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- PDB-8e8u: Structure of the LOR domain of human AASS -

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基本情報

登録情報
データベース: PDB / ID: 8e8u
タイトルStructure of the LOR domain of human AASS
要素Alpha-aminoadipic semialdehyde synthase, mitochondrial
キーワードOXIDOREDUCTASE / lysine metabolism / ketoglutarate / mitochondrial / reductase
機能・相同性
機能・相同性情報


saccharopine dehydrogenase (NADP+, L-lysine-forming) / saccharopine dehydrogenase (NAD+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-lysine-forming) activity / saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine catabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / Lysine catabolism / lysine biosynthetic process via aminoadipic acid ...saccharopine dehydrogenase (NADP+, L-lysine-forming) / saccharopine dehydrogenase (NAD+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-lysine-forming) activity / saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine catabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / Lysine catabolism / lysine biosynthetic process via aminoadipic acid / transcription corepressor activity / histone binding / mitochondrial matrix / intracellular membrane-bounded organelle / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
: / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding domain superfamily
類似検索 - ドメイン・相同性
Alpha-aminoadipic semialdehyde synthase, mitochondrial
類似検索 - 構成要素
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: 2.65 Å
データ登録者Khamrui, S. / Lazarus, M.B.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124838 米国
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R21HD102745 米国
引用ジャーナル: Open Biology / 年: 2022
タイトル: Characterization and structure of the human lysine-2-oxoglutarate reductase domain, a novel therapeutic target for treatment of glutaric aciduria type 1.
著者: Leandro, J. / Khamrui, S. / Suebsuwong, C. / Chen, P.J. / Secor, C. / Dodatko, T. / Yu, C. / Sanchez, R. / DeVita, R.J. / Houten, S.M. / Lazarus, M.B.
履歴
登録2022年8月25日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年10月5日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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: Alpha-aminoadipic semialdehyde synthase, mitochondrial
B: Alpha-aminoadipic semialdehyde synthase, mitochondrial
C: Alpha-aminoadipic semialdehyde synthase, mitochondrial
D: Alpha-aminoadipic semialdehyde synthase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)201,0146
ポリマ－200,9654
非ポリマー492
水72140
1
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial
D: Alpha-aminoadipic semialdehyde synthase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,5073
ポリマ－100,4832
非ポリマー241
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-12 kcal/mol
Surface area34380 Å2
手法PISA
2
B: Alpha-aminoadipic semialdehyde synthase, mitochondrial
C: Alpha-aminoadipic semialdehyde synthase, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,5073
ポリマ－100,4832
非ポリマー241
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-12 kcal/mol
Surface area34530 Å2
手法PISA
単位格子
Length a, b, c (Å)73.005, 131.944, 96.494
Angle α, β, γ (deg.)90.000, 100.720, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A
21(chain B and (resid 24 through 360 or resid 362 through 466))
31(chain C and (resid 24 through 356 or resid 361 through 466))
41(chain D and (resid 24 through 356 or resid 361 through 466))

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARGchain AAA24 - 4666 - 448
21ALAALAGLYGLY(chain B and (resid 24 through 360 or resid 362 through 466))BB24 - 3606 - 342
22SERSERARGARG(chain B and (resid 24 through 360 or resid 362 through 466))BB362 - 466344 - 448
31ALAALASERSER(chain C and (resid 24 through 356 or resid 361 through 466))CC24 - 3566 - 338
32GLYGLYARGARG(chain C and (resid 24 through 356 or resid 361 through 466))CC361 - 466343 - 448
41ALAALASERSER(chain D and (resid 24 through 356 or resid 361 through 466))DD24 - 3566 - 338
42GLYGLYARGARG(chain D and (resid 24 through 356 or resid 361 through 466))DD361 - 466343 - 448

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要素

#1: タンパク質
Alpha-aminoadipic semialdehyde synthase, mitochondrial / LKR/SDH


分子量: 50241.336 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: AASS / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: Q9UDR5, saccharopine dehydrogenase (NADP+, L-lysine-forming), saccharopine dehydrogenase (NAD+, L-glutamate-forming)
#2: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 40 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるか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: 2.27 Å3/Da / 溶媒含有率: 45.87 %
結晶化温度: 300 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8
詳細: 0.1 M Magnesium Formate, 25 mM Calcium Acetate, 11% PEG 3350

