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- PDB-4s37: Crystal structure of R2 pyocin membrane-piercing spike -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 4s37
タイトルCrystal structure of R2 pyocin membrane-piercing spike
要素Phage baseplate protein
キーワードMETAL BINDING PROTEIN / Cell Puncturing Device / Trimer / beta-helix / Iron-binding / Outer cell membrane piercing
機能・相同性Phage baseplate assembly protein V/Gp45 / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / metal ion binding / TRIETHYLENE GLYCOL / Baseplate assembly protein V
機能・相同性情報
生物種Pseudomonas aeruginosa (緑膿菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.2 Å
データ登録者Browning, C.B. / Leiman, P.G. / Shneider, M.M.
引用ジャーナル: To be Published
タイトル: Crystal structure of R2 pyocin membrane-piercing spike
著者: Browning, C.B. / Leiman, P.G. / Shneider, M.M.
履歴
登録2015年1月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年1月27日Provider: repository / タイプ: Initial release
改定 1.12017年11月22日Group: Advisory / Refinement description / カテゴリ: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
改定 1.22024年2月28日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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: Phage baseplate protein
B: Phage baseplate protein
C: Phage baseplate protein
D: Phage baseplate protein
E: Phage baseplate protein
F: Phage baseplate protein
G: Phage baseplate protein
H: Phage baseplate protein
I: Phage baseplate protein
J: Phage baseplate protein
K: Phage baseplate protein
L: Phage baseplate protein
M: Phage baseplate protein
N: Phage baseplate protein
O: Phage baseplate protein
P: Phage baseplate protein
Q: Phage baseplate protein
R: Phage baseplate protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)354,84986
ポリマ-349,98818
非ポリマー4,86168
43,8302433
1
A: Phage baseplate protein
B: Phage baseplate protein
C: Phage baseplate protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,17714
ポリマ-58,3313
非ポリマー84511
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area23230 Å2
ΔGint-257 kcal/mol
Surface area18840 Å2
手法PISA
2
D: Phage baseplate protein
E: Phage baseplate protein
F: Phage baseplate protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,19317
ポリマ-58,3313
非ポリマー86214
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area23590 Å2
ΔGint-248 kcal/mol
Surface area18820 Å2
手法PISA
3
G: Phage baseplate protein
H: Phage baseplate protein
I: Phage baseplate protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,37318
ポリマ-58,3313
非ポリマー1,04115
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area23690 Å2
ΔGint-265 kcal/mol
Surface area19010 Å2
手法PISA
4
J: Phage baseplate protein
K: Phage baseplate protein
L: Phage baseplate protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,34518
ポリマ-58,3313
非ポリマー1,01415
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area23510 Å2
ΔGint-260 kcal/mol
Surface area19470 Å2
手法PISA
5
M: Phage baseplate protein
N: Phage baseplate protein
O: Phage baseplate protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)59,14113
ポリマ-58,3313
非ポリマー81010
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area23190 Å2
ΔGint-247 kcal/mol
Surface area18640 Å2
手法PISA
6
P: Phage baseplate protein
Q: Phage baseplate protein
R: Phage baseplate protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)58,6196
ポリマ-58,3313
非ポリマー2883
543
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area21570 Å2
ΔGint-171 kcal/mol
Surface area18210 Å2
手法PISA
単位格子
Length a, b, c (Å)94.945, 137.471, 164.759
Angle α, β, γ (deg.)90.00, 106.56, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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タンパク質 , 1種, 18分子 ABCDEFGHIJKLMNOPQR

#1: タンパク質
Phage baseplate protein / VR2 protein


分子量: 19443.758 Da / 分子数: 18 / 由来タイプ: 組換発現 / 由来: (組換発現) Pseudomonas aeruginosa (緑膿菌)
遺伝子: VR2, gpV, D480_28305, JF43_02945, NCGM1900_0632, NCGM1984_0630
プラスミド: pET-28-based / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q9S581

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非ポリマー , 6種, 2501分子

#2: 化合物...
