[日本語] English
万見
- PDB-5c8j: A YidC-like protein in the archaeal plasma membrane -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 5c8j
タイトルA YidC-like protein in the archaeal plasma membrane
要素
  • Antibody fragment, heavy chain
  • Antibody fragment, light chain
  • Protein MJ0480
キーワードMEMBRANE PROTEIN / membrane protein insertase
機能・相同性
機能・相同性情報


small molecule binding / plasma membrane
類似検索 - 分子機能
Protein MJ0935 / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein EMC3/TMCO1-like / Integral membrane protein DUF106 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
類似検索 - ドメイン・相同性
Uncharacterized protein MJ0480
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Methanocaldococcus jannaschii (メタン生成菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.502 Å
データ登録者Borowska, M.T. / Dominik, P.K. / Anghel, S.A. / Kossiakoff, A.A. / Keenan, R.J.
資金援助 米国, 3件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM086487 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U01 GM094588 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM087519 米国
引用ジャーナル: Structure / 年: 2015
タイトル: A YidC-like Protein in the Archaeal Plasma Membrane.
著者: Borowska, M.T. / Dominik, P.K. / Anghel, S.A. / Kossiakoff, A.A. / Keenan, R.J.
履歴
登録2015年6月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02015年9月2日Provider: repository / タイプ: Initial release
改定 1.12015年9月16日Group: Database references
改定 1.22015年9月23日Group: Derived calculations
改定 1.32017年9月13日Group: Author supporting evidence / Derived calculations / カテゴリ: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
改定 1.42019年12月25日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.52024年10月9日Group: Data collection / Database references / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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

-
集合体

登録構造単位
A: Antibody fragment, heavy chain
B: Antibody fragment, light chain
C: Antibody fragment, heavy chain
D: Antibody fragment, light chain
E: Antibody fragment, heavy chain
F: Antibody fragment, light chain
G: Antibody fragment, heavy chain
H: Antibody fragment, light chain
I: Protein MJ0480
J: Protein MJ0480
K: Protein MJ0480
L: Protein MJ0480
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)292,70013
ポリマ－292,18912
非ポリマー5111
水00
1
A: Antibody fragment, heavy chain
B: Antibody fragment, light chain
I: Protein MJ0480


分子量 (理論値)分子数
合計 (水以外)73,0473
ポリマ－73,0473
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Antibody fragment, heavy chain
D: Antibody fragment, light chain
L: Protein MJ0480
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)73,5584
ポリマ－73,0473
非ポリマー5111
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Antibody fragment, heavy chain
F: Antibody fragment, light chain
J: Protein MJ0480


分子量 (理論値)分子数
合計 (水以外)73,0473
ポリマ－73,0473
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Antibody fragment, heavy chain
H: Antibody fragment, light chain
K: Protein MJ0480


分子量 (理論値)分子数
合計 (水以外)73,0473
ポリマ－73,0473
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)180.250, 251.420, 96.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
要素

#1: 抗体
Antibody fragment, heavy chain


分子量: 25591.508 Da / 分子数: 4 / 由来タイプ: 組換発現
詳細: OBTAINED BY PHAGE DISPLAY FROM A LIBRARY OF HUMAN IGG. ANTIBODY FRAGMENT; THE CDRS ARE COMPLETELY SYNTHETIC
由来: (組換発現) Homo sapiens (ヒト) / プラスミド: RH2.2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21-Gold(DE3)
#2: 抗体
Antibody fragment, light chain


分子量: 23298.830 Da / 分子数: 4 / 由来タイプ: 組換発現
詳細: OBTAINED BY PHAGE DISPLAY FROM A LIBRARY OF HUMAN IGG. ANTIBODY FRAGMENT; THE CDRS ARE COMPLETELY SYNTHETIC
由来: (組換発現) Homo sapiens (ヒト) / プラスミド: RH2.2 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21-Gold(DE3)
#3: タンパク質
Protein MJ0480


分子量: 24156.955 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (メタン生成菌)
株: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
遺伝子: MJ0480 / プラスミド: pET28a / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q57904
#4: 糖 ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


タイプ: D-saccharide / 分子量: 510.615 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C24H46O11 / コメント: 可溶化剤*YM
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.73 Å3/Da / 溶媒含有率: 66.99 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.08 M calcium acetate and 18% PEG3350

