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- PDB-6g31: Crystal structure of human geranylgeranyl diphosphate synthase mu... -

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基本情報

登録情報
データベース: PDB / ID: 6g31
タイトルCrystal structure of human geranylgeranyl diphosphate synthase mutant D188Y bound to zoledronate
要素Geranylgeranyl pyrophosphate synthase
キーワードTRANSFERASE (転移酵素) / geranylgeranyl diphosphate synthase / mevalonate pathway (メバロン酸経路) / prenyltransferase (プレニル基転移酵素) / GGPPS / bisphosphonates (ビスホスホネート)
機能・相同性
機能・相同性情報


isoprenoid metabolic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / 転移酵素; メチル基以外のアルキル基またはアリル基を移すもの; - / geranyl diphosphate biosynthetic process / ジメチルアリルtransトランスフェラーゼ / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity ...isoprenoid metabolic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / 転移酵素; メチル基以外のアルキル基またはアリル基を移すもの; - / geranyl diphosphate biosynthetic process / ジメチルアリルtransトランスフェラーゼ / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / prenyltransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / isoprenoid biosynthetic process / Activation of gene expression by SREBF (SREBP) / Z disc / perinuclear region of cytoplasm / 核質 / identical protein binding / metal ion binding / 細胞質基質 / 細胞質
類似検索 - 分子機能
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
ゾレドロン酸 / Geranylgeranyl pyrophosphate synthase
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3 Å
データ登録者Lisnyansky, M. / Kapelushnik, N. / Ben-Bassat, A. / Marom, M. / Loewenstein, A. / Khananshvili, D. / Giladi, M. / Haitin, Y.
資金援助 イスラエル, 4件
組織認可番号国
Other governmentIsraeli Science Foundation (ISF) grant 1721/16 イスラエル
Other governmentIsraeli Science Foundation (ISF) grant 1775/12 イスラエル
Other governmentIsrael Cancer Research Foundation (ICRF) grant 01214 イスラエル
German Research FoundationI-2425-418.13/2016 イスラエル
引用ジャーナル: Mol. Pharmacol. / 年: 2018
タイトル: Reduced Activity of Geranylgeranyl Diphosphate Synthase Mutant Is Involved in Bisphosphonate-Induced Atypical Fractures.
著者: Lisnyansky, M. / Kapelushnik, N. / Ben-Bassat, A. / Marom, M. / Loewenstein, A. / Khananshvili, D. / Giladi, M. / Haitin, Y.
履歴
登録2018年3月24日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年10月17日Provider: repository / タイプ: Initial release
改定 1.12018年10月24日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22018年11月7日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
改定 1.32024年1月17日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Geranylgeranyl pyrophosphate synthase
B: Geranylgeranyl pyrophosphate synthase
C: Geranylgeranyl pyrophosphate synthase
D: Geranylgeranyl pyrophosphate synthase
E: Geranylgeranyl pyrophosphate synthase
F: Geranylgeranyl pyrophosphate synthase
G: Geranylgeranyl pyrophosphate synthase
H: Geranylgeranyl pyrophosphate synthase
I: Geranylgeranyl pyrophosphate synthase
J: Geranylgeranyl pyrophosphate synthase
K: Geranylgeranyl pyrophosphate synthase
L: Geranylgeranyl pyrophosphate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)429,95260
ポリマ－425,81212
非ポリマー4,14048