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 35 / 由来タイプ: 合成 / : SO4
#3: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 19 / 由来タイプ: 合成 / : Cl
#4: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 7 / 由来タイプ: 合成 / : C2H6O2
#5: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 6 / 由来タイプ: 合成 / : Ca
#6: 化合物 ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 1 / 由来タイプ: 合成 / : C6H14O4
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2433 / 由来タイプ: 天然 / : H2O

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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: 2.94 Å3/Da / 溶媒含有率: 58.23 %
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: 8.5
詳細: 60% PEG 400, 100mM NaSO4, 100mM Bis-Tris, pH 8.5, 18mg/ml protein, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: SLS / ビームライン: X06SA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2011年2月7日
放射モノクロメーター: Si (111) / 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 Å / 相対比: 1
反射解像度: 2.2→49.26 Å / Num. obs: 203160 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / 冗長度: 4.4 % / Rmerge(I) obs: 0.05 / Rsym value: 0.063 / Net I/σ(I): 15.1
反射 シェル解像度: 2.2→2.32 Å / 冗長度: 4 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.2 / Num. unique all: 28488 / Rsym value: 0.467 / % possible all: 95.3

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解析

ソフトウェア
名称バージョン分類
RemDAqデータ収集
PHASER位相決定
PHENIX(phenix.refine: 1.8.2_1309)精密化
XDSデータ削減
SCALAデータスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 2.2→49.186 Å / SU ML: 0.24 / σ(F): 2 / 位相誤差: 19.62 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2079 10157 5 %
Rwork0.1625 --
obs0.1648 203160 99.12 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.2→49.186 Å
タンパク質核酸リガンド溶媒全体
原子数22839 0 238 2433 25510
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00424564
X-RAY DIFFRACTIONf_angle_d0.88933604
X-RAY DIFFRACTIONf_dihedral_angle_d10.7088652
X-RAY DIFFRACTIONf_chiral_restr0.0573742
X-RAY DIFFRACTIONf_plane_restr0.0034351
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.22560.28752910.23075536X-RAY DIFFRACTION86
2.2256-2.25170.24973400.2046449X-RAY DIFFRACTION100
2.2517-2.27920.2633380.20166421X-RAY DIFFRACTION100
2.2792-2.30810.25453420.19326498X-RAY DIFFRACTION100
2.3081-2.33840.23393380.18576418X-RAY DIFFRACTION100
2.3384-2.37050.2243400.17676465X-RAY DIFFRACTION100
2.3705-2.40430.23283380.1776427X-RAY DIFFRACTION100
2.4043-2.44020.21573430.17216518X-RAY DIFFRACTION100
2.4402-2.47830.24373380.17426414X-RAY DIFFRACTION100
2.4783-2.5190.23253390.1666440X-RAY DIFFRACTION100
2.519-2.56240.22633420.16686497X-RAY DIFFRACTION100
2.5624-2.6090.21433410.16526488X-RAY DIFFRACTION100
2.609-2.65920.23073400.16426459X-RAY DIFFRACTION100