-
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: APS / ビームライン: 24-ID-E / 波長: 0.9791 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2013年8月12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: 0.9791 Å / 相対比: 1
反射解像度: 3.5→76.4 Å / Num. obs: 55459 / % possible obs: 99 % / 冗長度: 6.8 % / Net I/σ(I): 8.9

-
位相決定

位相決定手法: 分子置換

-
解析

ソフトウェア
名称バージョン分類
PHENIX精密化
xia2データ削減
PHASER位相決定
PDB_EXTRACT3.15データ抽出
精密化構造決定の手法: 分子置換 / 解像度: 3.502→89.774 Å / SU ML: 0.51 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 32.56 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3024 2446 5.08 %
Rwork0.253 45725 -
obs0.2555 48171 86.24 %
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
原子変位パラメータBiso max: 283.73 Å2 / Biso mean: 114.6489 Å2 / Biso min: 34.92 Å2
精密化ステップサイクル: final / 解像度: 3.502→89.774 Å
タンパク質核酸リガンド溶媒全体
原子数17808 0 81 0 17889
Biso mean--195.98 --
残基数----2308
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00218336
X-RAY DIFFRACTIONf_angle_d0.49824990
X-RAY DIFFRACTIONf_chiral_restr0.0392834
X-RAY DIFFRACTIONf_plane_restr0.0043083
X-RAY DIFFRACTIONf_dihedral_angle_d11.74610743
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.502-3.57350.4962350.353774477924
3.5735-3.65120.3607770.32321310138743
3.6512-3.73620.4005950.33861757185257
3.7362-3.82960.35731140.30982159227370
3.8296-3.93310.33261400.29982505264582
3.9331-4.04890.38131440.29632915305994
4.0489-4.17960.33031760.285830813257100
4.1796-4.3290.30971890.259830303219100
4.329-4.50230.35411610.233930763237100
4.5023-4.70720.25431580.214430973255100
4.7072-4.95530.26751740.203730713245100
4.9553-5.26580.2381620.20631283290100
5.2658-5.67230.24331450.214131593304100
5.6723-6.2430.27981600.229431193279100
6.243-7.1460.3251660.25231493315100
7.146-9.00190.27491740.24253181335599
9.0019-89.80370.30421760.27943244342097
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)
15.17284.3087-0.49666.0789-0.36174.5591-0.3706-0.2174-0.4203-1.1520.0498-0.57580.55320.18220.33451.2296-0.07840.07960.44670.12110.8221-18.83343.6084-73.9227
27.55652.54550.88337.764-1.62374.25380.5045-0.93630.85281.17990.3322-0.4424-0.72180.34910.30541.169-0.0156-0.12520.6861-0.17490.756-19.13955.6292-56.9969
31.53041.54250.81363.27690.77181.2784-0.8738-0.2991-0.6952-1.14020.08960.30820.06350.16750.21051.3438-0.22320.33680.63510.08720.719-27.872228.9467-78.6692
40.5182-1.69660.13956.62511.24622.7388-1.05390.479-1.3659-1.44650.3795-0.29551.3398-0.14360.31611.6389-0.53530.45010.35140.02410.8967-44.51999.6549-77.2348
59.32580.6313-2.60583.3592-3.4947.2426-0.84750.3086-0.1166-0.10240.6676-0.18120.0202-0.46940.24781.0433-0.15750.1340.5636-0.11660.5527-40.957219.0325-80.3534
65.33310.9536-1.21958.2534-0.43755.16810.2033-0.79570.18431.0304-0.4291-1.02410.32110.49530.14580.8275-0.1427-0.1060.7170.17390.3761-25.395136.942-51.6022
73.39093.29681.64383.5061.5523.6409-0.1587-0.53490.07080.0303-0.59830.02170.1252-0.22020.85191.13450.05250.05650.40670.02380.7632-32.763320.8876-64.4317
84.5683-0.1828-0.49765.1871.66234.74270.643-0.0724-1.0150.1303-0.4769-1.1330.6578-0.3429-0.02911.0888-0.09950.26670.5444-0.00610.997-35.04623.7478-70.2696
93.3311.8973.11378.17523.58467.3230.21810.4548-0.2852-0.4728-0.66070.12260.8270.64380.27881.26330.15450.1620.86170.18570.363-27.1324120.6829-67.305