水0
1
A: Geranylgeranyl pyrophosphate synthase
B: Geranylgeranyl pyrophosphate synthase
E: Geranylgeranyl pyrophosphate synthase
F: Geranylgeranyl pyrophosphate synthase
I: Geranylgeranyl pyrophosphate synthase
J: Geranylgeranyl pyrophosphate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)214,97630
ポリマ－212,9066
非ポリマー2,07024
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17730 Å2
ΔGint-222 kcal/mol
Surface area70070 Å2
手法PISA
2
C: Geranylgeranyl pyrophosphate synthase
D: Geranylgeranyl pyrophosphate synthase
K: Geranylgeranyl pyrophosphate synthase
L: Geranylgeranyl pyrophosphate synthase
ヘテロ分子

G: Geranylgeranyl pyrophosphate synthase
H: Geranylgeranyl pyrophosphate synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)214,97630
ポリマ－212,9066
非ポリマー2,07024
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area17510 Å2
ΔGint-217 kcal/mol
Surface area70390 Å2
手法PISA
単位格子
Length a, b, c (Å)116.800, 134.240, 134.460
Angle α, β, γ (deg.)90.00, 102.67, 90.00
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
Geranylgeranyl pyrophosphate synthase / GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl ...GGPPSase / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Farnesyltranstransferase / Geranylgeranyl diphosphate synthase / Geranyltranstransferase


分子量: 35484.367 Da / 分子数: 12 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: GGPS1 / Variant: Asp188Tyr / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: O95749, 転移酵素; メチル基以外のアルキル基またはアリル基を移すもの; -, ジメチルアリルtransトランスフェラーゼ, geranylgeranyl diphosphate ...参照: UniProt: O95749, 転移酵素; メチル基以外のアルキル基またはアリル基を移すもの; -, ジメチルアリルtransトランスフェラーゼ, geranylgeranyl diphosphate synthase, (2E,6E)-farnesyl diphosphate synthase
#2: 化合物
ChemComp-ZOL / ZOLEDRONIC ACID / (1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID / ゾレドロン酸 / ゾレドロン酸


分子量: 272.090 Da / 分子数: 12 / 由来タイプ: 合成 / 式: C5H10N2O7P2 / コメント: 薬剤*YM
#3: 化合物...
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 36 / 由来タイプ: 合成 / 式: Mg

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実験情報

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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: 2.42 Å3/Da / 溶媒含有率: 49.07 %
結晶化温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.18M magnesium acetate tetrahydrate, 18% w/v PEG 3350, 0.18M sodium thiocyanate

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID30B / 波長: 0.976 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2018年2月9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: 0.976 Å / 相対比: 1
反射解像度: 2.779→48.619 Å / Num. obs: 98986 / % possible obs: 97.1 % / 冗長度: 3.27 % / Rmerge(I) obs: 0.222 / Net I/σ(I): 4.57
反射 シェル解像度: 2.779→2.793 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11.1_2575: ???)精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2Q80

2q80


解像度: 3→48.619 Å / SU ML: 0.7 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 37.5
Rfactor反射数%反射
Rfree0.3047 4042 5.07 %
Rwork0.2562 --
obs0.2586 79710 98.31 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 3→48.619 Å