2.6592-2.71340.22633400.16986462X-RAY DIFFRACTION100
2.7134-2.77240.21913380.17356421X-RAY DIFFRACTION100
2.7724-2.83690.23763410.17056477X-RAY DIFFRACTION100
2.8369-2.90790.23843420.17766486X-RAY DIFFRACTION100
2.9079-2.98650.22793410.16946486X-RAY DIFFRACTION100
2.9865-3.07430.22413400.16536457X-RAY DIFFRACTION100
3.0743-3.17360.19743400.16026461X-RAY DIFFRACTION100
3.1736-3.2870.19943400.16096454X-RAY DIFFRACTION100
3.287-3.41850.20943370.15756429X-RAY DIFFRACTION99
3.4185-3.57410.20853400.15626458X-RAY DIFFRACTION99
3.5741-3.76240.19743410.15126479X-RAY DIFFRACTION100
3.7624-3.99810.17753410.14386464X-RAY DIFFRACTION99
3.9981-4.30660.17333400.13346471X-RAY DIFFRACTION99
4.3066-4.73970.16993390.12616411X-RAY DIFFRACTION98
4.7397-5.42480.18593390.14296454X-RAY DIFFRACTION99
5.4248-6.83170.19933450.16596553X-RAY DIFFRACTION100
6.8317-49.1980.23133430.21166550X-RAY DIFFRACTION99
精密化 TLS

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.2264-0.3828-0.3620.63120.58180.53340.16-0.1234-0.28370.11540.0604-0.30770.77970.19880.33740.49990.0512-0.13390.23860.05590.455214.8425-13.823674.2575
20.48040.4486-0.10220.4591-0.05780.07250.1327-0.0371-0.17040.06240.0203-0.11030.17730.02570.00180.34830.0078-0.07940.22310.01750.23689.9733-2.957773.8254
30.04620.09130.05350.1570.09770.0862-0.1333-0.1186-0.14630.88220.00630.00220.13920.15160.00090.4593-0.0694-0.0060.36070.04360.33377.553913.643881.3519
40.18930.13890.00380.26220.10370.05660.2367-0.01490.14770.7923-0.08790.5518-0.12280.0144-0.00180.4067-0.07630.0570.26580.0690.33491.360620.187981.5833
50.0350.00510.02640.0073-0.01360.03340.25170.1976-0.25850.09170.1221-0.3070.11390.1184-00.4083-0.0563-0.1090.35220.03460.366517.475322.919174.2801
61.29070.38310.27830.15940.15630.1732-0.11190.3457-0.3397-0.0352-0.0872-0.873-0.13990.2429-0.17320.3738-0.0812-0.10960.30890.09550.361218.703529.639972.5451
70.01410.0534-0.03050.3238-0.16280.0762-0.06270.51450.01470.3633-0.07140.5062-0.21970.0035-0.00780.3021-0.0345-0.00220.36820.02080.38429.395640.433467.7536
80.0288-0.12830.02520.6122-0.10540.0229-0.10420.0417-0.0990.86460.16270.0792-0.19480.13560.00340.5578-0.0272-0.06820.3450.0520.282916.873546.134677.5972
90.3402-0.1972-0.22240.26340.00910.72010.1551-0.1880.30670.70750.3046-0.0869-0.51530.49430.01920.5945-0.0807-0.0560.32110.04360.379912.991356.269873.1276
100.32980.1923-0.13760.1274-0.08690.0690.1427-0.2501-0.20740.28550.02170.28050.3977-0.11240.16890.4647-0.0773-0.0530.23770.08740.3891-6.8395-11.310381.6347
110.46960.4164-0.30780.78830.10440.38940.0567-0.03540.02850.11930.05550.25860.1501-0.0309-00.3459-0.0324-0.03390.2790.08410.3598-1.47474.044274.1504
120.0011-0.0106-0.00020.0706-0.04770.03620.01770.1837-0.2029-0.30580.06390.31820.0943-0.0163-0.00020.4165-0.0266-0.0810.34280.0320.46163.543420.275562.2199
