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- PDB-7bim: A de novo designed nonameric coiled coil, CC-Type2-(GgLaId)4 -

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基本情報

登録情報
データベース: PDB / ID: 7bim
タイトルA de novo designed nonameric coiled coil, CC-Type2-(GgLaId)4
要素Nonameric de novo coiled coil CC-Type2-(GgLaId)4
キーワードDE NOVO PROTEIN (De novo) / coiled coil (コイルドコイル) / alpha-helical barrel / nonamer / synthetic
機能・相同性2-プロパノール
機能・相同性情報
生物種synthetic construct (人工物)
手法X線回折 / シンクロトロン / AB INITIO PHASING / 解像度: 1.64 Å
データ登録者Shelley, K.L. / Rhys, G.G. / Dawson, W.M. / Brady, R.L. / Woolfson, D.N.
資金援助 英国, 1件
組織認可番号国
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00661X/1 英国
引用ジャーナル: Chem Sci / 年: 2021
タイトル: Coiled coils 9-to-5: rational de novo design of alpha-helical barrels with tunable oligomeric states.
著者: Dawson, W.M. / Martin, F.J.O. / Rhys, G.G. / Shelley, K.L. / Brady, R.L. / Woolfson, D.N.
履歴
登録2021年1月12日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02021年4月21日Provider: repository / タイプ: Initial release
改定 1.12021年11月17日Group: Data collection / Database references / Structure summary
カテゴリ: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / struct
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct.pdbx_center_of_mass_x / _struct.pdbx_center_of_mass_y / _struct.pdbx_center_of_mass_z

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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: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
B: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
C: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
D: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
E: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
F: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
G: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
H: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
I: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
J: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
K: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
L: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
M: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
N: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
O: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
P: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Q: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
R: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
S: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
T: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
U: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
V: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
W: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
X: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Y: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Z: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
a: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
b: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
c: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
d: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
e: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
f: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
g: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
h: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
i: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
j: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)118,44882
ポリマ－114,43636
非ポリマー4,01246
水6,810378
1
A: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
B: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
C: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
D: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
E: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
F: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
G: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
H: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
I: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
ヘテロ分子


  • 登録者・ソフトウェアが定義した集合体
  • 根拠: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments ...根拠: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments indicate that that the sequence is hexameric in aqueous solution.
  • 29.6 kDa, 9 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)29,61821
ポリマ－28,6099
非ポリマー1,00912
水1629
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18860 Å2
ΔGint-142 kcal/mol
Surface area11570 Å2
手法PISA
2
J: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
K: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
L: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
M: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
N: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
O: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
P: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Q: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
R: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
ヘテロ分子


  • 登録者・ソフトウェアが定義した集合体
  • 根拠: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments ...根拠: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments indicate that that the sequence is hexameric in aqueous solution.
  • 29.7 kDa, 9 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)29,74222
ポリマ－28,6099
非ポリマー1,13313
水1629
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18910 Å2
ΔGint-150 kcal/mol
Surface area11720 Å2
手法PISA
3
S: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
T: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
U: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
V: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
W: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
X: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Y: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
Z: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
a: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
ヘテロ分子


  • 登録者・ソフトウェアが定義した集合体
  • 根拠: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments ...根拠: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments indicate that that the sequence is hexameric in aqueous solution.
  • 29.5 kDa, 9 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)29,53019
ポリマ－28,6099
非ポリマー92110
水1629
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18250 Å2
ΔGint-167 kcal/mol
Surface area11920 Å2
手法PISA
4
b: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
c: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
d: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
e: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
f: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
g: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
h: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
i: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
j: Nonameric de novo coiled coil CC-Type2-(GgLaId)4
ヘテロ分子


  • 登録者・ソフトウェアが定義した集合体
  • 根拠: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments ...根拠: Nonameric open barrel has only been observed in a crystalline environment. Same sequence also crystallises as a collapsed hexameric barrel, furthermore AUC (both SV and SE) experiments indicate that that the sequence is hexameric in aqueous solution.
  • 29.6 kDa, 9 ポリマー
  • Omokage検索でこの集合体の類似形状データを探す (詳細)
分子量 (理論値)分子数
合計 (水以外)29,55820
ポリマ－28,6099
非ポリマー94911
水1629
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18440 Å2
ΔGint-152 kcal/mol
Surface area11680 Å2
手法PISA
単位格子
Length a, b, c (Å)71.210, 128.080, 71.450
Angle α, β, γ (deg.)90.000, 110.670, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質・ペプチド ...
Nonameric de novo coiled coil CC-Type2-(GgLaId)4


