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- PDB-8y6f: The crystal structure of MMPs cleavable human heavy chain ferritin -

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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: 8y6f
タイトルThe crystal structure of MMPs cleavable human heavy chain ferritin
要素Ferritin
キーワードTRANSPORT PROTEIN / heavy chain ferritin / MMPs cleavable
機能・相同性
機能・相同性情報


: / ferric iron binding / ferrous iron binding / iron ion transport / cytoplasm
類似検索 - 分子機能
Ferritin iron-binding regions signature 1. / Ferritin iron-binding regions signature 2. / Ferritin, conserved site / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
類似検索 - ドメイン・相同性
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: 2.01 Å
データ登録者Yuan, C. / Huang, M.
資金援助 中国, 2件
組織認可番号
National Natural Science Foundation of China (NSFC)32371312 中国
National Natural Science Foundation of China (NSFC)22077016 中国
引用ジャーナル: Int.J.Biol.Macromol. / : 2024
タイトル: Engineered protein cages with enhanced extracellular drug release for elevated antitumor efficacy.
著者: Yan, W. / Li, H. / Ning, J. / Huang, S. / Jiang, L. / Xu, P. / Huang, M. / Yuan, C.
履歴
登録2024年2月2日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02024年7月17日Provider: repository / タイプ: Initial release

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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: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)273,69437
ポリマ-272,51112
非ポリマー1,18325
45,4162521
1
A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
ヘテロ分子

A: Ferritin
B: Ferritin
C: Ferritin
D: Ferritin
E: Ferritin
F: Ferritin
G: Ferritin
H: Ferritin
I: Ferritin
J: Ferritin
K: Ferritin
L: Ferritin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)547,38874
ポリマ-545,02124
非ポリマー2,36650
43224
タイプ名称対称操作
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area96560 Å2
ΔGint-731 kcal/mol
Surface area138900 Å2
手法PISA
単位格子
Length a, b, c (Å)219.660, 219.660, 148.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDモデル要素
11E-201-

CL

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要素

#1: タンパク質
Ferritin


分子量: 22709.229 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: FTH1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q6NZ44
#2: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / : Cl / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-FE / FE (III) ION


分子量: 55.845 Da / 分子数: 17 / 由来タイプ: 合成 / : Fe / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 4 / 由来タイプ: 合成 / : Na / タイプ: SUBJECT OF INVESTIGATION
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2521 / 由来タイプ: 天然 / : H2O
研究の焦点であるリガンドがあるかY

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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: 3.28 Å3/Da / 溶媒含有率: 62.53 %
結晶化温度: 285 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8 / 詳細: 0.1 M Tris 8.0, 1% PEG 8000, 20% isopropanol

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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: SSRF / ビームライン: BL10U2 / 波長: 0.9798 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2023年12月30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: 0.9798 Å / 相対比: 1
反射解像度: 2.01→32.47 Å / Num. obs: 237253 / % possible obs: 98.96 % / 冗長度: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1555 / Net I/σ(I): 8.68
反射 シェル解像度: 2.01→2.08 Å / Rmerge(I) obs: 0.6882 / Num. unique obs: 23455 / CC1/2: 0.909 / % possible all: 99.43