102.9846-2.10870.49214.81881.54682.70640.042-0.02140.36970.21880.1315-0.2-0.6350.45690.04311.0634-0.05850.15410.48680.17420.3429-19.1046123.6816-71.0976
112.79410.0173-1.48162.16481.11452.9710.40050.5697-0.2777-0.5026-0.7531-0.83220.0151-0.4257-0.09291.07990.0852-0.02370.46410.40280.7343-26.1409125.0285-74.7366
122.97193.00280.8984.77323.05992.9611-0.95330.26381.93191.0652-0.7079-0.037-2.1192-0.50171.56741.14610.2167-0.01550.6668-0.02540.8448-49.252157.079-67.0074
134.8592-0.74313.08743.5091-0.8878.4286-0.50090.35540.14820.9625-0.31510.3137-0.1192-0.18930.71751.1098-0.01440.0170.4034-0.0570.5785-44.1265147.2964-63.2452
145.129-2.631.15566.7498-0.673.6080.20980.14650.4512-1.3983-0.4773-1.3215-0.31640.4110.1781.34130.10640.29170.81910.32540.635-28.8088129.3947-91.1195
155.6326-3.70611.166.0038-0.31712.71360.62860.66970.8698-0.7184-0.6754-0.1129-0.24810.22710.13011.3573-0.07770.06290.82950.23540.7028-27.2519130.038-91.1035
162.3119-1.47150.10574.79833.26355.1682-0.22210.23470.6802-1.11350.1771-0.1994-1.01880.89660.64931.40550.1574-0.05280.50370.17060.6805-40.3319157.0446-74.7401
173.0155-0.12190.01781.56230.76541.8177-0.82720.5750.7837-0.55250.03290.2081-1.1652-0.11840.42161.3827-0.0109-0.26640.76330.33840.9922-37.6551155.0646-76.4487
182.79750.85562.04923.83871.85653.78810.1065-0.29270.7026-1.0787-0.24840.3222-1.0612-1.30050.75011.52740.2716-0.10530.56720.11510.8288-39.7921165.8272-70.3872
194.9592-3.63382.87739.7418-3.60573.86170.07980.27350.5795-0.6422-0.2187-1.1652-0.44450.20020.15971.50560.06070.00390.21430.0940.3644-31.6866121.515-51.1564
204.22781.46622.19484.0446-1.12912.19160.6431-0.0869-0.0387-0.618-0.4289-0.2587-0.1999-0.4893-0.07251.51190.01760.21260.7478-0.03930.4695-37.3779111.8974-49.5351
211.9290.5932.35813.3561-1.11914.0041-0.401-0.38620.45240.03070.1774-0.0415-0.0866-0.445-0.70981.5990.07710.27080.60050.1280.2685-37.4633120.4984-44.8035
220.9847-0.29251.83030.0839-0.53613.40040.703-0.1002-1.97340.831.36780.27151.249-0.1355-1.27141.4490.3828-0.06160.67380.06072.2432-35.754894.965-43.3205
231.14660.8887-0.4113.0080.11460.1390.5245-0.1630.2134-0.4349-0.54680.24530.1459-0.1052-0.28511.770.11180.3170.44630.23470.183-28.0697129.6604-43.5101
243.1517-3.57121.05046.8191-4.4934.3808-0.1437-0.36821.43142.4934-0.9017-1.3095-1.60471.02161.6451.9317-0.39070.2370.57940.37730.9215-9.8759145.8657-28.1488
254.2283-0.07592.22081.8428-1.47064.85260.3267-0.32941.20410.092-0.2349-0.20960.58630.4491-0.50141.23080.20050.04960.65570.03420.4998-20.7756136.6112-37.7038
261.9613-0.3891.57193.5275-2.1694.164-0.101-0.0889-0.08390.3847-0.9131-1.3446-1.70621.42540.47241.42120.42230.23632.06841.12620.5226-5.6404142.0787-31.8807
279.60022.48153.25463.9877-1.19645.891-0.59730.63160.2259-0.0067-0.0149-0.7737-0.92421.91821.02511.3122-0.0350.14831.02260.29680.7323-14.0811143.3779-42.9434
282.32321.7592-2.35883.707-2.30594.05290.4427-0.64290.0391.55-0.459-0.48791.26130.57780.22831.9763-0.00680.20410.63520.36240.3937-27.8592106.9451-28.5259
294.69430.32992.82111.04261.09733.1850.7392-0.9135-1.06231.0869-0.5046-0.53870.32360.47080.17251.83590.04670.00890.8710.28250.5975-25.8476106.7083-26.0964
309.74411.17473.71396.02310.96425.1480.0668-1.7909-0.06421.7043-0.98950.6756-0.88520.38330.52021.0710.01120.34381.04120.13630.5844-38.2173108.926-33.2308