分子量: 3178.767 Da / 分子数: 36 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#2: 化合物...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル / グリセリン


分子量: 92.094 Da / 分子数: 39 / 由来タイプ: 合成 / 式: C3H8O3
#3: 化合物
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / 2-プロパノ-ル / 2-プロパノール


分子量: 60.095 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C3H8O / コメント: alkaloid*YM
#4: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 378 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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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: 2.64 Å3/Da / 溶媒含有率: 53.5 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: 0.1 M ammonium acetate, 0.05 M Na HEPES, 12.5% v/v propan-2-ol. 25% v/v glycerol added to crystal as cryo-protectant prior to cryo-cooling.

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: DIAMOND / ビームライン: I04 / 波長: 0.9795 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2016年9月18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: 0.9795 Å / 相対比: 1
反射解像度: 1.64→66.85 Å / Num. obs: 146091 / % possible obs: 99.9 % / 冗長度: 6.8 % / Biso Wilson estimate: 18.486 Å2 / CC1/2: 0.9993 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Net I/σ(I): 14.25
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4.45-66.916.60.0294573310.9990.0120.03199
1.64-1.676.91.4291.473220.5260.5831.545100

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0258精密化
PDB_EXTRACT3.27データ抽出
xia20.5.48-g3279616-dials-1.3データ削減
xia20.5.48-g3279616-dials-1.3データスケーリング
Arcimboldo位相決定
精密化構造決定の手法: AB INITIO PHASING / 解像度: 1.64→66.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.079 / SU ML: 0.063 / 交差検証法: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.086 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: Repeated attempts to model solvent within the observed density in the centre of each barrel pore were inconsistent. Therefore we have included representative solvent molecules to fit the ...詳細: Repeated attempts to model solvent within the observed density in the centre of each barrel pore were inconsistent. Therefore we have included representative solvent molecules to fit the density as well as possible; however we note that the fit is poor, and that these solvent molecules do not make the expected stabilising contacts with the surrounding protein.
Rfactor反射数%反射Selection details
Rfree0.2055 7270 4.98 %RANDOM
Rwork0.1823 ---
obs0.1834 138782 99.92 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: MASK
原子変位パラメータBiso max: 139.17 Å2 / Biso mean: 33.214 Å2 / Biso min: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.42 Å2
2---1.09 Å20 Å2
3---0.73 Å2
精密化ステップサイクル: final / 解像度: 1.64→66.85 Å
タンパク質核酸リガンド溶媒全体
原子数8023 0 262 378 8663
Biso mean--58.78 42.17 -
残基数----1107
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198422
X-RAY DIFFRACTIONr_bond_other_d0.0030.028933
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.95911087
X-RAY DIFFRACTIONr_angle_other_deg1.2452.89620825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.21551077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.36225.909308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16151804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028948
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021308
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 1.64→1.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.29 544 -
Rwork0.292 10267 -
all-10811 -
