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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: 1dwf | |||||||||
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タイトル | Study on radiation damage on a cryocooled crystal. Part 2: Structure after irradiation with 9.1*10e15 photons/mm2 | |||||||||
![]() | MYROSINASE MA1 | |||||||||
![]() | HYDROLASE / GLYCOSIDASE / RADIATION DAMAGE / RADIOLYSIS / CRYO-COOLED | |||||||||
機能・相同性 | ![]() thioglucosidase / thioglucosidase activity / glucosinolate glucohydrolase activity / glucosinolate catabolic process / vacuole / beta-glucosidase activity / response to salt stress / carbohydrate metabolic process / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Burmeister, W.P. | |||||||||
![]() | ![]() タイトル: Structural Changes in a Cryo-Cooled Protein Crystal due to Radiation Damage 著者: Burmeister, W.P. #1: ![]() タイトル: The Crystal Structures of Sinapis Alba Myrosinase and a Covalent Glycosyl-Enzyme Intermediate Provide Insights Into the Substrate Recognition and Active-Side Machinery of an S-Glycosidase 著者: Burmeister, W.P. / Cottaz, S. / Driguez, H. / Iori, R. / Palmieri, S. / Henrissat, B. | |||||||||
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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ダウンロード
PDBx/mmCIF形式 | ![]() | 150.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 115.6 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
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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
-タンパク質 , 1種, 1分子 M
#1: タンパク質 | 分子量: 56848.117 Da / 分子数: 1 / 断片: RESIDUES 3-501 / 由来タイプ: 天然 詳細: AFTER IRRADIATION WITH 9.1*10E15 PHOTONS/MM2 OF PHOTONS 由来: (天然) ![]() |
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-糖 , 4種, 10分子 ![](data/chem/img/NAG.gif)
#2: 多糖 | #3: 多糖 | beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)- ...beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | #4: 多糖 | beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D- ...beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | #5: 糖 | ChemComp-NAG / |
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-非ポリマー , 4種, 802分子 ![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#6: 化合物 | ChemComp-ZN / | ||||
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#7: 化合物 | ChemComp-SO4 / #8: 化合物 | ChemComp-GOL / #9: 水 | ChemComp-HOH / | |
-詳細
構成要素の詳細 | THIS ENTRY IS THE 2ND STRUCTURE OF A SERIES OF STRUCTURES IN A STUDY ON RADIATION DAMAGE IN CRYO- ...THIS ENTRY IS THE 2ND STRUCTURE OF A SERIES OF STRUCTURES | ||
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非ポリマーの詳細 | GLYCOSYLAT配列の詳細 | THERE ARE SOME DISCREPANCIES IN THE SEQUENCE COMPARED TO ENTRY 1MYR AS THE X-RAY SEQUENCE HAS BEEN ...THERE ARE SOME DISCREPANC | |
-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: 3.2 Å3/Da / 溶媒含有率: 50 % 解説: DOSE 0.1*10E15 PHOTONS/MM2 USED FOR DATA COLLECTION, I/SIGMA VALUES ARE STRONGLY AFFECTED BY A FEW ZINGERS ON THE DETECTOR | |||||||||||||||||||||||||
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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: 6.5 詳細: HANGING DROP METHOD, 12 MG/ML PROTEIN IN 30 MM HEPES, PH 6.5, 0.05 % NAN3 PRECIPITANT 66% SATURATED AMMONIUM SULFATE, 100MM TRIS-HCL | |||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, ハンギングドロップ法 | |||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 1998年4月15日 / 詳細: BENT MULTILAYER MIRROR, SAGITALLY FOCUSING CRYSTAL |
放射 | モノクロメーター: C(111), GE(220) / 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: 0.9475 Å / 相対比: 1 |
反射 | 解像度: 2→34.9 Å / Num. obs: 51406 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / 冗長度: 3.4 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 12 |
反射 シェル | 解像度: 2→2.1 Å / 冗長度: 3 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 4 / Rsym value: 0.147 / % possible all: 99.8 |
反射 シェル | *PLUS % possible obs: 99.8 % |
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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: ![]() 開始モデル: PDB ENTRY 1MYR 解像度: 2→17.4 Å / Rfactor Rfree error: 0.0034 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / 交差検証法: THROUGHOUT / σ(F): 0 詳細: AN OVERALL TEMPERATURE FACTOR REFINEMENT AND AN OCCUPANCY REFINEMENT HAVE BEEN USED. THE AIM OF THE STUDY IS TO LOOK AT THE EVOLUTION OF THE OCCUPANCY OF GROUPS SENSITIVE TO RADIATION DAMAGE. ...詳細: AN OVERALL TEMPERATURE FACTOR REFINEMENT AND AN OCCUPANCY REFINEMENT HAVE BEEN USED. THE AIM OF THE STUDY IS TO LOOK AT THE EVOLUTION OF THE OCCUPANCY OF GROUPS SENSITIVE TO RADIATION DAMAGE. THE MODEL IS NOT SUPPOSED TO BE USED AS A MODEL OF MYROSINASE. A MODEL REPLACING ENTRY 1MYR WILL BE DEPOSITED LATER. NO COORDINATES ARE GIVEN FOR RESIDUES 1 - 2. PRO 501 IS THE LAST RESIDUE SEEN IN ELECTRON DENSITY. THE PROTEIN COULD EXTEND BEYOND PRO 501. THE OCCUPANCY OF CERTAIN GROUPS WHICH ARE SENSITIVE TO RADIATION DAMAGE HAS BEEN REFINED. DUE TO THIS REFINEMENT OCCUPANCIES DIFFERENT OR EVEN BIGGER THAT 1.0 ARE PRESENT IN THE STRUCTURE.
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原子変位パラメータ | Biso mean: 19.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2→17.4 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2→2.07 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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ソフトウェア | *PLUS 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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