タンパク質核酸リガンド溶媒全体
原子数23369 0 228 0 23597
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00924077
X-RAY DIFFRACTIONf_angle_d1.17633109
X-RAY DIFFRACTIONf_dihedral_angle_d6.89113847
X-RAY DIFFRACTIONf_chiral_restr0.0543892
X-RAY DIFFRACTIONf_plane_restr0.0084298
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.03530.411290.4332584X-RAY DIFFRACTION99
3.0353-3.07230.44221340.41512658X-RAY DIFFRACTION99
3.0723-3.11120.4451480.40792606X-RAY DIFFRACTION99
3.1112-3.15210.46491340.41072616X-RAY DIFFRACTION99
3.1521-3.19530.47981550.43092614X-RAY DIFFRACTION99
3.1953-3.24090.41841310.41152615X-RAY DIFFRACTION99
3.2409-3.28930.37531380.39592635X-RAY DIFFRACTION99
3.2893-3.34070.34141350.37912608X-RAY DIFFRACTION99
3.3407-3.39540.38551440.33492577X-RAY DIFFRACTION99
3.3954-3.4540.40181390.32672662X-RAY DIFFRACTION99
3.454-3.51680.37841250.32492579X-RAY DIFFRACTION99
3.5168-3.58440.36861360.3222622X-RAY DIFFRACTION98
3.5844-3.65750.33521530.30582602X-RAY DIFFRACTION99
3.6575-3.7370.31611590.28762570X-RAY DIFFRACTION98
3.737-3.82390.33651470.2862586X-RAY DIFFRACTION99
3.8239-3.91950.31871190.25772623X-RAY DIFFRACTION99
3.9195-4.02540.31261340.25872645X-RAY DIFFRACTION98
4.0254-4.14380.27231290.24052622X-RAY DIFFRACTION98
4.1438-4.27750.26021460.22332610X-RAY DIFFRACTION99
4.2775-4.43030.28291410.22132596X-RAY DIFFRACTION98
4.4303-4.60750.29811280.20742584X-RAY DIFFRACTION97
4.6075-4.81710.30641370.20722644X-RAY DIFFRACTION99
4.8171-5.07080.27751560.23092588X-RAY DIFFRACTION98
5.0708-5.38810.30681370.23972640X-RAY DIFFRACTION99
5.3881-5.80350.30311530.26152612X-RAY DIFFRACTION99
5.8035-6.38640.28311390.26232635X-RAY DIFFRACTION98
6.3864-7.30780.29691490.23992588X-RAY DIFFRACTION97
7.3078-9.19680.21351420.17542561X-RAY DIFFRACTION96
9.1968-48.62490.23571250.19282586X-RAY DIFFRACTION94
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.36390.13490.07050.4437-0.36980.49910.45310.0743-0.3964-0.6222-0.31480.12860.4290.1053-0.25491.07510.6994-0.16970.96392.33282.0593-13.3137-35.990270.0669
24.9478-2.0034-3.05453.3679-1.37784.8597-0.07370.684-0.99190.54660.187-0.48620.80940.6556-0.09240.86070.2415-0.12690.8514-0.06541.057742.2081-14.626210.441
31.8993-1.2214-1.76812.3316-0.16352.8497-0.07680.8078-0.7015-0.7732-0.562-0.95561.59950.70710.51511.60870.20990.02891.0082-0.27460.999153.1894-26.765-10.1784
44.4484-1.9443-3.57762.8129-0.01044.04940.36541.1636-0.7789-0.11740.30460.12251.2618-0.06030.62120.88960.25370.04941.2855-0.26860.673537.7587-15.86842.1415
52.9455-1.2035-2.40963.9217-0.15644.20780.4020.4520.4275-0.5751-0.0475-0.762-0.11511.1405-0.42130.53840.07790.11770.8019-0.03120.574347.7085-7.24380.5507
63.8014-1.0621-1.46713.94730.17782.05770.04681.31530.1885-0.9425-0.00440.06740.2999-0.168-0.36151.08420.07020.21621.2289-0.17770.532437.1729-11.8211-13.7649
72.3686-0.9690.34524.3564-0.68082.2242-0.39910.8453-0.2164-2.0313-0.3305-0.78140.88850.6475-0.48952.15130.24860.02310.4815-0.55970.857844.7869-22.9602-16.2951
84.0807-0.8709-1.13692.97620.60831.06330.04851.1254-0.2829-1.41970.19632.04680.9364-0.1122-0.05991.5581-0.0397-0.45191.22780.01370.989318.8847-19.8666-12.1986