obs--99.98 %
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)
10.7955-0.18960.09888.1914-1.09620.944-0.0111-0.04020.01930.14950.05480.3156-0.0389-0.0623-0.04370.07180.00820.02320.14540.00210.120458.03127.87923.774
20.67890.0596-0.09856.7246-0.7411.11680.02980.01620.0379-0.14310.03390.26280.001-0.1114-0.06370.04980.0171-0.00140.15590.01610.136654.76127.8816.253
31.66311.4456-0.404114.0362-1.81742.4061-0.06460.12470.084-0.75950.16520.44670.0933-0.1234-0.10060.05480.0056-0.04470.14340.02940.062257.03627.3948.351
40.99771.3007-0.17217.3916-0.56910.7057-0.06460.15740.0359-0.37840.1065-0.0360.0421-0.0537-0.0420.1439-0.0029-0.00280.16230.01950.086663.96926.6033.808
52.5252.51220.115814.56270.14041.9719-0.06290.2316-0.0178-0.58430.0463-0.4167-0.01350.05520.01650.06990.01410.03510.15270.02430.022872.14925.8674.903
61.86671.6450.069713.45030.77981.853-0.01750.1043-0.0334-0.0810.0509-0.6610.02790.1287-0.03340.01780.0070.0280.13550.01650.069277.78925.74810.819
72.15851.1762-0.274112.80410.56131.94630.0616-0.01250.03340.37020.0087-0.35180.03130.1938-0.07030.0122-0.0044-0.00640.11530.01460.063178.23625.88519.013
80.92550.0079-0.02929.26550.040.9688-0.001-0.08930.06120.42450.0486-0.06220.00810.043-0.04760.0774-0.0082-0.00130.1482-0.00250.100473.34326.78125.617
92.3016-0.90590.27213.1931-0.04642.0535-0.0203-0.17310.09560.67730.03430.2761-0.0683-0.0255-0.0140.04230.00350.02180.1205-0.00670.01865.44327.59327.525
100.78110.330.21959.38081.11980.8009-0.04430.05840.0038-0.33760.0646-0.0976-0.05540.0682-0.02030.0949-0.00890.02410.1477-0.01650.077360.89947.2739.017
110.5896-0.51830.05148.82241.1930.9606-0.00460.02110.0167-0.16950.0413-0.3307-0.03440.1032-0.03670.0740.00030.00680.1569-0.020.126465.69347.33845.661
120.7262-1.208-0.27487.18751.04010.9527-0.0311-0.0620.03950.13870.076-0.299-0.02960.0864-0.04490.07650.0125-0.02680.1627-0.01640.129565.19846.90153.905
131.1874-1.4929-0.30848.18770.65560.6788-0.0902-0.0795-0.01550.37210.0638-0.20640.01050.05340.02640.14370.0229-0.01910.1725-0.00560.091559.53246.13959.816
142.7442-1.98740.001513.3983-0.25071.4332-0.2259-0.2372-0.110.79710.21650.07590.0233-0.03150.00940.12460.03630.04270.1530.01410.020351.20645.64360.636
150.9263-0.67380.42946.1817-0.34750.7139-0.06-0.0823-0.07710.28910.09860.2432-0.0142-0.0819-0.03860.10460.01920.06010.16270.01810.138144.36945.41755.946
161.14480.05180.139314.116-0.42451.8988-0.0631-0.0609-0.09870.14750.15970.64230.0267-0.1326-0.09650.0063-0.00140.01620.12550.01870.142842.17945.27148.01
170.7146-0.0383-0.04278.2541-0.23690.7999-0.03150.0366-0.0373-0.29570.03240.28110.0114-0.0359-0.0010.0665-0.008-0.0280.1431-0.00610.133745.46145.98940.329
180.8229-0.0935-0.19268.81130.18550.7739-0.05180.0856-0.0353-0.47660.07110.1987-0.0286-0.0259-0.01920.1034-0.007-0.0180.1521-0.01060.093252.95646.60836.987
191.1620.89980.326413.78822.53733.07190.0140.1132-0.0339-0.10820.0205-0.6607-0.07190.1747-0.03450.0104-0.00740.03110.1742-0.0180.129129.5052647.858
201.45570.8992-0.247312.53132.29042.79330.0156-0.0076-0.03770.41990.1195-0.63710.0890.2026-0.1350.01680.0161-0.03480.1556-0.01710.130730.0624.77156.055
211.54160.0845-0.346814.0682.56512.387-0.0018-0.0472-0.01610.87790.0055-0.27260.16140.0772-0.00380.07890.0137-0.05090.1458-0.010.060525.25524.4762.812
221.6573-0.19150.170313.05691.71662.4429-0.0229-0.0713-0.05770.69750.0230.18590.009-0.0317-0.00010.07960.01420.020.1331-0.00710.008117.25324.57864.772