130.27160.35610.00890.9314-0.21510.09830.2031-0.32980.1081.2049-0.1750.2755-0.2697-0.0761-0.02380.5021-0.06050.03550.3030.04170.35895.810229.546780.0524
140.42440.05320.33170.4437-0.46170.8028-0.0825-0.05870.25380.638-0.1339-0.2503-0.57120.2288-0.17190.4184-0.1022-0.05580.31780.06930.25615.217847.445873.046
150.29820.0619-0.04520.1795-0.04560.02680.17410.2371-0.1613-0.34640.07640.57660.5419-0.06640.02170.6195-0.079-0.11240.27260.01980.3064-1.5407-15.962961.4498
160.33970.3959-0.11410.9589-0.09340.0521-0.13310.1796-0.1221-0.10330.40540.26170.4698-0.09750.37630.4773-0.0932-0.18870.29450.03240.3518-4.625-6.133156.2539
170.31810.14020.22510.7184-0.14360.22810.01460.1033-0.0965-0.20230.07560.06010.0737-0.09020.02330.323-0.0606-0.06550.21160.0080.21481.9246-0.744164.9271
180.0199-0.05880.00170.1298-0.00040.0007-0.06990.1162-0.10910.00820.1138-0.1755-0.06130.1574-0.00010.33760.0064-0.02640.42640.01280.345714.188112.636766.8839
190.01080.0144-0.00970.0292-0.01890.0093-0.0998-0.18430.190.1439-0.0761-0.68560.05960.34920.00040.3919-0.0115-0.10440.33120.06720.376218.866516.545273.7311
200.04140.07-0.01060.1045-0.01840.023-0.06720.26350.2879-0.08390.08490.3016-0.0927-0.07090.00040.2642-0.0520.00870.23120.04440.2816.390125.911164.4581
211.8056-0.4134-0.83250.4790.01160.6421-0.1230.4743-0.3019-0.409700.34660.087-0.22910.01120.2322-0.07270.02410.20910.05480.25386.165832.542866.1961
220.48530.0339-0.79930.0426-0.13541.48580.0917-0.411-0.00821.0755-0.1663-0.023-0.08180.3387-0.04410.524-0.05420.00860.22070.00940.2919.034540.051779.1613
230.2679-0.1495-0.2270.25190.1010.4039-0.0712-0.2960.48090.8568-0.0144-0.205-0.42790.43270.0090.5692-0.091-0.0440.34040.04030.369116.350651.632673.4909
240.31910.1196-0.09550.42740.18510.16990.1516-0.0366-0.2219-0.05580.0252-0.010.5351-0.23420.56920.61510.0149-0.20880.3595-0.09420.4413-12.4723-10.943915.2453
250.1712-0.28720.02780.60920.34740.77790.15190.0347-0.1356-0.07810.0072-0.24830.15740.2210.05380.32490.0317-0.11120.3331-0.0790.2977-6.31514.413321.7144
260.04120.03080.03280.05630.00420.01790.2034-0.0424-0.2242-0.46150.0415-0.24630.12250.27620.00010.30380.0324-0.02650.496-0.09910.35674.846720.59829.0153
270.4876-0.8313-0.01124.24230.54150.09430.07820.56260.0618-0.87390.10090.3487-0.0662-0.2445-0.18940.1273-0.0088-0.08820.2977-0.05580.2499-11.929831.019324.8652
281.00370.6179-0.21740.6836-0.70171.11130.0997-0.4019-0.0283-0.0014-0.19030.1267-0.23360.1736-0.0610.17880.0362-0.00140.3917-0.12320.3855-8.437640.278239.2082
290.0151-0.02270.05380.1292-0.04830.140.03680.11620.2839-0.2258-0.13120.2161-0.25250.1588-0.00010.25870.0395-0.03390.3516-0.04960.3799-5.942553.804633.199