93.2854-0.6883-1.24483.8250.29131.98850.13561.3536-1.9285-0.7009-0.35980.33831.1815-0.51160.10481.7815-0.1637-0.16431.2717-0.50861.058830.5313-30.6589-16.0527
105.84293.628-0.0454.7985-2.06641.4770.0433-0.18291.061-0.6365-0.7441-0.04790.48631.22140.47140.9571-0.05110.03241.19010.29560.850440.848813.2801-7.1231
114.2566-1.17760.2611.16420.28721.4334-0.0571.7591.3402-0.2872-0.3221-0.3278-0.48440.94560.13540.8632-0.35270.05070.71950.33060.469740.95738.3482-3.0401
126.7687-0.0734-0.20151.72950.61612.5508-0.46120.76940.1074-0.25890.1225-0.0922-0.33770.01640.26580.73120.0321-0.01060.72380.12240.47341.64853.98033.5478
130.24910.30510.66684.4534-0.97062.80560.49130.19870.76130.3326-0.29920.6196-0.35340.6567-0.0990.6179-0.0254-0.18650.99310.45880.995746.036617.295410.773
144.27172.64370.54364.92121.90212.82990.3954-0.06820.44410.036-0.87770.9924-0.0692-0.69510.45580.4918-0.014-0.06130.5208-0.15850.849426.949610.509323.0402
153.8287-1.8462-0.04822.12661.29452.80330.19460.36651.4208-0.67020.35620.4498-0.6108-0.381-0.48040.6993-0.3162-0.09080.6252-0.0640.689746.077123.198917.9632
167.8766-3.472-4.7991.7321.23046.40461.1411.76111.8428-0.86720.0674-0.3914-1.1991-0.3479-0.8180.9861-0.3598-0.20831.11370.56561.101844.831727.74228.3341
171.42720.6923-2.32263.2917-1.38513.8081-0.1852-0.9433-0.55760.4888-0.11420.42940.5682-0.25650.20840.6843-0.09180.18681.06430.06890.769535.4479-19.101677.6381
186.06342.39170.72942.28760.79630.5902-0.0057-0.1226-1.33660.7270.1719-0.10310.60540.3203-0.19131.57620.2168-0.00621.28070.49141.003647.4612-29.466890.9061
196.0936-3.30142.22126.5548-1.52777.3315-0.4244-0.18930.13742.053-0.5526-0.9513-0.48660.00911.50811.0046-0.1379-0.02351.07720.10080.693644.9830.218289.8178
201.2711-0.71630.81797.1915-3.28731.70220.411-0.16840.37740.6226-1.39331.3282-0.9711-1.52860.62320.98690.37640.14441.4183-0.26460.759225.127814.984382.1951
212.8667-0.93640.40873.1972-0.42052.52450.3188-1.15560.71410.7137-0.1919-0.0448-0.57690.3260.03370.7697-0.00870.0550.714-0.20730.523340.5868-0.746882.5772
221.40910.28291.40123.7314-1.17632.55310.1304-0.90760.13570.3606-0.14140.4973-0.3665-0.2694-0.07580.5890.00470.11850.6901-0.20350.592231.2783-3.925771.5488
233.1941-0.5586-2.03142.0913-0.30762.9563-0.61-0.81550.28430.9932-0.32920.13910.0162-0.20890.54340.95620.05380.03170.8687-0.23950.608230.84173.455467.2936
244.3198-2.4296-1.75753.8450.71760.62370.29370.23691.2182-0.3614-0.36890.0112-0.3444-1.02060.16710.60420.0405-0.10210.7899-0.19250.556237.02799.913164.4441
257.8109-0.1834-1.35684.79720.43064.24850.7341.01280.80680.1227-0.6888-1.35550.24610.2619-0.08960.3892-0.0042-0.06620.91680.18180.854252.78957.132553.4922
262.0093-0.3003-0.22694.8846-0.39894.33890.4234-0.24271.9726-0.1460.4658-0.0466-1.259-1.5518-0.03330.77680.3249-0.07271.0682-0.17541.263131.432419.088561.6894
274.3319-2.78180.97063.1991-2.36254.10570.1212-0.30511.01661.273-0.2396-1.0942-0.85510.5167-0.58580.9580.1408-0.23481.1623-0.92061.870531.734822.457972.358