315.2899-0.3462-0.97395.9114.26923.1851-0.9713-0.6102-0.42841.78470.0549-0.4541-1.1117-0.3885-0.01431.31-0.138-0.19090.95960.14680.4717-15.0184125.5839-18.5718
321.0047-0.14571.5342.8717-1.76883.328-0.07661.15860.2942-0.58190.343-0.3299-0.0960.18351.09011.1044-0.92210.16721.10650.44490.7435-19.2933152.0117-31.6705
332.6013-0.29961.19372.5549-1.55385.70950.31290.1083-0.5791-0.1126-0.56470.15480.054-0.43970.17771.1947-0.11860.21030.90370.04410.5968-21.3967137.956-21.5901
347.6017-1.45461.34333.9063-1.20812.4898-1.1416-1.69141.55870.52870.2951-0.1021-1.23810.44570.47481.56690.12110.01120.9227-0.31780.7728-21.1616148.0838-20.0432
354.8849-1.49580.9076.5421-1.05293.3977-0.56430.19490.03790.9172-0.1878-0.4576-0.2604-0.32811.0641.1678-0.01760.04350.8635-0.14490.5966-29.816650.6662-93.272
363.6438-0.7781.07063.66752.84496.56240.03210.3913-0.25020.8043-0.84110.52711.4593-1.93780.92091.5289-0.40770.00931.2683-0.22610.4915-36.976551.1924-95.9283
372.2636-1.6176-0.49881.53210.79351.26670.53730.02480.1933-0.71970.24690.7437-0.0757-1.5086-0.03872.01310.1328-1.13291.96491.00943.1649-34.337770.7384-100.7145
380.56990.74980.56915.0248-1.3633.7892-0.21550.4319-0.179-0.8616-0.7448-1.74121.02730.38210.53771.1003-0.07930.33861.144-0.01460.9172-19.236132.0379-105.1549
396.2332-0.3116-0.57727.3535-2.64849.3239-00.1432-0.2305-1.0862-0.8682-0.49310.51571.17940.95941.5669-0.27030.35891.0702-0.20090.7572-16.330728.5795-106.883
404.88553.4188-1.47743.61231.68156.6087-1.9801-0.1744-1.14682.62561.51440.06982.31640.44581.42022.19390.52310.68391.09820.27880.8916-7.668124.202-104.4334
412.7407-2.6834-1.04682.66131.0552.49261.06890.40810.54330.012-0.52160.4311-3.0151-0.7876-0.6362.98890.54050.06430.97240.20060.7989-26.61854.477-121.7195
421.01250.029-0.39221.4121-2.23314.98480.43731.1930.2033-1.3885-0.5729-0.3871-1.0638-0.2431-1.00162.43750.00630.58560.67350.4523-0.7006-25.365160.8221-112.9146
434.58861.7128-3.30651.65830.80426.1587-0.47110.3799-0.1307-0.1212-0.1639-1.4839-0.3068-0.3060.21791.49580.04920.13720.79940.07770.6296-20.978243.2049-117.0819
444.3831-0.0085-1.1234.452-5.24566.4858-1.47581.2345-0.5503-0.62480.58560.25810.659-2.0951-0.05032.8011-0.64460.27791.84290.04350.7661-19.485828.91-126.8121
451.9973-0.37120.29991.9032-0.31222.3549-1.26740.4609-0.97421.462-0.0040.38371.7649-0.003-0.07523.2326-0.32920.82951.2478-0.26570.9122-20.166524.4412-119.5491
461.4616-0.6350.75433.20181.76453.4236-0.9150.7433-0.91690.1597-0.22660.41531.4752-0.0476-0.91112.4522-0.09581.00291.3272-0.8351.1757-14.611918.6013-127.4266
479.01463.46111.08765.0979-2.18583.52040.3494-1.8115-0.16531.85520.03-0.7665-0.1883-0.29530.07481.3198-0.3012-0.71530.6588-0.19231.2321-0.685168.6476-55.8831
487.56552.2769-0.63473.994-0.09622.09340.2465-0.6661-1.12340.58960.00430.06430.2672-0.18931.80270.6729-0.194-0.80480.66120.20540.9232.773777.2412-60.4829
496.3251.9627-2.59027.17350.48223.588-0.95870.6384-0.9793-0.4743-0.719-0.25961.02150.13620.92271.1088-0.13910.17280.64030.13711.0491-8.395162.2745-68.0236
503.89072.8956-0.77159.0912-4.2262.90211.08570.00850.35580.4999-0.4131.4562-0.2959-0.4522-0.35880.70510.14360.14250.43090.02491.3783-13.998285.9388-67.307
515.40393.53030.20586.6749-4.05269.10661.2159-1.16920.51261.5904-0.84081.5255-0.95420.3945-0.66171.0024-0.0830.33230.5075-0.12691.263-11.320898.1492-67.9114
