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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: 1gzm | |||||||||
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タイトル | Structure of Bovine Rhodopsin in a Trigonal Crystal Form | |||||||||
![]() | RHODOPSIN | |||||||||
![]() | SIGNALING PROTEIN / PHOTORECEPTOR / RETINAL PROTEIN / VISUAL PIGMENT / G-PROTEIN COUPLED RECEPTOR / INTEGRAL MEMBRANE PROTEIN / PALMITATE / PHOSPHORYLATION | |||||||||
機能・相同性 | ![]() Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly ...Opsins / VxPx cargo-targeting to cilium / sperm head plasma membrane / rod bipolar cell differentiation / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / photoreceptor inner segment membrane / podosome assembly / G protein-coupled photoreceptor activity / 11-cis retinal binding / rod photoreceptor outer segment / cellular response to light stimulus / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / outer membrane / detection of temperature stimulus involved in thermoception / response to light intensity / photoreceptor cell maintenance / arrestin family protein binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction, visible light / G-protein alpha-subunit binding / phototransduction / photoreceptor outer segment / sperm midpiece / visual perception / guanyl-nucleotide exchange factor activity / microtubule cytoskeleton organization / photoreceptor disc membrane / cell-cell junction / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / zinc ion binding / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Li, J. | |||||||||
![]() | ![]() タイトル: Structure of Bovine Rhodopsin in a Trigonal Crystal Form 著者: Li, J. / Edwards, P. / Burghammer, M. / Villa, C. / Schertler, G.F.X. #1: ジャーナル: J.Mol.Biol. / 年: 2004 タイトル: Crystals of Native and Modified Bovine Rhodopsins and Their Heavy Atom Derivatives 著者: Edwards, P. / Li, J. / Burghammer, M. / Mcdowell, J.H. / Villa, C. / Hargrave, P.A. / Schertler, G.F.X. | |||||||||
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 | ![]() | 159.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 124.9 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 | ![]() | 4.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 4.2 MB | 表示 | |
XML形式データ | ![]() | 34.7 KB | 表示 | |
CIF形式データ | ![]() | 43.7 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 | ![]() 1f88S S: 精密化の開始モデル |
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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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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
-タンパク質 / 糖 , 2種, 6分子 AB
#1: タンパク質 | 分子量: 39057.492 Da / 分子数: 2 / 由来タイプ: 天然 詳細: DISULFIDE LINK BETWEEN A110 AND A187, AND B110 AND B187 由来: (天然) ![]() ![]() #2: 多糖 | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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-非ポリマー , 7種, 65分子 












#3: 化合物 | #4: 化合物 | ChemComp-PLM / #5: 化合物 | #6: 化合物 | #7: 化合物 | ChemComp-C8E / ( #8: 化合物 | #9: 水 | ChemComp-HOH / | |
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-詳細
構成要素の詳細 | LIGHT-ABSORBING MOLECULES THAT MEDIATE VISION. CONSIST OF AN APOPROTEIN, OPSIN, COVALENTLY BOUND TO ...LIGHT-ABSORBING MOLECULES THAT MEDIATE VISION. CONSIST OF AN APOPROTEIN |
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Has protein modification | Y |
-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: 3.07 Å3/Da / 溶媒含有率: 49 % 解説: DATA WERE COLLECTED USING MICROFOCUSED SYNCHROTRON SOURCE. | ||||||||||||||||||||||||||||||
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結晶化 | 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 詳細: VAPOUR DIFFUSION IN SITTING DROPS OF 15 MG/ML PROTEIN AND 0.2% C8E4, 0.05%LDAO AGAINST 0.8M LI2SO4, 1.6% PEG8000 AND 20% GLYCEROL, pH 8.5 | ||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 18 ℃ / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: Edwards, P., (2004) J. Mol. Biol., 343, 1439. | ||||||||||||||||||||||||||||||
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: 2000年10月15日 |
放射 | 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: 0.782 Å / 相対比: 1 |
反射 | 解像度: 2.65→46 Å / Num. obs: 26026 / % possible obs: 97 % / Observed criterion σ(I): 0 / 冗長度: 4.4 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 11 |
反射 シェル | 解像度: 2.65→2.79 Å / 冗長度: 1.6 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 1.4 / % possible all: 86 |
反射 | *PLUS % possible obs: 97 % |
反射 シェル | *PLUS % possible obs: 86.1 % |
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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 1F88 解像度: 2.65→46 Å / Rfactor Rfree error: 0.0066 / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 詳細: THE FOLLOWING HOH RESIDUES ARE EQUIVALENT BY NON- CRYSTALLOGRAPHIC SYMMETRY AND ARE EQUIVALENT TO THESE RESIDUES IN THE PRIMARY REFERENCE: U1 == V1, AND WATER RESIDUE 7 IN REFERENCE U2 == V3, ...詳細: THE FOLLOWING HOH RESIDUES ARE EQUIVALENT BY NON- CRYSTALLOGRAPHIC SYMMETRY AND ARE EQUIVALENT TO THESE RESIDUES IN THE PRIMARY REFERENCE: U1 == V1, AND WATER RESIDUE 7 IN REFERENCE U2 == V3, AND WATER RESIDUE 16 IN REFERENCE U3 == V4, AND WATER RESIDUE 8 IN REFERENCE U4 == V5, AND WATER RESIDUE 11 IN REFERENCE U5 == V6, AND WATER RESIDUE 4 IN REFERENCE U6 == V7, AND WATER RESIDUE 13 IN REFERENCE U7 == V11, AND WATER RESIDUE 6 IN REFERENCE U8 == V9, AND WATER RESIDUE 3 IN REFERENCE U9 == V19, AND WATER RESIDUE 15 IN REFERENCE U10 == V3, AND WATER RESIDUE 18 IN REFERENCE U11 == V13, AND WATER RESIDUE 5 IN REFERENCE U12 == V14, AND WATER RESIDUE 14 IN REFERENCE U13 == V15, AND WATER RESIDUE 19 IN REFERENCE U14 == V16, AND WATER RESIDUE 9 IN REFERENCE U15 == V17, AND WATER RESIDUE 1 IN REFERENCE U16 == V12, AND WATER RESIDUE 17 IN REFERENCE U17 == V18, AND WATER RESIDUE 20 IN REFERENCE U18 == V2, AND WATER RESIDUE 12 IN REFERENCE U19 == V19, AND WATER RESIDUE 2 IN REFERENCE U20 == V20, AND WATER RESIDUE 10 IN REFERENCE THE FOLLOWING CARBOHYDRATE RESIDUES ARE EQUIVALENT BY NON- CRYSTALLOGRAPHIC SYMMETRY: A1335 IS EQUIVALENT TO B1335 A1336 IS EQUIVALENT TO B1336 A1337 IS EQUIVALENT TO B1350 A1338 IS EQUIVALENT TO B1337 A1339 IS EQUIVALENT TO B1338 A1340 IS EQUIVALENT TO B1339
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溶媒の処理 | 溶媒モデル: FLAT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 56 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: 2.65→46 Å
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拘束条件 |
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Refine LS restraints NCS | Rms dev Biso : 1 Å2 / Rms dev position: 0.515 Å / Weight position: 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.65→2.74 Å / Rfactor Rfree error: 0.0275 / Total num. of bins used: 10
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Xplor file |
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精密化 | *PLUS 最低解像度: 46 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.202 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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LS精密化 シェル | *PLUS Rfactor Rfree: 0.315 / Rfactor Rwork: 0.312 |