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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: NSLS-II / ビームライン: 17-ID-1 / 波長: 0.9795 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2020年8月18日
放射モノクロメーター: Si / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9795 Å / 相対比: 1
反射解像度: 2.65→48.56 Å / Num. obs: 50249 / % possible obs: 96.4 % / 冗長度: 5.6 % / CC1/2: 0.974 / Rmerge(I) obs: 0.407 / Rpim(I) all: 0.178 / Rrim(I) all: 0.446 / Net I/σ(I): 2.7 / Num. measured all: 280133 / Scaling rejects: 43
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.65-2.745.62.3852615046740.4311.0452.6140.897
10.6-48.565.70.14644847810.9860.0610.1596.792.8

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解析

ソフトウェア
名称バージョン分類
Aimless0.7.4データスケーリング
PHENIX1.14_3260精密化
PDB_EXTRACT3.27データ抽出
autoPROCデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 8E8T

8e8t


解像度: 2.65→47.405 Å / SU ML: 0.44 / 交差検証法: THROUGHOUT / σ(F): 1.97 / 位相誤差: 36.91 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3194 2490 4.97 %
Rwork0.278 47579 -
obs0.2801 50069 95.97 %
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: 120.61 Å2 / Biso mean: 46.1736 Å2 / Biso min: 1.79 Å2
精密化ステップサイクル: final / 解像度: 2.65→47.405 Å
タンパク質核酸リガンド溶媒全体
原子数13490 0 2 40 13532
Biso mean--29.08 20.57 -
残基数----1724
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A8346X-RAY DIFFRACTION10.14TORSIONAL
12B8346X-RAY DIFFRACTION10.14TORSIONAL
13C8346X-RAY DIFFRACTION10.14TORSIONAL
14D8346X-RAY DIFFRACTION10.14TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6501-2.70110.35741290.3384271097
2.7011-2.75620.3841330.3415268098
2.7562-2.81610.37211400.3375271298
2.8161-2.88160.3451500.3391263098
2.8816-2.95370.4081380.3283269097
2.9537-3.03350.34481460.3226268698
3.0335-3.12280.34251530.3128265597
3.1228-3.22350.33611370.3079265297
3.2235-3.33870.35671380.3052269397
3.3387-3.47240.39371420.2892261996
3.4724-3.63030.35341320.2585263996
3.6303-3.82170.29991390.2582263596
3.8217-4.0610.31041240.254251791
4.061-4.37430.23811480.2293259295
4.3743-4.81410.26311410.2246262795
4.8141-5.50990.27211250.2529264595
5.5099-6.93840.31281490.2659261595
6.9384-47.40.28741260.2546258291
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)
12.5290.33210.09310.7583-0.00160.8008-0.07920.46380.6332-0.156-0.0565-0.1151-0.1058-0.0342-0.25610.23540.07140.14170.39830.04990.659950.143531.71295.7236
24.0591-1.15470.29343.7022.03161.9794-0.03710.33040.4966-0.1310.10250.2879-0.2325-0.20140.02570.35780.0941-0.02440.73950.15440.486337.088532.5522-0.9459
30.70340.0225-0.15240.59240.47390.4247-0.12890.35110.153-0.1973-0.0790.0671-0.1357-0.0654-0.00010.43670.0068-0.17140.6834-0.03810.240432.676824.7209-3.5103
42.5089-1.0661.80976.50521.20073.84450.18950.7155-0.1628-0.1084-0.0037-0.0847-0.03120.1258-0.10990.5997-0.12610.10050.80730.01930.631645.92212.1402-8.9391
50.2405-0.2678-0.07840.41140.07530.1140.17330.0571-0.0748-0.02070.07670.0414-0.0505-0.06870.45150.07170.15510.20120.0649-0.26360.643451.59834.763622.4955
60.473-0.4042-0.19030.53340.21330.3002-0.00710.0756-0.1172-0.0298-0.08150.10730.0194-0.0595-0.0990.37030.13360.11550.2696-0.15010.751553.3151-3.791914.6779