300.64030.0541-0.07660.012-0.09032.22430.2003-0.1203-0.5178-0.23040.1050.1431.191-0.04670.15750.70390.2209-0.32230.4111-0.17360.65584.4633-15.324227.2902
310.0394-0.08960.08580.4528-0.48230.72930.1213-0.2307-0.1805-0.42370.26840.01240.74530.3250.00650.59440.2433-0.17060.78-0.21790.626210.819-6.501825.1528
320.76530.19660.1950.5815-0.29530.4370.1738-0.0594-0.10970.0834-0.0015-0.1590.39030.2530.30120.36150.0802-0.12290.3629-0.0920.3332-0.294.019631.6705
330.327-0.28290.10530.4611-0.24460.15520.1071-0.38550.16190.49210.16140.18460.0590.18740.05230.2796-0.0316-0.07630.3044-0.04350.3536-10.935819.001440.2441
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1230.0726-0.0796-0.0861.99590.98480.5273-0.3364-0.6096-0.41571.31260.18020.10270.68830.5024-0.21770.56510.16630.06560.61340.22870.6072-56.45129.46339.6627
1240.02940.21210.02371.65870.21810.0299-0.02040.26650.04-0.28840.0694-0.35680.01810.1836-0.10470.20440.11940.04730.52360.09150.3654-48.758840.710828.7895
1250.1350.36820.14851.61831.22881.26820.0195-0.28490.2207-0.2780.1929-0.1194-0.36160.24690.1760.189-0.01410.02420.48080.04870.3074-56.608453.230831.0664
1260.02230.0183-0.02230.12930.0010.38820.2555-0.0166-0.24420.22190.16860.14430.0509-0.07340.16431.81060.21620.59630.63910.09452.3058-57.6388-14.963321.8606
1270.3701-0.5559-0.10150.93750.18210.0378-0.0030.0619-0.0428-0.1804-0.2068-0.20050.22390.1416-0.1082.41020.3130.69620.6383-0.03652.0572-64.2846-8.907419.6444
1280.6229-0.21460.68270.0883-0.24060.76070.28780.2545-0.9519-0.0866-0.3275-0.05241.44720.30970.0231.79180.2850.41890.66820.05921.3992-56.4858-1.5325.4026
1290.04370.0439-0.22930.0998-0.38621.6533-0.149-0.1389-0.2412-0.3693-0.0641-0.02040.3466-0.2382-0.05720.9020.34050.18170.58070.0250.8536-48.526814.4723.8951
1300.51710.3190.06240.2220.10970.1984-0.0534-0.1781-0.14230.12880.1471-0.54210.18190.30030.29820.660.97510.10450.94870.15310.869-43.261820.060429.0366
1310.0206-0.02430.01080.04230.01330.03020.3016-0.11910.0377-0.3002-0.11710.64140.1047-0.2159-0.00010.56310.05150.06070.4701-0.0460.5491-60.103525.062125.2666
1320.0043-0.02150.00650.0931-0.03430.0137-0.06670.2668-0.2975-0.2405-0.05930.61960.3705-0.14530.00040.34890.09160.04110.3580.04330.5202-61.351331.823526.6168
1330.1013-0.219-0.12910.46870.28130.1711-0.161-0.4343-0.10170.4140.1067-0.22430.14760.41530.03720.26290.08750.00860.70730.06210.4296-56.612840.549937.988
1340.9345-0.05810.42410.16350.09510.32290.1819-0.32610.2084-0.20940.0615-0.4009-0.23490.83190.17090.26670.01180.08570.60850.02030.4135-54.561253.198130.3746
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:44 )A9 - 44
2X-RAY DIFFRACTION2( CHAIN A AND RESID 45:95 )A45 - 95
3X-RAY DIFFRACTION3( CHAIN A AND RESID 96:111 )A96 - 111
4X-RAY DIFFRACTION4( CHAIN A AND RESID 112:120 )A112 - 120