230.74090.2817-0.01829.61250.56230.8862-0.0065-0.02810.00670.22080.02510.3271-0.0108-0.061-0.01860.09480.01410.02630.1564-0.00840.10559.83525.81561.313
240.87410.3810.02956.54630.24981.04370.00560.04380.0433-0.0680.00230.2192-0.0115-0.0764-0.00790.05670.01680.01080.1613-0.00540.12576.48427.22853.931
251.13141.0550.12597.3160.3790.6942-0.06790.11760.0593-0.34520.08580.2424-0.0454-0.0408-0.01790.10080.006-0.01330.17490.00040.10698.74128.08146.002
261.26371.36030.1687.74060.70580.8075-0.0670.160.0437-0.35530.08640.0911-0.0788-0.0342-0.01940.1253-0.0050.00970.1870.00090.076215.43228.17441.436
272.06931.73130.4512.31950.74812.1857-0.06730.2007-0.0582-0.4640.1237-0.375-0.14810.1387-0.05640.0576-0.0130.04940.1889-0.00850.045523.82427.38842.051
282.4422-1.79680.082913.1896-2.01952.1379-0.0848-0.1982-0.00250.6247-0.0061-0.1691-0.135-0.01830.09080.0384-0.0175-0.00220.1675-0.00390.018728.13847.06831.272
291.0208-1.05240.23187.3235-1.72251.1692-0.0595-0.0718-0.01510.30130.07480.1169-0.0685-0.0894-0.01540.0654-0.00410.01450.17-0.00220.110421.3545.8126.753
301.4813-0.1680.121810.5768-1.85032.0612-0.00570.0352-0.01820.0350.0650.37870.0232-0.1495-0.05920.0016-0.00550.00890.1531-0.00870.076119.05644.57718.92
310.9319-0.1151-0.03037.0541-1.12251.0219-0.02830.0948-0.0312-0.22260.02430.19650.0434-0.02490.00410.0813-0.0005-0.00720.1617-0.00970.103922.52644.06511.338
320.75460.2017-0.03457.6264-1.04091.0539-0.07840.1053-0.0328-0.39490.09110.14290.07240.0111-0.01270.11080.00710.00920.1667-0.00410.0929.7344.0597.69
331.9893-0.28840.1814.4183-0.59352.0266-0.12890.2111-0.0846-0.56150.1459-0.23320.05570.1577-0.01710.05280.01270.04020.16160.00080.04737.77245.0189.549
340.9696-0.16760.29757.51970.04710.9709-0.01460.0318-0.0385-0.16680.017-0.2484-0.02330.1626-0.00240.05750.00760.03610.1670.01710.13442.55647.58416.314
351.0067-0.8295-0.05298.1852-0.41130.88730.0022-0.05160.00020.0023-0.0331-0.3453-0.03340.10130.03090.0572-0.00190.00050.17290.01850.134842.00547.3524.338
361.6455-1.97760.068511.5025-0.65721.5736-0.0843-0.16060.05950.31880.0984-0.4304-0.05190.0487-0.01410.0208-0.0192-0.01160.16830.00560.073836.36347.4430.341
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 30
2X-RAY DIFFRACTION2B0 - 30
3X-RAY DIFFRACTION3C0 - 30
4X-RAY DIFFRACTION4D0 - 30
5X-RAY DIFFRACTION5E0 - 29
6X-RAY DIFFRACTION6F0 - 30
7X-RAY DIFFRACTION7G0 - 29
8X-RAY DIFFRACTION8H0 - 30
9X-RAY DIFFRACTION9I0 - 30
10X-RAY DIFFRACTION10J0 - 30
11X-RAY DIFFRACTION11K0 - 30
12X-RAY DIFFRACTION12L0 - 30
13X-RAY DIFFRACTION13M0 - 30
14X-RAY DIFFRACTION14N0 - 29
15X-RAY DIFFRACTION15O0 - 29
16X-RAY DIFFRACTION16P0 - 30
17X-RAY DIFFRACTION17Q0 - 29
18X-RAY DIFFRACTION18R0 - 30
19X-RAY DIFFRACTION19S0 - 30
20X-RAY DIFFRACTION20T0 - 30
21X-RAY DIFFRACTION21U0 - 30
22X-RAY DIFFRACTION22V0 - 29
23X-RAY DIFFRACTION23W0 - 30
24X-RAY DIFFRACTION24X0 - 30
25X-RAY DIFFRACTION25Y0 - 30
26X-RAY DIFFRACTION26Z0 - 30
27X-RAY DIFFRACTION27a0 - 30
28X-RAY DIFFRACTION28b0 - 29
29X-RAY DIFFRACTION29c0 - 30
30X-RAY DIFFRACTION30d0 - 30
31X-RAY DIFFRACTION31e0 - 30
32X-RAY DIFFRACTION32f0 - 30
33X-RAY DIFFRACTION33g0 - 30
34X-RAY DIFFRACTION34h0 - 28
35X-RAY DIFFRACTION35i0 - 30
36X-RAY DIFFRACTION36j0 - 30

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万見について

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お知らせ

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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

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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