70.8874-0.7556-0.14745.3759-2.32411.7204-0.11490.272-0.6031-0.10250.01960.22160.55840.06210.08850.64160.12460.01180.5217-0.36081.110351.0897-17.435114.1215
81.6937-0.3229-0.68360.71230.49991.5029-0.09760.6302-0.41940.04770.06860.19510.2977-0.26380.08070.34730.02610.13570.5021-0.26520.454751.4931-11.523611.4698
91.46730.44210.59980.17780.20310.25690.20070.7884-0.5228-0.2549-0.05890.1340.50920.2128-0.11980.56950.1174-0.12811.0859-0.4450.980940.1655-13.6408-7.4765
101.1929-0.2274-0.21980.2584-0.06190.09450.00280.3886-0.4038-0.0897-0.07570.19620.1223-0.06950.00880.2346-0.05950.04020.4382-0.25510.777342.9949-10.489211.9935
112.1710.04080.55810.92910.14482.7194-0.08780.2127-0.45710.00880.07420.21040.2449-0.2631-0.01460.5587-0.03530.04250.47150.04231.018136.5318-8.602913.8174
122.0794-0.38960.89161.09850.85791.82860.22920.20750.0086-0.215-0.01040.2068-0.4186-0.7002-0.22040.45060.02690.06920.38340.03750.873935.98680.600510.7601
131.3825-0.2985-0.67630.6005-0.19772.1339-0.11180.1799-0.4858-0.0238-0.06560.41290.4567-0.28120.26630.3480.06280.05380.2927-0.03960.814237.3076.259518.1062
142.5580.17570.37492.03120.04850.5027-0.03790.2531-0.0006-0.0284-0.123-0.0281-0.1720.1309-0.03750.34230.181-0.01230.57270.13470.357353.993620.9717-1.9217
151.6757-0.6483-0.5190.49680.01180.93330.08950.87690.2827-0.4459-0.0861-0.0103-0.1237-0.1994-0.10110.67180.01770.0690.99930.16380.696442.184327.4247-14.276
161.0768-0.31660.46950.2263-0.17280.2134-0.0080.30140.0673-0.1620.06990.1553-0.0977-0.1285-0.01610.62240.1016-0.3180.81290.12450.422727.39318.8106-10.763
170.1733-0.2677-0.21420.7790.31390.28430.0212-0.12590.22780.188-0.03510.1004-0.2576-0.0629-0.09690.37940.15140.00580.3046-0.37310.39653.427630.879147.1763
181.621.43680.74173.4005-1.3362.20880.2178-0.01380.51690.0394-0.13140.2145-0.4152-0.17020.10330.32440.0169-0.0420.5877-0.06120.424510.988334.60252.1623
191.45570.31280.35481.5912-0.35130.52340.1212-0.12650.1840.12690.0314-0.2105-0.15440.2162-0.0090.2954-0.12910.10060.399-0.27560.614820.692227.546756.733
206.14432.81560.28719.0564-1.06774.4792-0.0041-0.8341-0.53930.5238-0.09330.27240.4197-0.29510.09420.5858-0.04010.01990.67850.06520.53319.036812.177463.1095
210.1329-0.1511-0.05670.2934-0.05660.152-0.098-0.0613-0.11580.0324-0.11190.03020.0627-0.0976-0.22570.00540.23530.00790.0171-0.3030.52783.27354.813131.4585
220.8949-0.40390.24060.8863-0.56640.362-0.0645-0.0736-0.1530.15520.06350.08320.0063-0.03640.07770.15840.12210.0978-0.0270.01050.11233.9208-3.283340.0325
231.2119-0.88280.83291.4109-0.67451.56180.1538-0.2066-0.2025-0.0730.10190.07420.29170.1333-0.19260.17960.04040.04390.1923-0.00910.39571.8234-11.370540.6803
241.03330.51260.79381.04111.06872.72120.0828-0.474-0.45430.1967-0.0389-0.29540.62960.20510.01990.29370.073-0.06580.21120.00920.554714.7892-12.943862.063
250.640.8111-0.22481.57140.49131.95210.004-0.0989-0.30810.086-0.1814-0.34830.31350.15880.16720.2964-0.00110.16240.18250.10230.576912.2566-10.410743.2348
261.0927-0.1566-0.61221.43920.79644.753-0.1911-0.3950.01090.08880.0444-0.27360.18660.26480.01290.26660.1389-0.04020.59780.19650.503820.6783-7.737245.1779
271.1343-0.00240.08372.49022.16792.1253-0.065-0.15590.12560.02040.1586-0.2264-0.17730.24330.0110.27120.0527-0.16170.27420.08070.1615.6445-5.231136.3041