5X-RAY DIFFRACTION5( CHAIN A AND RESID 121:130 )A121 - 130
6X-RAY DIFFRACTION6( CHAIN A AND RESID 131:145 )A131 - 145
7X-RAY DIFFRACTION7( CHAIN A AND RESID 146:155 )A146 - 155
8X-RAY DIFFRACTION8( CHAIN A AND RESID 156:165 )A156 - 165
9X-RAY DIFFRACTION9( CHAIN A AND RESID 166:176 )A166 - 176
10X-RAY DIFFRACTION10( CHAIN B AND RESID 4:44 )B4 - 44
11X-RAY DIFFRACTION11( CHAIN B AND RESID 45:111 )B45 - 111
12X-RAY DIFFRACTION12( CHAIN B AND RESID 112:120 )B112 - 120
13X-RAY DIFFRACTION13( CHAIN B AND RESID 121:145 )B121 - 145
14X-RAY DIFFRACTION14( CHAIN B AND RESID 146:177 )B146 - 177
15X-RAY DIFFRACTION15( CHAIN C AND RESID 6:25 )C6 - 25
16X-RAY DIFFRACTION16( CHAIN C AND RESID 26:44 )C26 - 44
17X-RAY DIFFRACTION17( CHAIN C AND RESID 45:95 )C45 - 95
18X-RAY DIFFRACTION18( CHAIN C AND RESID 96:111 )C96 - 111
19X-RAY DIFFRACTION19( CHAIN C AND RESID 112:120 )C112 - 120
20X-RAY DIFFRACTION20( CHAIN C AND RESID 121:130 )C121 - 130
21X-RAY DIFFRACTION21( CHAIN C AND RESID 131:145 )C131 - 145
22X-RAY DIFFRACTION22( CHAIN C AND RESID 146:155 )C146 - 155
23X-RAY DIFFRACTION23( CHAIN C AND RESID 156:177 )C156 - 177
24X-RAY DIFFRACTION24( CHAIN D AND RESID 4:44 )D4 - 44
25X-RAY DIFFRACTION25( CHAIN D AND RESID 45:111 )D45 - 111
26X-RAY DIFFRACTION26( CHAIN D AND RESID 112:120 )D112 - 120
27X-RAY DIFFRACTION27( CHAIN D AND RESID 121:145 )D121 - 145
28X-RAY DIFFRACTION28( CHAIN D AND RESID 146:155 )D146 - 155
29X-RAY DIFFRACTION29( CHAIN D AND RESID 156:176 )D156 - 176
30X-RAY DIFFRACTION30( CHAIN E AND RESID 6:25 )E6 - 25
31X-RAY DIFFRACTION31( CHAIN E AND RESID 26:44 )E26 - 44
32X-RAY DIFFRACTION32( CHAIN E AND RESID 45:111 )E45 - 111
33X-RAY DIFFRACTION33( CHAIN E AND RESID 112:120 )E112 - 120
34X-RAY DIFFRACTION34( CHAIN E AND RESID 121:130 )E121 - 130
35X-RAY DIFFRACTION35( CHAIN E AND RESID 131:145 )E131 - 145
36X-RAY DIFFRACTION36( CHAIN E AND RESID 146:155 )E146 - 155
37X-RAY DIFFRACTION37( CHAIN E AND RESID 156:177 )E156 - 177
38X-RAY DIFFRACTION38( CHAIN F AND RESID 2:25 )F2 - 25
39X-RAY DIFFRACTION39( CHAIN F AND RESID 26:44 )F26 - 44
40X-RAY DIFFRACTION40( CHAIN F AND RESID 45:85 )F45 - 85
41X-RAY DIFFRACTION41( CHAIN F AND RESID 86:95 )F86 - 95
42X-RAY DIFFRACTION42( CHAIN F AND RESID 96:111 )F96 - 111
43X-RAY DIFFRACTION43( CHAIN F AND RESID 112:120 )F112 - 120
44X-RAY DIFFRACTION44( CHAIN F AND RESID 121:130 )F121 - 130
45X-RAY DIFFRACTION45( CHAIN F AND RESID 131:145 )F131 - 145
46X-RAY DIFFRACTION46( CHAIN F AND RESID 146:155 )F146 - 155
47X-RAY DIFFRACTION47( CHAIN F AND RESID 156:165 )F156 - 165
48X-RAY DIFFRACTION48( CHAIN F AND RESID 166:176 )F166 - 176
49X-RAY DIFFRACTION49( CHAIN G AND RESID 2:44 )G2 - 44