286.2057-0.8467-0.2858.3995-1.1555.0728-0.3856-1.46991.3690.78190.4982-0.7714-0.64260.6663-0.15150.5966-0.1045-0.05050.858-0.36690.690721.24466.601139.7835
290.40860.9777-0.78553.4551-1.47911.60960.2047-0.62280.77750.7041-0.9118-0.3214-0.1857-0.08710.43731.30360.1179-0.43441.8312-0.4840.89335.761518.934556.2302
300.7746-0.6041-0.7192.4220.23382.7735-0.1885-1.09230.53690.255-0.2018-0.3747-0.0471-0.12120.35230.5487-0.135-0.07251.0023-0.29270.590312.23094.534342.7044
313.45490.51890.04853.6185-0.58181.0387-0.5337-0.27090.66650.17240.10780.3107-0.64130.79710.41180.59120.0053-0.07521.0915-0.28910.6827-3.64483.434743.4129
321.1717-0.38992.17342.12060.89355.56030.1732-1.25991.04220.3614-0.1411-0.2624-0.75740.76720.60160.7665-0.13490.06851.2824-0.54140.947-3.566714.27240.3389
330.70670.01171.20442.1225-1.20033.011-0.3624-0.82961.2551-0.36190.26840.2357-0.824-0.27880.18250.57960.08-0.0190.8504-0.42171.0252-11.734715.071529.5207
341.56770.61481.68410.7193-0.33014.55460.08980.05160.12840.9307-0.0303-0.4739-1.48120.98740.10571.1851-0.37730.06351.3201-1.14381.5873-1.950226.634546.2738
351.7034-1.82842.58914.0164-3.27594.06891.1645-0.1636-1.9001-0.2734-0.75880.7061-0.08591.8783-0.1430.47730.03660.0431.72550.15571.0384.5727-21.156745.3909
364.016-1.3711-0.05761.51270.27751.2539-0.123-0.6368-0.5067-0.02580.15390.02180.191-0.01490.00620.534-0.05020.03610.62160.04260.665420.1317-18.693138.3279
375.4052-0.6872-1.98234.172-0.54043.2478-0.41441.2880.5312-1.3681.06671.39650.2834-0.861-0.53530.65950.0077-0.18061.39920.18910.649855.30794.200137.9956
380.3190.19790.08730.3211-0.27131.05840.1392-0.1780.11220.2874-0.34830.0909-0.3830.3256-0.32540.7775-0.8560.05922.12351.9030.934871.629917.396721.5467
390.8640.0614-0.29092.43010.76162.6613-0.27540.95780.9506-0.22470.1275-0.07120.06480.98480.22530.60360.0466-0.00220.8750.49210.787864.58822.247634.9094
401.5277-1.03341.57261.75430.02023.44730.27660.56540.9158-0.33770.4605-0.5096-0.0346-0.30240.72760.4040.1625-0.2751.89320.84640.602780.03152.919731.8368
410.4208-0.35840.4253.2776-0.86180.5657-0.05080.34730.86090.49760.89320.7334-0.3922-0.4636-0.28050.57260.0092-0.11921.220.61931.129780.422412.266442.9291
421.6621-0.40050.12880.9661.32914.4503-0.23-0.01350.7967-0.29950.27540.2681-0.08130.8733-0.01680.5877-0.0466-0.07050.96540.31130.940988.150112.865448.889
430.6972-1.03550.42184.8509-0.9562.9943-0.2064-0.3232-0.21751.01210.31710.573-1.2447-0.5995-0.4530.9919-0.0534-0.16861.5811.11321.153378.244424.759632.3372
442.18840.7881-0.84558.41160.21552.8633-0.6195-0.2325-0.3356-0.67781.468-1.15910.23960.8538-0.19520.76160.33220.32371.69290.04020.479780.7535-15.386738.356
451.72521.57780.59111.89830.57580.2083-0.4222-0.092-0.67870.4524-0.80560.7330.6461-0.71490.86011.43580.95870.33692.1323-0.16680.688264.7663-30.1823.0394
463.3008-0.40471.10192.4161-1.98785.5376-0.17990.94890.1728-0.2738-0.4506-0.18010.65491.4340.69680.62970.16130.12850.97330.26320.687170.914-15.403235.7837
472.92430.01741.31013.5812-0.78133.4539-0.52970.1377-0.1365-0.00930.1923-0.35070.56250.91160.42940.43130.0586-0.00650.6408-0.04970.564157.4062-10.67233.6152