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.20.1_4487: ???)精密化
xia2データスケーリング
xia2データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.01→23.52 Å / SU ML: 0.24 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 36.9 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2867 11641 4.93 %
Rwork0.2447 --
obs0.2468 235979 99.04 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 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: 2.01→23.52 Å
タンパク質核酸リガンド溶媒全体
原子数16767 0 25 2521 19313
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.901
X-RAY DIFFRACTIONf_dihedral_angle_d5.1962253
X-RAY DIFFRACTIONf_chiral_restr0.0482440
X-RAY DIFFRACTIONf_plane_restr0.0073059
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.030.34833960.30087425X-RAY DIFFRACTION99
2.03-2.060.32853840.29217438X-RAY DIFFRACTION99
2.06-2.080.33773660.28337429X-RAY DIFFRACTION100
2.08-2.110.33663650.28167451X-RAY DIFFRACTION99
2.11-2.140.31983870.27567436X-RAY DIFFRACTION99
2.14-2.170.30844310.26577382X-RAY DIFFRACTION99
2.17-2.20.30073710.27117470X-RAY DIFFRACTION99
2.2-2.230.30494040.2677402X-RAY DIFFRACTION99
2.23-2.260.31624030.277452X-RAY DIFFRACTION99
2.26-2.30.31983530.27617431X-RAY DIFFRACTION99
2.3-2.340.32333960.27377415X-RAY DIFFRACTION99
2.34-2.380.32854160.26887389X-RAY DIFFRACTION99
2.38-2.430.31153760.25837455X-RAY DIFFRACTION99
2.43-2.480.29853530.25317484X-RAY DIFFRACTION99
2.48-2.530.28693640.24737462X-RAY DIFFRACTION99
2.53-2.590.30923760.25117459X-RAY DIFFRACTION99
2.59-2.660.29483900.24317461X-RAY DIFFRACTION99
2.66-2.730.27583780.24127448X-RAY DIFFRACTION99
2.73-2.810.284110.24197413X-RAY DIFFRACTION99
2.81-2.90.31163760.24967452X-RAY DIFFRACTION99
2.9-30.31463830.24337452X-RAY DIFFRACTION99
3-3.120.28144180.23837456X-RAY DIFFRACTION99
3.12-3.260.27893820.24027476X-RAY DIFFRACTION99
3.26-3.430.25543940.23697499X-RAY DIFFRACTION99
3.43-3.650.24353740.22277490X-RAY DIFFRACTION99
3.65-3.930.24863680.21737590X-RAY DIFFRACTION99
3.93-4.320.25243950.2067575X-RAY DIFFRACTION99
4.32-4.940.23423960.20877627X-RAY DIFFRACTION99
4.94-6.210.29964080.24447693X-RAY DIFFRACTION99
6.21-23.520.27024270.23197726X-RAY DIFFRACTION97
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)
10.9038-0.2259-0.25550.33760.44020.33010.03140.12340.2687-0.0504-0.00260.02550.11-0.03820.05740.1854-0.0104-0.02170.11690.00280.112826.986838.155336.7288
24.15170.9373-2.8980.3886-0.77792.15170-0.22290.0972-0.08090.01430.01150.03630.0518-0.05050.13990.0488-0.00780.11850.00020.128329.658940.385541.9876
35.22562.1175-1.0122.57290.16311.465-0.66061.28650.0214-0.92060.33320.07630.5594-0.29920.02190.3193-0.0031-0.07550.39090.05940.11133.083234.159927.1078
45.65670.2097-1.5310.11050.27560.9585-0.0994-0.0303-0.0492-0.04210.0581-0.01620.0143-0.01860.04630.1779-0.0009-0.01840.08670.00050.097221.623548.42535.0697
54.9923-1.4575-0.95120.9217-0.24350.60890.1557-0.0723-0.0413-0.1416-0.0636-0.0391-0.1834-0.0921-0.04570.1170.0264-0.03810.1489-0.02380.115442.642453.387228.8127
6-0.00350.0838-0.10622.8921.30431.02540.10590.06540.0204-0.3869-0.23150.063-0.2690.02720.04660.0996-0.0331-0.01770.10780.02470.108238.264387.561136.63