521.32550.6854-1.7286.0983-3.29453.26470.37140.8312-0.4804-1.38340.46921.5511.4048-0.3669-0.1810.78680.0706-0.29580.76230.11541.0224-11.488586.888-84.1248
532.32123.55390.5026.58561.27390.32610.3964-1.05690.1020.7564-0.1142-1.25970.6231-0.28110.00460.8113-1.25230.52632.8884-1.44942.0961-61.296689.7071-48.0853
546.880.67013.4724.85450.37369.00670.882-0.2287-2.01071.61950.12041.41271.3294-2.2727-0.30331.2408-0.33110.03851.36410.09761.318-54.03180.002-55.6335
553.6795-0.74452.45414.71165.34439.54120.94261.08830.17130.9728-0.61130.4861-0.3992-1.4879-0.30071.024-0.18790.3270.9943-0.1240.768-44.765787.7601-62.6441
562.87920.7016-2.3144.26160.22473.1186-0.2433-0.72520.62830.6039-1.1841.17790.2333-0.89560.6461.23470.1488-0.31761.2356-0.27640.6965-44.714768.9581-78.4324
571.1242.9245-1.61398.7143-3.23733.23220.80490.36361.76290.12540.00191.2567-0.8439-1.4916-0.77940.82330.39720.11321.051-0.14261.4629-44.529287.8761-83.73
580.0982-0.0763-0.06090.0641-0.00481.09370.04610.19890.03930.0012-0.27950.0270.1458-0.1709-0.41151.71771.2021-0.78225.5816-1.60211.8803-60.248374.7372-96.5212
594.3472-5.8131-1.68379.39413.17691.571.0768-0.62411.9724-1.93910.3089-0.5807-1.58510.2029-0.61852.9560.6650.33161.4249-0.6841.6175-47.587384.7015-92.3812
605.2698-1.0224-2.53979.15025.73676.1267-0.10540.95190.0349-0.7248-0.36821.361-0.0771-1.01040.05370.9247-0.008-0.06371.3167-0.06480.748-49.410880.0523-83.3569
612.2554-4.22280.92889.0194-4.44176.95510.34470.15470.4354-0.94670.6562-0.1953-1.1333-1.46910.12270.77660.12720.14391.1459-0.52841.9227-45.80896.2591-65.9489
628.81295.18583.31225.29020.51562.89610.8206-1.1652-2.4335-0.70770.7568-0.97081.69580.9388-1.19651.25630.1501-0.17391.0855-0.33722.1251-44.492177.4665-60.4552
636.8691-3.9054-0.60072.14050.25241.7444-0.43821.4030.1623-1.5557-0.6382-1.43140.4852-0.1833-0.16731.16340.11420.7540.36240.12621.1422-1.10998.3117-87.3615
648.3559-4.8144-2.52583.16621.89593.17570.26690.3411-1.74511.6214-0.24570.59570.79680.39330.07171.09610.1044-0.05240.751-0.05871.31812.056694.0384-81.0439
653.43051.00511.30832.48820.48191.33360.06120.3419-0.3355-0.1629-0.5043-0.91920.0354-0.0584-0.13430.4953-0.15360.06590.40760.04670.4116-14.065289.4775-76.09
666.93032.7115-0.61336.87582.56925.51810.7922-0.8158-0.02280.8162-0.53271.0174-0.29970.5941-0.31031.4-0.04430.09390.57710.20260.9509-11.062675.6832-65.8653
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 102 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 117 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 142 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 163 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 232 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 76 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 77 through 140 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 141 through 215 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 36 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 37 through 102 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 103 through 141 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 142 through 161 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 162 through 234 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 64 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 65 through 103 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 104 through 151 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 152 through 173 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 174 through 215 )D0