482.46890.33590.98713.5828-1.20062.8887-0.29560.3856-0.4306-0.1867-0.1354-0.12990.61750.10990.22350.71930.1340.1790.7765-0.00850.631853.6655-18.219932.4348
492.53321.55831.02812.7712-0.75962.19640.1990.2082-0.43580.1934-0.4368-0.00841.42770.5589-0.0110.86640.15530.09270.589-0.00840.592954.3252-25.798938.1421
502.78980.5534-0.87082.6508-0.96196.8419-0.19840.0985-0.69830.98210.02020.18381.1001-0.54670.07490.68830.04190.07230.29470.07860.712946.6828-25.550548.8556
510.87150.66550.11461.85380.70290.3041-0.2820.5349-0.8101-0.268-0.2273-0.35531.5750.80170.45861.38410.4020.08120.9265-0.45111.361756.5712-37.121630.5749
523.32681.98590.66965.212-1.08326.2356-0.384-0.3590.1240.2786-0.42520.5134-0.2447-0.70630.6720.37640.3482-0.00490.9545-0.31830.9985-23.41735.44112.7161
530.2932-0.13520.31523.3488-0.68654.4722-0.11240.7730.3713-0.05270.13780.605-1.6662-0.72250.22910.70050.2971-0.24680.91570.31351.1015-33.308220.1936-5.1952
543.39560.10020.95043.3104-0.26924.5621-0.2091.04120.2214-0.20970.1764-0.0878-0.7973-0.1369-0.00670.7352-0.0117-0.04420.5031-0.10850.6473-20.36845.6977-1.4629
554.26981.1796-1.24051.54212.05848.6735-0.5546-0.09540.0849-0.40831.08570.5416-0.23511.261-0.44981.63080.0578-0.01881.00260.31630.8967-18.979410.9592-14.784
560.0128-0.09910.18092.1814-0.3292.3429-0.9033-0.03410.7297-0.89690.5312-0.6221-1.28721.1502-0.01861.6249-0.1015-0.14711.01450.14561.3259-15.740319.6399-11.0111
575.7571-1.05064.33922.1147-0.00133.6431-0.02320.2597-0.0748-0.17991.0071-0.3737-0.54520.5042-1.12271.2504-0.66360.11681.1759-0.06691.34313.226914.6041-10.7366
585.1805-2.9916-0.59993.04680.90810.27040.34321.34710.9275-0.6597-0.086-0.1781-1.8108-0.3143-0.07891.3044-0.24720.02251.13531.17710.9424-14.278626.5937-18.3292
590.23440.26530.12550.37890.38610.7327-0.26310.18720.66820.0435-0.13730.008-0.72710.3699-0.03322.14520.01370.0438-0.45950.65421.731-18.798730.6537-9.5719
604.1862.1616-1.70632.0294-2.45046.2476-0.64460.7721-0.5831-1.70080.25010.34610.32890.00440.34041.0676-0.0477-0.12371.0376-0.35390.6031-21.6031-18.2776-8.2157
612.11660.296-0.33212.7313-0.67060.849-0.3560.3201-0.199-0.63390.13840.02630.7075-0.49270.08350.8363-0.2287-0.09831.0069-0.31560.695-22.2481-10.47711.5304
627.48942.13380.91162.1969-0.5593.20740.10170.0798-1.4602-0.17590.1826-0.62870.3423-0.04-0.3350.6631-0.0505-0.03740.6069-0.30450.8133-18.4282-23.558315.5251
635.80582.8423-0.83015.3498-0.33266.06720.4333-0.24980.14-0.07250.517-0.3125-1.4646-1.6991-1.0430.75940.16690.16121.22060.32790.7261-15.71052.961864.5207
640.10380.297-0.13271.99661.14413.7080.6732-0.51540.71070.058-0.4197-1.205-1.2871.2931-0.39830.9374-0.41270.10791.76760.14941.3305-9.699418.876183.8721
652.8460.01161.48764.01860.54463.54450.5283-0.818-0.0990.2803-0.19440.3012-0.5335-0.0758-0.36820.6428-0.0234-0.01041.20180.22350.6012-18.15574.472575.6491
661.9297-0.2296-0.07543.57120.86873.32930.1695-0.3578-0.01531.0330.2145-0.1954-0.14030.0251-0.25310.9308-0.0537-0.12931.60420.24230.8653-21.33773.546990.9273