70.384-1.6971-1.24547.21715.17063.6483-0.11750.0568-0.03860.72740.03870.14340.28440.0601-0.05520.17440.0367-0.00660.22770.03360.138341.786783.162341.5721
82.9042.3052.83537.31234.1917.7913-0.2659-0.18030.3519-0.3377-0.12780.7635-0.6588-0.44840.29760.1601-0.01980.01030.12990.01090.165230.946794.743839.2245
90.4695-0.8376-0.43691.880.24030.54120.08840.15890.00160.0579-0.18370.25970.1458-0.19470.1080.1259-0.019-0.00770.14420.0340.156746.356190.236732.9933
100.19140.252-0.05645.91831.0460.69550.06740.0561-0.02030.0794-0.1021-0.00960.1416-0.03520.09960.11730.0370.0310.16650.03950.180153.611972.157928.9737
110.32070.13420.01681.9543-1.02430.43310.02350.0931-0.0122-0.0555-0.03470.0590.1201-0.04310.02940.1721-0.0150.01320.1399-0.02850.112876.655426.885936.8001
120.05880.22210.02263.5735-2.68952.1314-0.11040.0425-0.02390.40470.14010.0549-0.2011-0.1078-0.06360.13450.01880.01150.1612-0.00510.096275.783128.976440.9745
130.0668-0.5810.35313.3736-1.99021.31350.05980.0944-0.0418-0.2117-0.0585-0.12170.07960.00650.06510.1555-0.0114-0.01060.1852-0.05490.153768.57124.219233.0439
140.67-0.10150.05165.3256-0.17630.03850.07550.21560.1676-0.0791-0.227-0.0661-0.09310.26220.06530.10510.07060.030.1814-0.02370.093861.299742.478228.4171
150.445-0.38030.2551.06930.77571.49010.2323-0.1086-0.12470.3454-0.00480.01630.04650.07420.07680.1237-0.10770.0540.30080.02520.1997107.344175.671249.7406
161.81430.10861.03270.492-0.29740.64570.04640.1521-0.1002-0.01560.02110.0343-0.13080.1156-0.06210.1342-0.02320.02490.2011-0.01480.124582.25676.809533.1033
176.06021.76954.03430.52321.1442.60840.0171-0.0501-0.1570.0730.08330.0221-0.0857-0.0611-0.06660.13630.04050.0370.15840.04480.14681.97573.055141.0971
186.1475-2.24533.77281.7379-2.58244.74430.07020.85770.3817-0.1682-0.3369-0.11920.05990.59730.15920.21240.00190.090.19370.01170.176592.096682.138936.4127
194.74070.60931.34320.38150.32951.3448-0.00830.70620.5944-0.3289-0.0819-0.0097-0.13310.45710.16160.1504-0.02120.01250.27720.00430.149787.440468.602528.9188
204.18280.84511.0021.48950.16372.6418-0.028-0.1713-0.1631-0.0284-0.0443-0.0209-0.14730.3863-0.0040.1414-0.01710.01640.1942-0.00190.127598.937165.092344.0312
215.5021-1.06110.83151.02530.460.6174-0.05930.1718-0.0382-0.03530.09160.0366-0.02970.1086-0.01940.1330.02510.00890.1630.09070.157972.564161.177928.8798
221.60330.731-0.18793.05440.35791.9566-0.06950.06420.2098-0.38590.1175-0.0096-0.2562-0.4792-0.13360.1289-0.0298-0.00540.24420.02060.14926.005774.158951.7016
230.7199-0.2446-0.52291.8187-0.83761.05670.1024-0.0157-0.0186-0.1033-0.07320.22220.19090.12810.0250.1008-0.0882-0.00270.154-0.02830.13346.271750.485670.3676
240.4479-1.9931.09758.3981-4.60232.5039-0.0570.1103-0.04760.3688-0.1484-0.0163-0.1561-0.05250.26010.1476-0.04170.00520.17590.00810.115613.588954.571667.4896
252.6194-0.0214-0.61151.8172-0.78241.45580.2492-0.1515-0.111-0.1580.29010.54560.0956-0.7006-0.125-0.036-0.0561-0.08290.3720.02470.14381.037560.436967.102
261.1218-0.77520.20064.6691-2.14481.03090.125-0.0563-0.09550.071-0.04740.2744-0.0528-0.1412-0.12350.1638-0.0423-0.02340.1995-0.06420.09246.928450.678357.4761
271.2554-1.43751.01785.2109-3.37935.3295-0.1086-0.28070.01310.1636-0.126-0.3516-0.06710.13830.14270.0823-0.01720.01760.12390.00640.085214.426338.100560.775