50X-RAY DIFFRACTION50( CHAIN G AND RESID 45:111 )G45 - 111
51X-RAY DIFFRACTION51( CHAIN G AND RESID 112:120 )G112 - 120
52X-RAY DIFFRACTION52( CHAIN G AND RESID 121:145 )G121 - 145
53X-RAY DIFFRACTION53( CHAIN G AND RESID 146:176 )G146 - 176
54X-RAY DIFFRACTION54( CHAIN H AND RESID 2:25 )H2 - 25
55X-RAY DIFFRACTION55( CHAIN H AND RESID 26:54 )H26 - 54
56X-RAY DIFFRACTION56( CHAIN H AND RESID 55:111 )H55 - 111
57X-RAY DIFFRACTION57( CHAIN H AND RESID 112:120 )H112 - 120
58X-RAY DIFFRACTION58( CHAIN H AND RESID 121:130 )H121 - 130
59X-RAY DIFFRACTION59( CHAIN H AND RESID 131:155 )H131 - 155
60X-RAY DIFFRACTION60( CHAIN H AND RESID 156:178 )H156 - 178
61X-RAY DIFFRACTION61( CHAIN I AND RESID 3:44 )I3 - 44
62X-RAY DIFFRACTION62( CHAIN I AND RESID 45:111 )I45 - 111
63X-RAY DIFFRACTION63( CHAIN I AND RESID 112:120 )I112 - 120
64X-RAY DIFFRACTION64( CHAIN I AND RESID 121:145 )I121 - 145
65X-RAY DIFFRACTION65( CHAIN I AND RESID 146:155 )I146 - 155
66X-RAY DIFFRACTION66( CHAIN I AND RESID 156:177 )I156 - 177
67X-RAY DIFFRACTION67( CHAIN J AND RESID 2:25 )J2 - 25
68X-RAY DIFFRACTION68( CHAIN J AND RESID 26:44 )J26 - 44
69X-RAY DIFFRACTION69( CHAIN J AND RESID 45:111 )J45 - 111
70X-RAY DIFFRACTION70( CHAIN J AND RESID 112:120 )J112 - 120
71X-RAY DIFFRACTION71( CHAIN J AND RESID 121:130 )J121 - 130
72X-RAY DIFFRACTION72( CHAIN J AND RESID 131:145 )J131 - 145
73X-RAY DIFFRACTION73( CHAIN J AND RESID 146:155 )J146 - 155
74X-RAY DIFFRACTION74( CHAIN J AND RESID 156:176 )J156 - 176
75X-RAY DIFFRACTION75( CHAIN K AND RESID 2:44 )K2 - 44
76X-RAY DIFFRACTION76( CHAIN K AND RESID 45:95 )K45 - 95
77X-RAY DIFFRACTION77( CHAIN K AND RESID 96:120 )K96 - 120
78X-RAY DIFFRACTION78( CHAIN K AND RESID 121:130 )K121 - 130
79X-RAY DIFFRACTION79( CHAIN K AND RESID 131:145 )K131 - 145
80X-RAY DIFFRACTION80( CHAIN K AND RESID 146:155 )K146 - 155
81X-RAY DIFFRACTION81( CHAIN K AND RESID 156:177 )K156 - 177
82X-RAY DIFFRACTION82( CHAIN L AND RESID 2:44 )L2 - 44
83X-RAY DIFFRACTION83( CHAIN L AND RESID 45:68 )L45 - 68
84X-RAY DIFFRACTION84( CHAIN L AND RESID 69:95 )L69 - 95
85X-RAY DIFFRACTION85( CHAIN L AND RESID 96:111 )L96 - 111
86X-RAY DIFFRACTION86( CHAIN L AND RESID 112:120 )L112 - 120
87X-RAY DIFFRACTION87( CHAIN L AND RESID 121:130 )L121 - 130
88X-RAY DIFFRACTION88( CHAIN L AND RESID 131:145 )L131 - 145
89X-RAY DIFFRACTION89( CHAIN L AND RESID 146:155 )L146 - 155
90X-RAY DIFFRACTION90( CHAIN L AND RESID 156:176 )L156 - 176
91X-RAY DIFFRACTION91( CHAIN M AND RESID 5:44 )M5 - 44
92X-RAY DIFFRACTION92( CHAIN M AND RESID 45:95 )M45 - 95
93X-RAY DIFFRACTION93( CHAIN M AND RESID 96:111 )M96 - 111
94X-RAY DIFFRACTION94( CHAIN M AND RESID 112:120 )M112 - 120
95X-RAY DIFFRACTION95( CHAIN M AND RESID 121:145 )M121 - 145