672.09032.08170.04182.8028-0.31932.97060.40991.81880.19950.4854-0.3220.3673-1.0454-0.9816-0.29511.0042-0.1877-0.05161.5720.25770.8185-19.836116.143392.1234
682.1024-1.6794.31879.9366-2.79139.27390.30890.80251.3655-0.23150.1599-0.2207-0.48792.1677-0.46080.99670.02270.30851.2961-0.04350.9223-38.310512.196483.8204
693.613-0.26823.10677.1638-0.3692.8934-0.388-0.3861-0.33491.23490.76961.2905-0.1023-1.603-0.51351.0550.09620.22491.16470.30871.0726-45.097311.956391.0413
709.61451.8804-1.59863.62841.76432.9813-0.0512-2.75732.80560.5715-0.31880.7743-0.8664-1.33490.24081.5772-0.1440.18811.5909-0.54571.2197-22.293824.604994.9847
713.0341-0.23811.32022.7304-1.73354.33310.09480.39990.15811.37490.4492-0.5303-0.1537-0.6386-0.6340.90190.1613-0.06860.85550.31661.0418-26.719-13.148690.285
723.86610.81553.44272.08150.92743.0431-0.5884-1.76640.17460.4365-0.5068-0.89450.74161.92330.73550.71420.1373-0.01561.71130.60991.1917-8.7276-28.6580.6919
730.9947-0.616-0.30281.5980.02761.9438-0.0098-0.57260.06210.1475-0.2729-0.17680.39980.56590.07810.85540.1239-0.02071.30330.74630.9779-18.0429-12.503775.2417
741.1826-0.586-0.36031.7285-1.11041.9265-0.4546-0.8281-0.62460.3093-0.2526-0.2843-0.28180.1498-0.06270.71150.216-0.21740.96061.06531.0979-9.2318-23.412971.2627
758.80482.111-1.17364.72561.1020.84930.19550.2667-0.51550.0367-0.09740.37450.0767-0.4957-0.25420.60070.10180.02211.06380.54051.1783-30.9494-20.539354.463
762.4912-0.59160.9832.75680.10624.39861.1747-0.6051-0.9785-0.60170.0170.37590.53051.0291-0.43280.88610.56520.08571.08520.65811.2939-11.551-31.688260.056
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 279 through 296 )
2X-RAY DIFFRACTION2chain 'I' and (resid 5 through 26 )
3X-RAY DIFFRACTION3chain 'I' and (resid 27 through 42 )
4X-RAY DIFFRACTION4chain 'I' and (resid 43 through 84 )
5X-RAY DIFFRACTION5chain 'I' and (resid 85 through 110 )
6X-RAY DIFFRACTION6chain 'I' and (resid 111 through 165 )
7X-RAY DIFFRACTION7chain 'I' and (resid 166 through 189 )
8X-RAY DIFFRACTION8chain 'I' and (resid 190 through 240 )
9X-RAY DIFFRACTION9chain 'I' and (resid 241 through 294 )
10X-RAY DIFFRACTION10chain 'J' and (resid 6 through 42 )
11X-RAY DIFFRACTION11chain 'J' and (resid 43 through 68 )
12X-RAY DIFFRACTION12chain 'J' and (resid 69 through 166 )
13X-RAY DIFFRACTION13chain 'J' and (resid 167 through 194 )
14X-RAY DIFFRACTION14chain 'J' and (resid 195 through 255 )
15X-RAY DIFFRACTION15chain 'J' and (resid 256 through 278 )
16X-RAY DIFFRACTION16chain 'J' and (resid 279 through 296 )
17X-RAY DIFFRACTION17chain 'K' and (resid 5 through 135 )
18X-RAY DIFFRACTION18chain 'K' and (resid 136 through 295 )
19X-RAY DIFFRACTION19chain 'L' and (resid 6 through 26 )
20X-RAY DIFFRACTION20chain 'L' and (resid 27 through 42 )
21X-RAY DIFFRACTION21chain 'L' and (resid 43 through 106 )
22X-RAY DIFFRACTION22chain 'L' and (resid 107 through 135 )
23X-RAY DIFFRACTION23chain 'L' and (resid 136 through 166 )
24X-RAY DIFFRACTION24chain 'L' and (resid 167 through 223 )
25X-RAY DIFFRACTION25chain 'L' and (resid 224 through 255 )
26X-RAY DIFFRACTION26chain 'L' and (resid 256 through 277 )