281.812-2.21041.36284.0006-1.68465.64140.304-0.3273-0.10250.2928-0.21420.62680.1350.0505-0.01120.1422-0.0060.04370.28160.00810.194117.086829.490473.5685
290.4191-0.80560.28062.0953-0.06280.8276-0.11680.22030.05880.2228-0.0872-0.28550.1032-0.3857-0.10360.0764-0.05170.06790.1908-0.02290.16615.993740.632896.5361
300.01870.3133-0.0861.6847-1.28271.2358-0.0782-0.04970.1353-0.29510.04170.342-0.266-0.2978-0.06270.0081-0.11890.05010.2523-0.00420.13866.278964.278977.8455
31-0.0014-0.13190.11344.4201-3.41722.49920.0327-0.02780.02570.2287-0.1314-0.0977-0.22540.19510.17440.1833-0.01270.01530.2308-0.01250.130513.648959.930981.0634
322.1516-2.42792.75184.3808-4.1225.1542-0.0158-0.1255-0.49120.09970.47920.72540.4211-0.4615-0.05840.19-0.0150.10830.2227-0.03690.22430.780350.060681.8723
338.12097.9258-1.33928.3768-1.77381.689-0.9949-0.32370.2199-0.9740.62371.22290.3085-0.69140.09710.3627-0.09970.10460.52490.05260.35821.347772.547373.0216
340.34281.2757-0.79185.6994-4.17383.1138-0.0150.11940.0796-0.05560.35890.55450.1251-0.3011-0.38720.1171-0.04240.03010.18250.01030.17725.172167.347790.2536
351.25331.4088-0.69954.3411-3.11432.3879-0.0156-0.2518-0.1698-0.0135-0.1126-0.126-0.01780.38570.10530.1345-0.00890.0190.1668-0.02110.12211.46854.099998.0444
361.35751.136-2.71962.6673-2.53495.1942-0.0526-0.06720.12060.09350.15520.0481-0.1114-0.3016-0.07940.1403-0.0395-0.04130.2022-0.0480.110115.576480.573981.9131
370.5935-0.3645-0.88110.22610.08321.17910.0717-0.0840.1401-0.11550.0364-0.02520.05310.0054-0.16150.2539-0.10950.00130.17410.01590.138458.8565109.457563.2699
382.8930.532-1.82570.0334-0.35111.01980.04190.0596-0.1823-0.0781-0.0909-0.04670.103-0.04760.07710.2646-0.0651-0.00480.1557-0.00360.115750.9543101.574670.7475
395.4276-1.4388-4.09353.28691.39197.19920.2189-0.4070.0810.3535-0.20860.1987-0.66410.2001-0.14810.3217-0.01280.00280.13550.01280.174360.4438113.794867.1139
403.36820.907-1.73810.8691-0.6720.82150.0745-0.21720.2894-0.06940.00660.0506-0.01530.1238-0.06350.2557-0.0244-0.03570.15580.0090.139746.8616105.56858.4641
415.31361.3552-0.83883.8768-0.16116.75430.02080.24220.2683-0.0477-0.26260.2215-0.0645-0.33810.23430.2279-0.09680.00530.26080.02040.142129.509797.67973.4211
420.9692-0.3649-1.00330.260.26631.55170.009-0.31510.0733-0.01890.1068-0.0408-0.09220.3122-0.12590.2427-0.1017-0.00290.138-0.00330.141558.9949108.70181.9973
434.40410.1637-1.94280.0134-0.22471.4097-0.14250.0148-0.1394-0.0170.06040.14620.122-0.01330.0660.1538-0.01430.00660.0967-0.02110.115457.4716104.331481.205
444.0545-0.7356-2.09980.62160.95141.49490.06160.19960.2942-0.03470.0218-0.1365-0.2247-0.0071-0.14810.2046-0.0203-0.04290.14660.01190.143264.4087108.509889.509
452.0144-1.5966-1.69061.66012.51714.61150.11350.11470.2265-0.03460.0694-0.1484-0.14080.2472-0.17210.2134-0.01030.00850.1091-0.00820.162980.597999.431281.8911
461.3802-0.1025-1.47870.1935-0.08841.8458-0.14640.07240.03960.05490.1042-0.020.3849-0.00260.00780.14150.0048-0.01110.1472-0.01990.094236.394825.381939.2019
473.75720.3123-3.3402-0.0274-0.2062.79540.0124-0.32940.0428-0.0390.08750.0034-0.06780.13510.0510.19150.07840.01180.18690.05420.130738.687429.424745.4398