19X-RAY DIFFRACTION19chain 'E' and (resid 4 through 20 )E0
20X-RAY DIFFRACTION20chain 'E' and (resid 21 through 86 )E0
21X-RAY DIFFRACTION21chain 'E' and (resid 87 through 102 )E0
22X-RAY DIFFRACTION22chain 'E' and (resid 103 through 117 )E0
23X-RAY DIFFRACTION23chain 'E' and (resid 118 through 142 )E0
24X-RAY DIFFRACTION24chain 'E' and (resid 143 through 161 )E0
25X-RAY DIFFRACTION25chain 'E' and (resid 162 through 195 )E0
26X-RAY DIFFRACTION26chain 'E' and (resid 196 through 210 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 211 through 233 )E0
28X-RAY DIFFRACTION28chain 'F' and (resid 2 through 64 )F0
29X-RAY DIFFRACTION29chain 'F' and (resid 65 through 91 )F0
30X-RAY DIFFRACTION30chain 'F' and (resid 92 through 103 )F0
31X-RAY DIFFRACTION31chain 'F' and (resid 104 through 116 )F0
32X-RAY DIFFRACTION32chain 'F' and (resid 117 through 129 )F0
33X-RAY DIFFRACTION33chain 'F' and (resid 130 through 173 )F0
34X-RAY DIFFRACTION34chain 'F' and (resid 174 through 214 )F0
35X-RAY DIFFRACTION35chain 'G' and (resid 4 through 43 )G0
36X-RAY DIFFRACTION36chain 'G' and (resid 44 through 102 )G0
37X-RAY DIFFRACTION37chain 'G' and (resid 103 through 117 )G0
38X-RAY DIFFRACTION38chain 'G' and (resid 118 through 152 )G0
39X-RAY DIFFRACTION39chain 'G' and (resid 153 through 195 )G0
40X-RAY DIFFRACTION40chain 'G' and (resid 196 through 232 )G0
41X-RAY DIFFRACTION41chain 'H' and (resid 2 through 19 )H0
42X-RAY DIFFRACTION42chain 'H' and (resid 20 through 64 )H0
43X-RAY DIFFRACTION43chain 'H' and (resid 65 through 140 )H0
44X-RAY DIFFRACTION44chain 'H' and (resid 141 through 151 )H0
45X-RAY DIFFRACTION45chain 'H' and (resid 152 through 189 )H0
46X-RAY DIFFRACTION46chain 'H' and (resid 190 through 214 )H0
47X-RAY DIFFRACTION47chain 'I' and (resid 5 through 44 )I0
48X-RAY DIFFRACTION48chain 'I' and (resid 45 through 121 )I0
49X-RAY DIFFRACTION49chain 'I' and (resid 122 through 143 )I0
50X-RAY DIFFRACTION50chain 'I' and (resid 144 through 161 )I0
51X-RAY DIFFRACTION51chain 'I' and (resid 162 through 175 )I0
52X-RAY DIFFRACTION52chain 'I' and (resid 176 through 194 )I0
53X-RAY DIFFRACTION53chain 'J' and (resid 5 through 22 )J0
54X-RAY DIFFRACTION54chain 'J' and (resid 23 through 121 )J0
55X-RAY DIFFRACTION55chain 'J' and (resid 122 through 161 )J0
56X-RAY DIFFRACTION56chain 'J' and (resid 162 through 175 )J0
57X-RAY DIFFRACTION57chain 'J' and (resid 176 through 194 )J0
58X-RAY DIFFRACTION58chain 'K' and (resid 5 through 22 )K0
59X-RAY DIFFRACTION59chain 'K' and (resid 23 through 42 )K0
60X-RAY DIFFRACTION60chain 'K' and (resid 43 through 161 )K0
61X-RAY DIFFRACTION61chain 'K' and (resid 162 through 175 )K0
62X-RAY DIFFRACTION62chain 'K' and (resid 176 through 194 )K0
63X-RAY DIFFRACTION63chain 'L' and (resid 5 through 98 )L0
64X-RAY DIFFRACTION64chain 'L' and (resid 99 through 130 )L0
65X-RAY DIFFRACTION65chain 'L' and (resid 131 through 161 )L0
66X-RAY DIFFRACTION66chain 'L' and (resid 162 through 194 )L0

+
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

+
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