27X-RAY DIFFRACTION27chain 'L' and (resid 278 through 296 )
28X-RAY DIFFRACTION28chain 'A' and (resid 5 through 26 )
29X-RAY DIFFRACTION29chain 'A' and (resid 27 through 42 )
30X-RAY DIFFRACTION30chain 'A' and (resid 43 through 110 )
31X-RAY DIFFRACTION31chain 'A' and (resid 111 through 165 )
32X-RAY DIFFRACTION32chain 'A' and (resid 166 through 214 )
33X-RAY DIFFRACTION33chain 'A' and (resid 215 through 278 )
34X-RAY DIFFRACTION34chain 'A' and (resid 279 through 296 )
35X-RAY DIFFRACTION35chain 'B' and (resid 6 through 42 )
36X-RAY DIFFRACTION36chain 'B' and (resid 43 through 296 )
37X-RAY DIFFRACTION37chain 'C' and (resid 4 through 26 )
38X-RAY DIFFRACTION38chain 'C' and (resid 27 through 42 )
39X-RAY DIFFRACTION39chain 'C' and (resid 43 through 110 )
40X-RAY DIFFRACTION40chain 'C' and (resid 111 through 173 )
41X-RAY DIFFRACTION41chain 'C' and (resid 174 through 214 )
42X-RAY DIFFRACTION42chain 'C' and (resid 215 through 278 )
43X-RAY DIFFRACTION43chain 'C' and (resid 279 through 296 )
44X-RAY DIFFRACTION44chain 'D' and (resid 6 through 21 )
45X-RAY DIFFRACTION45chain 'D' and (resid 22 through 42 )
46X-RAY DIFFRACTION46chain 'D' and (resid 43 through 108 )
47X-RAY DIFFRACTION47chain 'D' and (resid 109 through 135 )
48X-RAY DIFFRACTION48chain 'D' and (resid 136 through 166 )
49X-RAY DIFFRACTION49chain 'D' and (resid 167 through 214 )
50X-RAY DIFFRACTION50chain 'D' and (resid 215 through 277 )
51X-RAY DIFFRACTION51chain 'D' and (resid 278 through 295 )
52X-RAY DIFFRACTION52chain 'E' and (resid 5 through 21 )
53X-RAY DIFFRACTION53chain 'E' and (resid 22 through 46 )
54X-RAY DIFFRACTION54chain 'E' and (resid 47 through 135 )
55X-RAY DIFFRACTION55chain 'E' and (resid 136 through 166 )
56X-RAY DIFFRACTION56chain 'E' and (resid 167 through 205 )
57X-RAY DIFFRACTION57chain 'E' and (resid 206 through 249 )
58X-RAY DIFFRACTION58chain 'E' and (resid 250 through 282 )
59X-RAY DIFFRACTION59chain 'E' and (resid 283 through 296 )
60X-RAY DIFFRACTION60chain 'F' and (resid 6 through 42 )
61X-RAY DIFFRACTION61chain 'F' and (resid 43 through 166 )
62X-RAY DIFFRACTION62chain 'F' and (resid 167 through 296 )
63X-RAY DIFFRACTION63chain 'G' and (resid 3 through 21 )
64X-RAY DIFFRACTION64chain 'G' and (resid 22 through 42 )
65X-RAY DIFFRACTION65chain 'G' and (resid 43 through 108 )
66X-RAY DIFFRACTION66chain 'G' and (resid 109 through 165 )
67X-RAY DIFFRACTION67chain 'G' and (resid 166 through 191 )
68X-RAY DIFFRACTION68chain 'G' and (resid 192 through 214 )
69X-RAY DIFFRACTION69chain 'G' and (resid 215 through 255 )
70X-RAY DIFFRACTION70chain 'G' and (resid 256 through 295 )
71X-RAY DIFFRACTION71chain 'H' and (resid 6 through 21 )
72X-RAY DIFFRACTION72chain 'H' and (resid 22 through 42 )
73X-RAY DIFFRACTION73chain 'H' and (resid 43 through 152 )
74X-RAY DIFFRACTION74chain 'H' and (resid 153 through 193 )
75X-RAY DIFFRACTION75chain 'H' and (resid 194 through 255 )
76X-RAY DIFFRACTION76chain 'H' and (resid 256 through 278 )

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る