480.9732-1.0636-0.18251.3915-0.68773.866-0.0310.6507-0.3126-0.37050.16970.38220.0956-0.63520.33980.2540.02370.0070.071-0.09270.075235.633125.790132.0745
493.6617-0.908-2.60410.57620.44211.8069-0.12740.3514-0.2305-0.1006-0.00870.0716-0.0524-0.20420.08550.2101-0.0645-0.01940.1494-0.01260.125540.892216.902243.1526
502.8047-2.5405-2.30322.6481.59372.35520.19880.0472-0.0456-0.1532-0.07290.1634-0.05550.0535-0.10210.1510.0264-0.03840.1485-0.01450.082231.017819.766260.7911
512.37160.39480.36630.47430.34830.2472-0.1114-0.10590.24470.08730.06960.0621-0.0209-0.06070.04030.1949-0.00760.03490.0951-0.01530.122639.686590.3904111.9831
523.70710.20933.4736-0.0597-0.0863.3150.08250.0015-0.0366-0.0359-0.02450.00480.08480.0036-0.12310.1590.04580.01860.1267-0.05490.146535.059285.2139101.2723
534.5751-0.41040.6131.64570.50210.6488-0.1302-0.5130.93170.012-0.18950.3134-0.0011-0.31240.18610.28-0.00590.01840.11120.05540.296529.605290.0394111.0499
544.2791-0.23312.41110.17370.27433.0008-0.08050.2010.1033-0.09830.0397-0.0223-0.3170.01790.05150.1833-0.0667-0.00770.11910.01750.153643.308298.6574106.0217
553.09972.24851.3441.88361.47321.4527-0.01230.0151-0.0309-0.05860.03530.0130.0439-0.2083-0.02440.15960.01340.06550.1387-0.00470.130731.010295.045387.4493
560.14030.2340.10322.11720.74370.52840.0060.05460.07880.0284-0.03250.09320.07330.11390.06070.128-0.0061-0.0360.17060.03180.110925.38678.239638.9274
570.0005-0.3589-0.27452.51462.26321.9992-0.09890.14810.01810.16330.1704-0.15970.0587-0.0115-0.13140.19290.0886-0.07910.12150.02510.165629.474376.198245.447
581.25210.4264-0.38872.4011-0.61532.0279-0.0609-0.15080.0677-0.4892-0.06280.4769-0.4403-0.05450.05960.18470.045-0.03490.1599-0.02720.114125.887979.118632.0305
590.23810.04870.24731.58981.95142.3399-0.273-0.1448-0.02560.00060.48930.0781-0.3728-0.2057-0.0450.0666-0.1190.00090.20230.03190.151617.071674.0343.0284
602.1821.49341.76553.12052.96593.4714-0.0783-0.0132-0.0068-0.32940.03330.0122-0.53110.03610.00850.1840.02470.01860.16820.03860.106119.754283.79660.6543
610.884-0.14170.23880.1333-0.13010.91030.06110.21930.01840.0023-0.02160.0528-0.12080.2992-0.06360.17760.0127-0.01970.1035-0.03410.15578.434189.356339.1894
624.91880.45614.87870.09920.34964.80880.07480.12540.31120.0587-0.08570.09370.24490.1844-0.06130.17670.05870.02650.1883-0.02630.132276.423785.218545.623
638.1672-1.9972.15770.7539-0.11963.6931-0.05050.65960.6256-0.04810.1706-0.1263-0.18880.60690.15220.228-0.002-0.03640.04660.07870.226279.215388.906432.0574
642.9647-0.33423.07660.6066-1.04443.9973-0.17930.26840.0649-0.13790.0542-0.10910.03360.16380.05470.2462-0.05390.0470.1605-0.0250.113774.151697.861243.1768
653.3909-0.93853.42810.8357-0.88194.40480.0545-0.1832-0.16630.0450.06050.0196-0.0474-0.16190.050.21870.03540.02050.12110.0040.091483.744995.173660.642
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 184 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 49 )
7X-RAY DIFFRACTION7chain 'B' and (resid 50 through 77 )
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 87 )
9X-RAY DIFFRACTION9chain 'B' and (resid 88 through 138 )
10X-RAY DIFFRACTION10chain 'B' and (resid 139 through 184 )
11X-RAY DIFFRACTION11chain 'C' and (resid 6 through 49 )
12X-RAY DIFFRACTION12chain 'C' and (resid 50 through 87 )