282.39581.4667-0.80120.9554-0.45470.290.1447-0.0604-0.08450.1234-0.3188-0.87430.3760.7810.16070.3420.0849-0.09530.68540.20320.783120.90897.45339.9772
291.93490.3037-0.79541.39440.01881.60970.0183-0.1615-0.2342-0.0678-0.1933-0.36960.2230.34390.52670.10810.12610.16420.23210.2660.384723.48821.567333.6497
301.0503-0.5621-0.1850.7160.14070.6529-0.0923-0.0589-0.12760.14120.1272-0.05470.06240.22330.00530.02740.1021-0.04950.0780.06180.323114.47148.230936.8117
311.1689-0.1072-0.92330.6602-0.09411.99820.0207-0.58320.17230.2553-0.03060.0988-0.30480.1633-0.42020.29890.03140.20030.4979-0.19770.35446.029526.300163.8941
321.0573-0.8872-0.36990.970.68210.81750.0926-0.86490.00050.2997-0.2185-0.0498-0.29920.16360.01260.54660.0260.22710.53040.02210.467823.238321.66865.9546
331.07160.0213-0.13711.47580.14541.0514-0.21870.2515-0.506-0.3361-0.05280.11430.3153-0.13860.110.35710.02260.08740.4101-0.25390.64783.7094-6.7646.5949
343.13450.5792-0.06422.4386-0.84251.4913-0.08330.2089-0.0783-0.05660.1261-0.320.34410.215-0.02050.3120.07940.07820.5975-0.16060.570517.5433-3.6757-0.9618
350.8803-0.8802-0.04812.81450.43121.6132-0.16130.0155-0.1367-0.14410.2577-0.47490.14470.3383-0.06010.4460.02540.17740.6152-0.29120.479518.3575-1.1607-6.3516
366.1364-1.8839-2.19789.1899-0.95114.2020.01350.67920.1879-0.27230.02160.0787-0.0345-0.1467-0.03630.8232-0.12380.07870.5889-0.00820.68766.754215.3164-10.3486
371.22370.0031-0.07110.05010.04870.38550.03990.13530.3743-0.097-0.1457-0.0238-0.1251-0.0752-0.09540.2490.07190.1430.2257-0.0130.68232.667823.824619.2009
383.59130.3064-1.47343.3488-1.04676.7444-0.06930.02360.38240.44960.48250.0927-0.58140.3692-0.46370.7858-0.13850.18230.3188-0.04490.69910.512340.417222.5644
392.4576-0.2515-0.29870.7460.66722.43120.24860.78560.5393-0.06550.0491-0.148-0.36220.1083-0.26620.51610.0070.11130.47790.17980.7419.048236.6411-1.7245
401.6203-0.2452-0.36170.57220.01731.63640.09710.20610.13820.0498-0.1227-0.3542-0.01050.1653-0.00770.41630.04230.05620.31850.10611.059413.818734.02195.1135
411.41920.9208-0.40254.33580.19040.1689-0.03820.48130.1644-0.36970.2865-0.4896-0.35130.8326-0.27740.401-0.09130.28630.7610.06170.670119.694330.0917-2.2025
420.60680.1131-0.17860.48021.15863.14690.07460.02870.1208-0.10440.0194-0.2353-0.24380.4123-0.12640.2940.07730.22030.43870.32350.754122.888635.37812.6133
432.82051.16260.95863.94822.06875.69610.1681-0.30890.35750.11130.0431-0.0811-0.34780.2488-0.16010.4896-0.0440.10230.3104-0.10830.950114.064930.724520.9865
441.21270.08370.7480.57110.89731.72560.06120.36330.4306-0.143-0.2699-0.7484-0.08120.50830.18140.46730.2192-0.13480.60290.01270.881122.40124.39259.8553
452.72870.26441.23591.3331.1312.5226-0.1517-0.02560.4245-0.09650.1004-0.2422-0.16750.3264-0.03460.20380.09660.07460.20370.04620.432417.442718.202917.9792
462.71990.39080.70764.99081.05463.2203-0.23650.4596-0.3569-0.2596-0.03830.10230.3254-0.16010.12710.4384-0.0169-0.1250.4125-0.15250.30831.90710.5168-5.0193
471.81740.06020.19510.58060.11610.30910.08430.6997-0.1591-0.41860.2399-0.00760.13450.0229-0.05870.65570.0344-0.11160.8441-0.11890.418915.9909-0.7957-15.1713