96X-RAY DIFFRACTION96( CHAIN M AND RESID 146:155 )M146 - 155
97X-RAY DIFFRACTION97( CHAIN M AND RESID 156:176 )M156 - 176
98X-RAY DIFFRACTION98( CHAIN N AND RESID 6:44 )N6 - 44
99X-RAY DIFFRACTION99( CHAIN N AND RESID 45:111 )N45 - 111
100X-RAY DIFFRACTION100( CHAIN N AND RESID 112:120 )N112 - 120
101X-RAY DIFFRACTION101( CHAIN N AND RESID 121:145 )N121 - 145
102X-RAY DIFFRACTION102( CHAIN N AND RESID 146:155 )N146 - 155
103X-RAY DIFFRACTION103( CHAIN N AND RESID 156:176 )N156 - 176
104X-RAY DIFFRACTION104( CHAIN O AND RESID 4:15 )O4 - 15
105X-RAY DIFFRACTION105( CHAIN O AND RESID 16:44 )O16 - 44
106X-RAY DIFFRACTION106( CHAIN O AND RESID 45:95 )O45 - 95
107X-RAY DIFFRACTION107( CHAIN O AND RESID 96:111 )O96 - 111
108X-RAY DIFFRACTION108( CHAIN O AND RESID 112:130 )O112 - 130
109X-RAY DIFFRACTION109( CHAIN O AND RESID 131:155 )O131 - 155
110X-RAY DIFFRACTION110( CHAIN O AND RESID 156:177 )O156 - 177
111X-RAY DIFFRACTION111( CHAIN P AND RESID 11:25 )P11 - 25
112X-RAY DIFFRACTION112( CHAIN P AND RESID 26:44 )P26 - 44
113X-RAY DIFFRACTION113( CHAIN P AND RESID 45:111 )P45 - 111
114X-RAY DIFFRACTION114( CHAIN P AND RESID 112:120 )P112 - 120
115X-RAY DIFFRACTION115( CHAIN P AND RESID 121:145 )P121 - 145
116X-RAY DIFFRACTION116( CHAIN P AND RESID 146:155 )P146 - 155
117X-RAY DIFFRACTION117( CHAIN P AND RESID 156:176 )P156 - 176
118X-RAY DIFFRACTION118( CHAIN Q AND RESID 12:25 )Q12 - 25
119X-RAY DIFFRACTION119( CHAIN Q AND RESID 26:44 )Q26 - 44
120X-RAY DIFFRACTION120( CHAIN Q AND RESID 45:68 )Q45 - 68
121X-RAY DIFFRACTION121( CHAIN Q AND RESID 69:111 )Q69 - 111
122X-RAY DIFFRACTION122( CHAIN Q AND RESID 112:120 )Q112 - 120
123X-RAY DIFFRACTION123( CHAIN Q AND RESID 121:145 )Q121 - 145
124X-RAY DIFFRACTION124( CHAIN Q AND RESID 146:155 )Q146 - 155
125X-RAY DIFFRACTION125( CHAIN Q AND RESID 156:177 )Q156 - 177
126X-RAY DIFFRACTION126( CHAIN R AND RESID 9:25 )R9 - 25
127X-RAY DIFFRACTION127( CHAIN R AND RESID 26:44 )R26 - 44
128X-RAY DIFFRACTION128( CHAIN R AND RESID 45:95 )R45 - 95
129X-RAY DIFFRACTION129( CHAIN R AND RESID 96:111 )R96 - 111
130X-RAY DIFFRACTION130( CHAIN R AND RESID 112:120 )R112 - 120
131X-RAY DIFFRACTION131( CHAIN R AND RESID 121:130 )R121 - 130
132X-RAY DIFFRACTION132( CHAIN R AND RESID 131:145 )R131 - 145
133X-RAY DIFFRACTION133( CHAIN R AND RESID 146:155 )R146 - 155
134X-RAY DIFFRACTION134( CHAIN R AND RESID 156:177 )R156 - 177

+
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://pdbjlvh1.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

+
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

+
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

+
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。

-
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