13X-RAY DIFFRACTION13chain 'C' and (resid 88 through 138 )
14X-RAY DIFFRACTION14chain 'C' and (resid 139 through 184 )
15X-RAY DIFFRACTION15chain 'D' and (resid 6 through 14 )
16X-RAY DIFFRACTION16chain 'D' and (resid 15 through 49 )
17X-RAY DIFFRACTION17chain 'D' and (resid 50 through 76 )
18X-RAY DIFFRACTION18chain 'D' and (resid 77 through 91 )
19X-RAY DIFFRACTION19chain 'D' and (resid 92 through 124 )
20X-RAY DIFFRACTION20chain 'D' and (resid 125 through 138 )
21X-RAY DIFFRACTION21chain 'D' and (resid 139 through 184 )
22X-RAY DIFFRACTION22chain 'E' and (resid 6 through 14 )
23X-RAY DIFFRACTION23chain 'E' and (resid 15 through 49 )
24X-RAY DIFFRACTION24chain 'E' and (resid 50 through 76 )
25X-RAY DIFFRACTION25chain 'E' and (resid 77 through 91 )
26X-RAY DIFFRACTION26chain 'E' and (resid 92 through 138 )
27X-RAY DIFFRACTION27chain 'E' and (resid 139 through 159 )
28X-RAY DIFFRACTION28chain 'E' and (resid 160 through 184 )
29X-RAY DIFFRACTION29chain 'F' and (resid 6 through 14 )
30X-RAY DIFFRACTION30chain 'F' and (resid 15 through 49 )
31X-RAY DIFFRACTION31chain 'F' and (resid 50 through 77 )
32X-RAY DIFFRACTION32chain 'F' and (resid 78 through 87 )
33X-RAY DIFFRACTION33chain 'F' and (resid 88 through 96 )
34X-RAY DIFFRACTION34chain 'F' and (resid 97 through 124 )
35X-RAY DIFFRACTION35chain 'F' and (resid 125 through 138 )
36X-RAY DIFFRACTION36chain 'F' and (resid 139 through 184 )
37X-RAY DIFFRACTION37chain 'G' and (resid 6 through 42 )
38X-RAY DIFFRACTION38chain 'G' and (resid 43 through 76 )
39X-RAY DIFFRACTION39chain 'G' and (resid 77 through 91 )
40X-RAY DIFFRACTION40chain 'G' and (resid 92 through 159 )
41X-RAY DIFFRACTION41chain 'G' and (resid 160 through 184 )
42X-RAY DIFFRACTION42chain 'H' and (resid 6 through 49 )
43X-RAY DIFFRACTION43chain 'H' and (resid 50 through 87 )
44X-RAY DIFFRACTION44chain 'H' and (resid 88 through 138 )
45X-RAY DIFFRACTION45chain 'H' and (resid 139 through 184 )
46X-RAY DIFFRACTION46chain 'I' and (resid 6 through 49 )
47X-RAY DIFFRACTION47chain 'I' and (resid 50 through 76 )
48X-RAY DIFFRACTION48chain 'I' and (resid 77 through 91 )
49X-RAY DIFFRACTION49chain 'I' and (resid 92 through 138 )
50X-RAY DIFFRACTION50chain 'I' and (resid 139 through 184 )
51X-RAY DIFFRACTION51chain 'J' and (resid 6 through 42 )
52X-RAY DIFFRACTION52chain 'J' and (resid 43 through 77 )
53X-RAY DIFFRACTION53chain 'J' and (resid 78 through 96 )
54X-RAY DIFFRACTION54chain 'J' and (resid 97 through 138 )
55X-RAY DIFFRACTION55chain 'J' and (resid 139 through 184 )
56X-RAY DIFFRACTION56chain 'K' and (resid 6 through 49 )
57X-RAY DIFFRACTION57chain 'K' and (resid 50 through 76 )
58X-RAY DIFFRACTION58chain 'K' and (resid 77 through 91 )
59X-RAY DIFFRACTION59chain 'K' and (resid 92 through 138 )
60X-RAY DIFFRACTION60chain 'K' and (resid 139 through 184 )
61X-RAY DIFFRACTION61chain 'L' and (resid 6 through 49 )
62X-RAY DIFFRACTION62chain 'L' and (resid 50 through 76 )
63X-RAY DIFFRACTION63chain 'L' and (resid 77 through 91 )
64X-RAY DIFFRACTION64chain 'L' and (resid 92 through 138 )
65X-RAY DIFFRACTION65chain 'L' and (resid 139 through 184 )

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万見について

-
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