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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: 1lsh | |||||||||
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タイトル | LIPID-PROTEIN INTERACTIONS IN LIPOVITELLIN | |||||||||
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![]() | LIPID BINDING PROTEIN / LIPOVITELLIN / VITELLOGENIN / LIPOPROTEIN / PLASMA APOLIPOPROTE APOLIPOPROTEIN B / APOB / MICROSOMAL TRIGLYCERIDE TRANSFER PR BOUNDARY LIPID / PHOSPHOLIPID STRUCTURE | |||||||||
機能・相同性 | ![]() | |||||||||
生物種 | ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Thompson, J.R. / Banaszak, L.J. | |||||||||
![]() | ![]() タイトル: Lipid-protein interactions in lipovitellin. 著者: Thompson, J.R. / Banaszak, L.J. #1: ![]() タイトル: The Structural Basis of Lipid Interactions in Lipovitellin, a Souble Lipoprotein 著者: Anderson, T.A. / Levitt, D.G. / Banaszak, L.J. | |||||||||
履歴 |
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Remark 99 | The disulfide bond S-S involving residues 156 and 182 in chain A is formed between the alternate ...The disulfide bond S-S involving residues 156 and 182 in chain A is formed between the alternate conformers B of these residues. | |||||||||
Remark 600 | HETEROGEN DUE TO LACK OF ELECTRON DENSITY, ONLY VARYING PARTS OF PHOSPHOLIPID MOLECULES COULD BE ...HETEROGEN DUE TO LACK OF ELECTRON DENSITY, ONLY VARYING PARTS OF PHOSPHOLIPID MOLECULES COULD BE MODELED. THE FIRST SEVEN MOLECULES WERE MODELED AS PHOSPHATIDYLCHOLINE WITH AN ALTERNATE CONFORMATION FOR ONE OF THE ACYL CHAINS IN MOLECULES 1 AND 5. MOLECULES 2-7 WERE MODELED AS UNKNOWN PHOSPHOLIPID BUT ARBITARILY CALLED PHOSPHATIDYLCHOLINE. ADDITIONAL 43 METHYLENE CHAIN FRAGMENTS WITH BETWEEN 20 AND 5 CARBON ATOMS EACH WERE MODELED. THREE OF THE HYDROCARBON SEGMENTS ARE BRANCHED BUT NOT MODELED AS PHOSPHOLIPID BECAUSE IT WAS IMPOSSIBLE TO IDENTIFY WHICH PORTION OF ELECTRON DENSITY BELONGED TO THE ACYL CHAINS AND POLAR HEADGROUPS. THE 43 MOLECULES NAMED UPL (ARBITARILY CALLED UNKNOWN BRANCHED PHOSPHOLIPID FRAGMENT) WAS SIMPLY MEANT TO REPRESENTS METHYLENE CHAIN FRAGMENTS. | |||||||||
Remark 999 | SEQUENCE LIPOVITELLIN IS PROTEOLYTICALLY PROCESSED FROM ITS PRECURSOR PRODUCING FOUR POLYPEPTIDES. ...SEQUENCE LIPOVITELLIN IS PROTEOLYTICALLY PROCESSED FROM ITS PRECURSOR PRODUCING FOUR POLYPEPTIDES. PRECISE CLEAVED LENGTHS OF FRAGMENTS LV-1N, LV-1C AND LV-2 ARE NOT KNOWN. BOTH LV-1N AND LV-1C ARE PRESENTED HERE AS SINGLE ENTITY WITH CHAIN A TO CORRESSPOND WITH HOMOGENEOUS SINGLE POLYPEPTIDE IN LIPOVITELLINS OF OTHER SPECIES. ONE OF THE FRAGMENTS, PHOVITIN CONSISTING OF 232 RESIDUES (1074-1305) IN THE SWS ENTRY WAS PRESENT IN THE CRYSTAL BUT NONE OF ITS RESIDUE COULD BE MODELED DUE TO LACK OF ELECTRON DENSITY. |
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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 | ![]() | 309.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 230.6 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 | ![]() | 7.6 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 7.8 MB | 表示 | |
XML形式データ | ![]() | 71.9 KB | 表示 | |
CIF形式データ | ![]() | 104.3 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-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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詳細 | The biological assembly is a dimer believed to be generated by the crystallographic c2 dyad -x,y,-z |
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要素
#1: タンパク質 | 分子量: 117469.508 Da / 分子数: 1 / 断片: LV1n, LV1c / 由来タイプ: 天然 / 詳細: Egg Yolk / 由来: (天然) ![]() | ||||
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#2: タンパク質 | 分子量: 35110.094 Da / 分子数: 1 / 断片: LV2 / 由来タイプ: 天然 / 詳細: Egg Yolk / 由来: (天然) ![]() | ||||
#3: 化合物 | ChemComp-PLD / #4: 化合物 | ChemComp-UPL / #5: 水 | ChemComp-HOH / | |
-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: 2.32 Å3/Da / 溶媒含有率: 46.94 % | ||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.2 詳細: Protein stock:10 mg/ml lipovitellin, 0.25 mM sodium citrate; Well: 0.55-0.61 M sodium citrate, 1mM thioglycerol, 1 mM EDTA, 0.05% sodium azide, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||
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: CUSTOM-MADE / 検出器: CCD / 日付: 1998年2月7日 / 詳細: vertically focusing mirror |
放射 | モノクロメーター: double crystal Si220 monochromator,double crystal Si111 monochromator 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: 1.0332 Å / 相対比: 1 |
反射 | 解像度: 1.9→30 Å / Num. all: 82007 / Num. obs: 82007 / % possible obs: 74.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 1.54 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.064 / Net I/σ(I): 12.2 |
反射 シェル | 解像度: 1.9→1.99 Å / % possible all: 30.1 |
反射 | *PLUS 最低解像度: 30 Å / Rmerge(I) obs: 0.064 |
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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: LIPOVITELLIN (ROOM TEMP) 解像度: 1.9→21.6 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber 詳細: Used OUTIER program (Randy Read) to reject 312 reflections in the range 30-5.9 Angstrom
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 180.794 Å2 / ksol: 0.383954 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 49 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.9→21.6 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.9→1.99 Å / Rfactor Rfree error: 0.072 / Total num. of bins used: 8
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Xplor file |
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ソフトウェア | *PLUS バージョン: 0.9,1.0,1.1 / 分類: refinement | ||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 1.9 Å / 最低解像度: 30 Å | ||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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