechuate 3,4-Dioxygenase from Pseudomonas Aeruginosa 著者: Ohlendorf, D.H. / Weber, P.C. / Lipscomb, J.D. | ||||||||||||
履歴 |
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Remark 700 | SHEET SHEETS S1X AND S2X ARE HOMOLOGOUS EIGHT-STRANDED SHEETS WITH TOPOLOGY (-5, -1, 7, -5, 1, 1X, ...SHEET SHEETS S1X AND S2X ARE HOMOLOGOUS EIGHT-STRANDED SHEETS WITH TOPOLOGY (-5, -1, 7, -5, 1, 1X, 1). EACH SHEET IS FOLDED IN HALF WITH THE EDGES SEALED BY A 4 RESIDUE SEGMENT (37 - 40 OR 361 - 364) WHICH FORMS H-BONDS WITH EACH EDGE STRAND. |
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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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ダウンロード
PDBx/mmCIF形式 | ![]() | 540.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 436.5 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
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
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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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper:
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要素
#1: タンパク質 | 分子量: 22278.812 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() #2: タンパク質 | 分子量: 26696.287 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() #3: 化合物 | ChemComp-FE / #4: 水 | ChemComp-HOH / | 構成要素の詳細 | IF ALL THE COORDINATES FOR THE SIX PROTOMERS ARE AVERAGED, THE RMS DEVIATION OF EACH PROTOMER FROM ...IF ALL THE COORDINATE | 配列の詳細 | THE SEQUENCE PRESENTED IN THIS ENTRY IS BASED ON THE NUCLEOTIDE SEQUENCE PRESENTED IN GENBANK ENTRY ...THE SEQUENCE PRESENTED IN THIS ENTRY IS BASED ON THE NUCLEOTIDE | |
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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: 2.83 Å3/Da / 溶媒含有率: 56.57 % | |||||||||||||||||||||||||
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結晶化 | *PLUS 温度: 4 ℃ / pH: 8.4 / 手法: free interface diffusion / 詳細: or hanging drop vapor diffusion | |||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
反射 | Num. obs: 164157 / % possible obs: 95.7 % |
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解析
ソフトウェア | 名称: PROLSQ / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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精密化 | 解像度: 2.15→5 Å / σ(F): 0 詳細: THIS NONSTANDARD UNIT CELL WAS CHOSEN OVER THE EQUIVALENT C2 CELL (A = 223.26, B = 127.03, C = 134.18, BETA = 61.08) BECAUSE OF THE CONVENIENCE OF HAVING A BETA ANGLE NEAR 90 DEGREES AND TO ...詳細: THIS NONSTANDARD UNIT CELL WAS CHOSEN OVER THE EQUIVALENT C2 CELL (A = 223.26, B = 127.03, C = 134.18, BETA = 61.08) BECAUSE OF THE CONVENIENCE OF HAVING A BETA ANGLE NEAR 90 DEGREES AND TO MAINTAIN CONSISTENCY WITH THE INITIAL CRYSTALLIZATION REPORT. TO CONVERT FROM FRAC_I2 TO FRAC_C2 USE THE FOLLOWING: [ 1.0 ][ 0.0 ][ 0.0 ] (XFRAC_I2) (XFRAC_C2) [ 0.0 ][ 1.0 ][ 0.0 ] X (YFRAC_I2) = (YFRAC_C2) [ -1.0 ][ 0.0 ][ 1.0 ] (ZFRAC_I2) (ZFRAC_C2) THE COORDINATES HAVE BEEN DEPOSITED IN THE ORTHOGONAL COORDINATES DEFINED BY THE LOCAL SYMMETRY OF THE COMPLEX (23). DURING REFINEMENT THE THERMAL FACTORS OF ATOMS THAT ARE HYDROGEN BONDED TO EACH OTHER WERE RESTRAINED TO BE SIMILAR. THE OCCUPANCIES OF THE SOLVENTS WERE ALLOWED TO VARY ONLY IN STEPS OF 0.200. BEFORE THE GENERATION OF A MAP THE OCCUPANCIES OF NCS-RELATED SOLVENTS WERE AVERAGED AND QUANTIZED TO A MULTIPLE OF 0.100.
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精密化ステップ | サイクル: LAST / 解像度: 2.15→5 Å
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拘束条件 |
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ソフトウェア | *PLUS 名称: PROLSQ / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS Num. reflection all: 136440 / Rfactor all: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS |