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- PDB-4ovm: Crystal structure of SgcJ protein from Streptomyces carzinostaticus -

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基本情報

登録情報
データベース: PDB / ID: 4ovm
タイトルCrystal structure of SgcJ protein from Streptomyces carzinostaticus
要素uncharacterized protein SgcJ
キーワードUNKNOWN FUNCTION / neocarzinostatin biosynthesis / unknown funciton / PSI-biology / Midwest Center for Structural Genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro / Structural Genomics
機能・相同性Domain of unknown function DUF4440 / Domain of unknown function (DUF4440) / Steroid delta5-4-isomerase / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DUF4440 domain-containing protein
機能・相同性情報
生物種Streptomyces carzinostaticus subsp. neocarzinostaticus (バクテリア)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2.719 Å
データ登録者Chang, C. / Bigelow, L. / Clancy, S. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Babnigg, G. ...Chang, C. / Bigelow, L. / Clancy, S. / Bingman, C.A. / Yennamalli, R. / Lohman, J.R. / Ma, M. / Shen, B. / Phillips Jr., G.N. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
引用ジャーナル: J.Antibiot. / : 2016
タイトル: Crystal structure of SgcJ, an NTF2-like superfamily protein involved in biosynthesis of the nine-membered enediyne antitumor antibiotic C-1027.
著者: Huang, T. / Chang, C.Y. / Lohman, J.R. / Rudolf, J.D. / Kim, Y. / Chang, C. / Yang, D. / Ma, M. / Yan, X. / Crnovcic, I. / Bigelow, L. / Clancy, S. / Bingman, C.A. / Yennamalli, R.M. / ...著者: Huang, T. / Chang, C.Y. / Lohman, J.R. / Rudolf, J.D. / Kim, Y. / Chang, C. / Yang, D. / Ma, M. / Yan, X. / Crnovcic, I. / Bigelow, L. / Clancy, S. / Bingman, C.A. / Yennamalli, R.M. / Babnigg, G. / Joachimiak, A. / Phillips, G.N. / Shen, B.
履歴
登録2013年11月20日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年12月25日Provider: repository / タイプ: Initial release
改定 1.12014年1月22日Group: Structure summary
改定 1.22014年4月23日Group: Other / Structure summary
改定 1.32014年8月6日Group: Database references / Structure summary
改定 1.42015年2月25日Group: Derived calculations
改定 1.52016年11月2日Group: Database references / Other / Structure summary
改定 1.62017年9月27日Group: Derived calculations / カテゴリ: pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
改定 1.72023年3月22日Group: Database references / Structure summary / カテゴリ: audit_author / database_2
Item: _audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.82024年11月6日Group: Data collection / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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: uncharacterized protein SgcJ
B: uncharacterized protein SgcJ
C: uncharacterized protein SgcJ
D: uncharacterized protein SgcJ
E: uncharacterized protein SgcJ
F: uncharacterized protein SgcJ
G: uncharacterized protein SgcJ
H: uncharacterized protein SgcJ
I: uncharacterized protein SgcJ
J: uncharacterized protein SgcJ


分子量 (理論値)分子数
合計 (水以外)156,30710
ポリマ-156,30710
非ポリマー00
18010
1
A: uncharacterized protein SgcJ
B: uncharacterized protein SgcJ


分子量 (理論値)分子数
合計 (水以外)31,2612
ポリマ-31,2612
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-12 kcal/mol
Surface area11580 Å2
手法PISA
2
C: uncharacterized protein SgcJ
D: uncharacterized protein SgcJ


分子量 (理論値)分子数
合計 (水以外)31,2612
ポリマ-31,2612
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-12 kcal/mol
Surface area11490 Å2
手法PISA
3
E: uncharacterized protein SgcJ
F: uncharacterized protein SgcJ


分子量 (理論値)分子数
合計 (水以外)31,2612
ポリマ-31,2612
非ポリマー00
181
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-13 kcal/mol
Surface area11520 Å2
手法PISA
4
G: uncharacterized protein SgcJ
H: uncharacterized protein SgcJ


分子量 (理論値)分子数
合計 (水以外)31,2612
ポリマ-31,2612
非ポリマー00
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-15 kcal/mol
Surface area11170 Å2
手法PISA
5
I: uncharacterized protein SgcJ
J: uncharacterized protein SgcJ


分子量 (理論値)分子数
合計 (水以外)31,2612
ポリマ-31,2612
非ポリマー00
181
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-14 kcal/mol
Surface area10780 Å2
手法PISA
単位格子
Length a, b, c (Å)98.318, 52.827, 131.796
Angle α, β, γ (deg.)90.000, 90.140, 90.000
Int Tables number4
Space group name H-MP1211

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要素

#1: タンパク質
uncharacterized protein SgcJ


分子量: 15630.715 Da / 分子数: 10 / 由来タイプ: 組換発現
由来: (組換発現) Streptomyces carzinostaticus subsp. neocarzinostaticus (バクテリア)
プラスミド: pMCSG57 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)magic / 参照: UniProt: Q84HC7
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 10 / 由来タイプ: 天然 / : H2O
Has protein modificationY

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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: 2.24 Å3/Da / 溶媒含有率: 45.01 %
結晶化温度: 289 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.2 M Sodium Formate, 20% w/v PEG 3350 / PH範囲: 6.0-7.0

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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: APS / ビームライン: 19-ID / 波長: 0.97935 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2012年8月3日
放射モノクロメーター: Si(111) double crystal / 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: 0.97935 Å / 相対比: 1
反射解像度: 2.72→50 Å / Num. all: 36971 / Num. obs: 36879 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / 冗長度: 7.1 % / Biso Wilson estimate: 43.53 Å2 / Rmerge(I) obs: 0.084 / Χ2: 0.906 / Net I/av σ(I): 21.801 / Net I/σ(I): 11.5 / Num. measured all: 262129
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.72-2.777.20.9592.7118260.922100
2.77-2.827.20.88318170.903100
2.82-2.877.20.7718210.883100
2.87-2.937.20.64918640.89100
2.93-2.997.20.47118050.879100
2.99-3.067.20.36218280.907100
3.06-3.147.20.2918570.885100
3.14-3.227.20.22417910.875100
3.22-3.327.20.17918680.845100
3.32-3.437.20.1318130.873100
3.43-3.557.20.11518580.886100
3.55-3.697.20.09818240.901100
3.69-3.867.20.08318420.95799.9
3.86-4.067.10.07118680.941100
4.06-4.327.10.06618471.045100
4.32-4.657.10.06118551.028100
4.65-5.1270.05918520.968100
5.12-5.866.80.05318910.857100
5.86-7.386.90.0518770.897100
7.38-506.60.04618750.77995.4

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解析

ソフトウェア
名称バージョン分類NB
HKL-3000データ削減
PHENIX(phenix.refine: 1.8.1_1168)精密化
HKL-3000位相決定
SCALEPACKデータスケーリング
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.719→37.992 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / 交差検証法: FREE R-VALUE / σ(F): 0 / 位相誤差: 28.27 / 立体化学のターゲット値: MLHL
Rfactor反射数%反射Selection details
Rfree0.2562 1940 5.91 %Random
Rwork0.2165 30861 --
obs0.2189 32801 88.58 %-
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: 224.37 Å2 / Biso mean: 71.7697 Å2 / Biso min: 22.32 Å2
精密化ステップサイクル: LAST / 解像度: 2.719→37.992 Å
タンパク質核酸リガンド溶媒全体
原子数9230 0 0 10 9240
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.0029475
X-RAY DIFFRACTIONf_angle_d0.64812935
X-RAY DIFFRACTIONf_chiral_restr0.0421452
X-RAY DIFFRACTIONf_plane_restr0.0031673
X-RAY DIFFRACTIONf_dihedral_angle_d10.7363270
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7188-2.78680.4102630.33351011107440
2.7868-2.86210.3278740.32881287136153
2.8621-2.94630.35321060.32551732183870
2.9463-3.04140.35041370.30182169230689
3.0414-3.150.35051410.26832351249294
3.15-3.27610.28311560.2522436259298
3.2761-3.42510.29071520.22592402255499
3.4251-3.60560.25321540.213624842638100
3.6056-3.83130.23691570.205224722629100
3.8313-4.12680.22751590.182424802639100
4.1268-4.54140.22281560.16524952651100
4.5414-5.19720.17961600.159324902650100
5.1972-6.54240.23721600.21325382698100
6.5424-37.99580.25841650.22712514267997
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)
10.4674-0.77821.81374.2586-3.88397.24040.5845-0.58170.6188-0.6574-0.9541-1.55830.45540.68840.68030.33520.03160.07240.8237-0.04950.856864.970618.032235.7944
22.10022.80841.85165.8571.63065.72050.38070.2878-1.50052.34160.4119-1.16271.48650.3018-0.26550.66780.1468-0.0010.9828-0.05810.653666.941929.745727.7793
38.75881.67691.97846.27070.98392.4477-0.13081.504-0.3778-0.23060.3725-0.01660.33240.6627-0.09560.56780.02370.1060.8438-0.03850.383754.612127.528822.885
44.81794.57852.13234.32421.44723.6576-0.34761.56660.5157-0.34740.14891.07920.6932-0.32310.04040.6361-0.0927-0.00161.07320.01270.531160.571634.43821.0395
58.1109-1.1092-0.15212.6616-0.85178.2732-0.1045-0.3785-1.3412-0.67470.4786-0.90880.78980.3069-0.38540.45570.00820.03170.2779-0.05960.410556.443320.613438.4301
67.89060.1758-6.99898.30742.53447.08340.1462-2.74430.39512.0615-0.5089-2.10380.59952.72980.10370.5351-0.3335-0.10611.29830.10730.744665.962641.384235.7927
76.5471-0.6055-1.13176.5832-0.73924.9986-0.01741.0407-0.321-0.4321-0.0561-0.11590.58440.23750.13160.26040.01890.00890.4015-0.0680.266755.268425.945132.9808
87.34653.89095.08633.26460.14248.9912-0.97091.9775-0.9833-1.2124-0.46243.31390.7286-0.46750.68540.6298-0.1601-0.24180.5748-0.13610.875434.853614.074427.6801
97.7923-3.18870.43479.97210.76696.40181.03110.2562-1.1543-1.69960.0380.760.1882-1.3296-0.83040.536-0.15140.05860.62990.06770.54733.772422.121839.2092
100.36270.44191.35462.0042-3.59627.75260.1196-0.5093-1.25971.6158-0.14022.6093-0.5413-2.2822-0.07760.36850.01740.02240.29310.0230.595444.897628.357639.8508
113.3972-4.2043-2.72865.31684.01146.49960.1901-0.8337-0.16870.29540.0290.2185-0.3903-0.5224-0.28550.5001-0.01510.09230.65020.10230.352841.662826.541547.0676
123.96312.91653.95037.25543.48184.06020.3244-0.1537-0.0196-0.00460.11560.3990.1207-0.5591-0.42580.38930.09570.06240.5321-0.04310.455131.233933.682942.2583
138.1646-5.51931.12618.8041-2.60356.3651-0.4610.7653-0.8627-0.70440.64731.01340.04180.4057-0.16570.454-0.1253-0.01710.4909-0.14920.481142.09220.264525.8727
144.6207-2.6294-0.72933.2265-1.22427.080.11470.1606-0.0289-0.61370.08431.00790.3199-0.8542-0.08840.1519-0.0741-0.06810.6416-0.03390.394238.490427.905832.3978
152.0574-0.1301-1.46052.07231.40656.1724-0.79022.2248-0.8457-0.7481-0.04430.43760.2591-0.3333-0.07530.8486-0.0850.11570.9224-0.20110.635686.940444.66885.0014
164.31993.05930.81355.99031.00860.237-0.06420.2183-0.0113-0.7785-0.0248-0.01830.0785-0.32770.01980.5637-0.03380.07660.62710.15410.443586.270845.617722.2664
175.63371.7374-1.65644.7787-1.54612.13320.3669-0.1936-0.10440.1319-0.2068-0.0130.048-0.2996-0.03140.4807-0.11580.0670.7090.18280.452885.038943.113429.1947
183.77651.58811.33494.3597-1.86224.5219-0.16110.01840.1512-0.51290.17990.29850.1813-0.2922-0.04480.4880.0156-0.0350.51760.0490.348580.128751.701414.6221
196.9112-0.16030.29626.95740.45065.459-0.32080.3603-0.2242-0.28720.1476-0.0975-0.18760.24040.17740.3695-0.06-0.02180.39780.0770.201288.632551.727815.3696
203.6197-0.1268-0.58581.25382.98679.61851.4919-0.4585-0.56631.30090.0362-1.5795-0.59470.9347-0.92520.6062-0.37160.00021.00810.09720.9433107.899163.25520.6324
213.1522-1.14260.80356.2623-5.04847.2482-2.16390.41280.05281.0421-0.4616-0.8107-2.19231.60131.70291.5821-0.3743-0.29620.93540.19741.230499.933874.337320.3679
223.7287-0.39983.49372.2296-3.62891.9944-1.08740.38340.4888-0.5466-0.1290.0803-2.17451.66260.15280.7471-0.662-0.32731.03560.65940.871399.457972.444812.6809
235.95172.4447-5.2232.4239-2.75914.8533-0.41771.3418-0.7859-0.49390.3620.3977-0.41130.15130.94581.0126-0.4737-0.11591.11310.17350.746397.291664.28047.3269
242.0003-2.7323-8.28133.0714-1.59851.9964-0.0526-0.03392.5408-0.16860.74240.5167-3.65050.6617-0.40960.7838-0.1364-0.18610.79790.21360.77388.645565.190615.7679
252.45311.61480.46543.4997-0.62385.106-1.00190.37832.35270.63730.03680.9078-1.120.37510.84711.0929-0.215-0.39950.77480.45741.232688.881270.878111.0501
262.87512.83961.53822.80611.53010.844-1.64071.2451.8906-0.58490.71221.1311-2.49930.60560.78611.02730.0115-0.37180.69690.2071.233191.177178.593321.8907
278.3096-3.0068-4.70188.97364.57873.84060.182-0.1413-0.0644-1.14670.4465-1.2121-1.26770.3764-0.47770.5821-0.04280.0510.5520.10240.4374101.554458.476725.9379
286.2717-3.4599-0.32289.14012.79385.9002-0.3483-0.10130.5162-0.6862-0.27670.1009-1.37370.42020.42940.5176-0.0765-0.06920.4520.09890.377195.835565.870127.0708
293.54442.9917-1.6223.3898-2.07982.1142-1.0920.69531.0344-0.70671.00240.4510.19251.1558-0.16330.5246-0.27010.11010.9550.18290.163699.707360.071117.6719
304.7052.32251.72343.1415-0.00131.5371-0.90311.10410.4316-0.52990.20640.0089-1.23440.5034-0.35680.4829-0.09730.03530.41960.16940.322295.107461.765318.2212
311.61140.36761.8052.3849-1.24433.2324-0.8783-1.5441-0.87251.1501-0.55940.1169-0.34020.1601-3.58631.1498-0.26360.22110.34980.5656-0.1693108.161145.931461.6547
323.83224.242-4.61534.7901-5.3315.9091-0.0102-0.41410.37431.5558-0.7760.0036-1.33261.23980.03110.6406-0.0951-0.03030.6070.01990.5106113.93639.605150.9659
334.9431-2.79311.353.3261-3.41544.0834-0.04590.0917-0.5548-0.3571-0.3283-0.23610.4161-0.13220.05270.3841-0.04490.0630.3281-0.13380.4924104.015646.316743.8457
348.7067-6.2418-1.09994.49260.84625.11540.68410.6016-0.0894-1.8286-0.23350.37970.23930.5094-0.01680.53130.0005-0.02580.3778-0.11840.5996107.761740.015540.1164
354.87981.87372.92953.85232.80123.9498-0.12731.22810.2315-0.93150.5456-0.0921-1.02680.28610.42550.25050.02910.05720.6212-0.04020.4499119.273241.350643.4802
364.3412-5.9089-0.72029.78221.2596.5678-0.88620.5182-0.54761.65480.76170.5274-1.0305-1.06520.4350.658-0.2812-0.21380.3065-0.14760.179110.327354.326260.0361
373.3667-3.1683-0.90546.62883.23187.2023-1.0846-0.8755-1.06510.77350.4589-0.12060.79720.22510.56210.6231-0.11170.02150.30740.06660.3884114.565250.138753.7704
382.5948-1.7175-0.19893.10540.64924.1499-0.94640.30390.0378-0.03470.37220.06430.28210.09730.06960.4799-0.10410.13380.2863-0.08510.2836110.288552.352751.9524
394.6127-1.23683.17154.03840.664.2368-0.38250.03610.15940.43740.23970.3314-0.3793-0.60260.1310.52720.06890.00820.1362-0.05510.3626106.042950.986451.1002
408.46043.6774-0.34734.27831.10845.1678-0.2675-0.77480.6534-0.64740.93461.6271-0.1112-0.3209-0.41280.74460.2004-0.08270.69710.17910.94487.756664.452345.6085
419.65436.30420.34684.2017-0.65446.9185-0.45371.08390.42260.51960.2154-0.1081-0.4422-0.7202-0.21061.0111-0.0191-0.15250.54650.01270.970499.724974.040342.8745
424.91193.36461.20533.3694-2.17688.76510.3426-1.84091.83490.0798-0.28750.9972-0.5274-0.6601-0.02990.87360.1111-0.01010.3442-0.1280.7526101.204672.385552.8013
434.08580.23411.02976.36314.94034.0053-0.6604-0.24192.09280.2330.9134-0.0916-2.5527-0.71-0.74810.76290.3669-0.03490.471-0.17060.6418106.924864.713753.062
441.72961.3814-0.04892.6166-1.6151.3505-0.3816-0.08311.3930.8025-0.2946-0.8582-0.6728-0.45980.28490.8639-0.0041-0.15570.4516-0.05351.0617110.890972.468148.3846
456.6202-1.145-0.86065.18291.81975.87990.01250.4159-0.17340.5896-0.01460.3714-0.7276-0.8490.02110.36650.0720.05160.2813-0.07580.264795.42758.474243.8676
461.93642.2145-0.65879.01753.78353.34840.16841.40861.4989-2.3688-1.00771.2723-1.98520.0412-0.1711.1982-0.2001-0.080.72580.32960.8762108.221371.039831.1878
474.58830.0086-0.23394.31841.34212.6953-0.29650.26470.55730.62570.089-0.3418-1.1076-1.3459-0.04780.50570.0821-0.04540.2885-0.02440.375999.905361.185845.5753
484.06171.77311.36864.4433-2.33272.8307-0.7970.2211-0.51221.1536-1.6218-0.3025-1.01080.0302-1.35280.62050.26360.1653-0.1776-0.45350.1487102.376362.149246.8067
492.00882.14770.8556.299-1.28214.16720.42371.1354-0.1217-1.40080.25060.31161.18570.2857-0.99791.28320.1287-0.4139-0.01330.07690.87462.30344.722947.9394
504.5492-4.6661-3.03475.17463.90729.7376-0.61320.6279-0.0798-0.3821-0.93191.3758-0.6065-0.59871.20330.9658-0.1626-0.22650.96520.24610.986674.672842.09944.7823
512.00840.3086-0.61856.2101-0.79334.8244-0.32940.51910.6793-0.2234-0.15071.1463-1.00720.65370.3230.760.0411-0.21520.599-0.09590.716676.806539.020257.5091
522.043-2.0555-1.1945.75774.18443.1246-0.69330.79240.2908-0.9049-0.5352-0.2767-1.3472-0.39271.19440.7342-0.1507-0.08180.67850.02840.892183.461540.520252.8859
539.027-0.79544.91315.8060.89044.43240.21790.8382-0.0842-0.0513-0.1253-0.7339-0.71431.5250.08840.4631-0.10730.04640.9713-0.10720.501881.195135.081442.7829
543.2174-2.2247-1.01212.9742-0.60447.22130.3269-1.25330.48471.01150.95830.52630.1012-0.3418-0.79070.35910.1099-0.32620.5359-0.2190.60160.637736.292552.6673
553.79263.9802-1.10372.00535.94077.8388-0.81081.90281.4348-1.3832-0.92891.293-0.65840.78281.48490.64350.0994-0.13261.11810.1490.609875.161630.100436.7865
564.68731.46280.81395.13820.34376.0448-0.05920.8455-0.35780.00490.16040.05320.60080.109-0.11560.37070.1363-0.12680.4672-0.10620.42568.516630.654150.4411
577.7522-1.20811.5039.095-0.40974.41760.0054-0.10560.0974-0.27880.3135-0.1365-0.4447-0.4278-0.46830.25530.02480.02940.4171-0.02080.277269.159433.55654.6591
583.5326-1.73650.89815.64872.1151.76770.455-0.095-0.56151.02190.4090.8056-1.15810.61550.01670.81170.44730.42661.4946-0.679-0.269565.031830.858677.0682
592.2620.6842-1.80461.72290.09472.45770.22692.18112.21120.7571.08750.771-0.514-0.1909-1.08170.9852-0.0324-0.0761.01160.2040.973462.781718.496372.7363
608.8127-0.0376-0.08098.4864-3.75076.4619-0.2861-1.2224-1.36210.18130.90140.48871.0097-1.8487-0.56630.6679-0.0352-0.08230.95610.11440.701857.779621.934761.3887
611.5407-0.22530.07679.7013-0.33552.8322-0.6362-0.1328-0.0303-1.16270.89880.86180.0054-0.5123-0.20530.67420.1637-0.04080.7845-0.04240.477168.140221.759568.6181
623.40032.70130.23552.19470.57621.6648-0.4405-0.91990.66850.70640.41861.1352-0.8701-0.62040.06050.68460.28150.17620.6313-0.05350.490867.505235.388968.6083
638.53290.37799.94445.54461.61291.95821.0215-1.5003-0.74590.7677-0.53810.9582.3693-1.4438-1.09040.83040.2639-0.25760.3458-0.0250.636276.442413.348968.922
646.46530.0429-0.30076.4440.26457.4122-0.1396-0.01460.59080.45040.14750.6401-0.2698-0.70240.04620.35840.1279-0.04240.43-0.00690.384166.36629.589565.3008
659.23883.33573.83682.19380.2818.92320.4001-0.9929-0.90320.39160.5555-0.108-0.4739-1.117-0.88420.62430.10230.00751.12270.13390.849760.729554.02588.7535
660.5543-0.0801-0.12361.10120.2583-0.09460.1834-0.94170.3142-0.7514-0.24531.44930.5009-1.04010.00640.8747-0.1052-0.3250.82380.0551.123361.06151.5756-0.8225
676.01342.61080.64237.702-2.89578.91880.0816-0.5273-0.3573-0.5051-0.14050.81210.5167-0.3910.02190.4668-0.0204-0.11950.70270.03540.352770.802452.81633.3952
688.6686-6.9179-5.31562.20725.18384.6567-0.936-1.41860.35250.73231.21450.17150.51370.3430.02390.712-0.139-0.11650.52320.04940.597167.851955.4816-2.0044
694.92590.19331.83825.6201-2.51337.4754-0.50661.1536-0.0128-0.70810.0775-0.0707-0.71291.22140.38371.118-0.1981-0.15670.77950.03520.606876.082465.2021-13.9932
703.1494-0.7282-0.71473.0907-2.69453.60040.16591.6810.1021-0.6672-0.0733-0.0447-0.10681.2879-0.08061.0001-0.21270.04330.99410.10390.699784.876764.9593-11.188
718.1692-0.8896-2.56143.22942.12285.20470.46360.2348-0.6782-0.80330.17610.27180.12570.1536-0.42760.9238-0.0674-0.26350.57520.10350.558272.681160.0063-18.6754
723.80660.28150.24590.9847-2.04924.5889-0.06240.84870.3851-0.73260.09930.05340.25940.015-0.07450.76-0.0575-0.37330.60970.08210.61568.956860.705-14.8494
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 26 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 36 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 59 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 81 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 82 through 103 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 104 through 113 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 114 through 143 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 24 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 48 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 53 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 54 through 70 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 71 through 81 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 82 through 103 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 104 through 142 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 15 through 26 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 27 through 60 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 61 through 73 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 74 through 116 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 117 through 143 )C0
20X-RAY DIFFRACTION20chain 'D' and (resid 18 through 26 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 27 through 36 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 37 through 43 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 44 through 48 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 49 through 53 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 54 through 70 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 71 through 81 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 82 through 90 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 91 through 117 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 118 through 129 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 130 through 142 )D0
31X-RAY DIFFRACTION31chain 'E' and (resid 18 through 26 )E0
32X-RAY DIFFRACTION32chain 'E' and (resid 27 through 36 )E0
33X-RAY DIFFRACTION33chain 'E' and (resid 37 through 60 )E0
34X-RAY DIFFRACTION34chain 'E' and (resid 61 through 73 )E0
35X-RAY DIFFRACTION35chain 'E' and (resid 74 through 81 )E0
36X-RAY DIFFRACTION36chain 'E' and (resid 82 through 90 )E0
37X-RAY DIFFRACTION37chain 'E' and (resid 91 through 113 )E0
38X-RAY DIFFRACTION38chain 'E' and (resid 114 through 127 )E0
39X-RAY DIFFRACTION39chain 'E' and (resid 128 through 143 )E0
40X-RAY DIFFRACTION40chain 'F' and (resid 15 through 24 )F0
41X-RAY DIFFRACTION41chain 'F' and (resid 25 through 36 )F0
42X-RAY DIFFRACTION42chain 'F' and (resid 37 through 46 )F0
43X-RAY DIFFRACTION43chain 'F' and (resid 47 through 51 )F0
44X-RAY DIFFRACTION44chain 'F' and (resid 52 through 81 )F0
45X-RAY DIFFRACTION45chain 'F' and (resid 82 through 103 )F0
46X-RAY DIFFRACTION46chain 'F' and (resid 104 through 116 )F0
47X-RAY DIFFRACTION47chain 'F' and (resid 117 through 127 )F0
48X-RAY DIFFRACTION48chain 'F' and (resid 128 through 143 )F0
49X-RAY DIFFRACTION49chain 'G' and (resid 18 through 26 )G0
50X-RAY DIFFRACTION50chain 'G' and (resid 27 through 36 )G0
51X-RAY DIFFRACTION51chain 'G' and (resid 37 through 60 )G0
52X-RAY DIFFRACTION52chain 'G' and (resid 61 through 73 )G0
53X-RAY DIFFRACTION53chain 'G' and (resid 74 through 81 )G0
54X-RAY DIFFRACTION54chain 'G' and (resid 82 through 103 )G0
55X-RAY DIFFRACTION55chain 'G' and (resid 104 through 113 )G0
56X-RAY DIFFRACTION56chain 'G' and (resid 114 through 125 )G0
57X-RAY DIFFRACTION57chain 'G' and (resid 126 through 143 )G0
58X-RAY DIFFRACTION58chain 'H' and (resid 18 through 26 )H0
59X-RAY DIFFRACTION59chain 'H' and (resid 27 through 36 )H0
60X-RAY DIFFRACTION60chain 'H' and (resid 37 through 70 )H0
61X-RAY DIFFRACTION61chain 'H' and (resid 71 through 90 )H0
62X-RAY DIFFRACTION62chain 'H' and (resid 91 through 103 )H0
63X-RAY DIFFRACTION63chain 'H' and (resid 104 through 116 )H0
64X-RAY DIFFRACTION64chain 'H' and (resid 117 through 143 )H0
65X-RAY DIFFRACTION65chain 'I' and (resid 18 through 43 )I0
66X-RAY DIFFRACTION66chain 'I' and (resid 44 through 90 )I0
67X-RAY DIFFRACTION67chain 'I' and (resid 91 through 124 )I0
68X-RAY DIFFRACTION68chain 'I' and (resid 131 through 143 )I0
69X-RAY DIFFRACTION69chain 'J' and (resid 19 through 59 )J0
70X-RAY DIFFRACTION70chain 'J' and (resid 60 through 70 )J0
71X-RAY DIFFRACTION71chain 'J' and (resid 71 through 90 )J0
72X-RAY DIFFRACTION72chain 'J' and (resid 91 through 142 )J0

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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