481.95521.5075-0.54234.42621.27861.0326-0.0291-0.190.15820.25140.0847-0.47230.0560.3551-0.0570.47530.1741-0.16990.83710.02920.629731.64485.8401-8.7461
497.0365-1.43313.79591.1257-1.21894.3696-0.1447-0.2002-0.24440.01170.08280.1664-0.0243-0.25850.03930.21260.0457-0.04340.4142-0.01250.815843.9766-6.410248.8393
500.3129-0.4110.31761.1521-0.30990.3413-0.1137-0.0517-0.35480.22860.0951-0.10640.22650.0816-0.13680.24170.17770.08230.15360.11240.543352.4749-7.184647.2277
512.94270.7101-0.68256.0245-0.04174.21650.0422-0.4549-0.5830.15040.11140.01220.2666-0.0003-0.08410.43670.0518-0.01250.45330.15650.368343.5221-6.194153.9006
520.591-0.16370.26141.05460.37550.70920.0306-0.3119-0.36240.0870.14510.22090.187-0.1523-0.03940.41320.02730.0020.33260.17920.69535.1093-1.850657.3615
532.0314-1.656-2.25735.16830.17214.47260.0024-0.5925-0.01660.2358-0.0722-0.0639-0.19210.15560.05970.8896-0.0820.10960.6495-0.00060.312548.410914.425163.9804
540.2198-0.08920.04620.07850.01430.16070.05010.0065-0.06730.0373-0.04840.0017-0.034-0.0771-0.09340.27870.121-0.16240.0561-0.02720.287851.611519.492931.4042
550.4170.0853-0.11410.5683-0.28360.62780.1153-0.15570.14270.10510.0037-0.0598-0.18240.11040.17880.23940.0489-0.04360.0699-0.11510.189653.242229.721839.0447
564.7846-0.0133-0.23769.2835-0.64356.0180.0251-0.22250.63790.15060.0429-0.0639-0.67850.1228-0.04680.4091-0.07040.18160.5299-0.10370.674250.708942.814137.2707
572.7940.149-0.48250.9294-0.08621.68120.0141-0.6699-0.0046-0.01060.04240.052-0.06750.05070.09570.0547-0.0246-0.09680.1567-0.07880.465346.763836.783352.0768
580.0666-0.0275-0.09640.12280.0090.1847-0.0314-0.01760.01780.0624-0.017-0.0022-0.1268-0.05970.03140.2299-0.0765-0.07180.0879-0.09380.00641.259135.483347.5281
591.3787-0.0692-0.56390.8599-0.40951.23330.16130.01070.0385-0.2038-0.03750.2759-0.1153-0.3635-0.22080.3120.1653-0.16060.6359-0.18640.619834.349432.379745.1686
600.28490.0810.08460.5232-0.43471.35950.00950.03870.00380.0315-0.02080.0133-0.0074-0.04750.01190.45180.07610.05450.339-0.13720.041239.842229.828236.029
611.6117-1.88580.76022.3549-1.47522.673-0.05570.1425-0.4776-0.39050.01360.47020.4566-0.5007-0.02860.3294-0.05610.02490.7369-0.18820.54831.626122.394541.6284
623.9032-2.54690.34131.9746-0.69581.6539-0.1463-0.1297-0.35470.08070.07660.28880.0018-0.1223-0.06580.2510.1083-0.11390.2853-0.02640.75336.639515.567833.9281
631.75020.96150.75871.4676-1.40713.8706-0.01150.22220.2561-0.22140.13460.5325-0.0665-0.5609-0.0780.35770.1084-0.21620.7222-0.22080.904226.842529.295734.4088
641.6950.078-0.07760.48160.47760.5-0.0075-0.5342-0.18950.2879-0.1081-0.01340.1599-0.12720.13720.31760.02390.12120.34860.06410.626341.43545.460355.9945
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 24:93)A24 - 93
2X-RAY DIFFRACTION2(chain A and resid 94:108)A94 - 108
3X-RAY DIFFRACTION3(chain A and resid 109:136)A109 - 136
4X-RAY DIFFRACTION4(chain A and resid 137:146)A137 - 146
5X-RAY DIFFRACTION5(chain A and resid 147:211)A147 - 211
6X-RAY DIFFRACTION6(chain A and resid 212:243)A212 - 243
7X-RAY DIFFRACTION7(chain A and resid 244:253)A244 - 253
8X-RAY DIFFRACTION8(chain A and resid 254:272)A254 - 272
9X-RAY DIFFRACTION9(chain A and resid 273:294)A273 - 294
10X-RAY DIFFRACTION10(chain A and resid 295:309)A295 - 309
11X-RAY DIFFRACTION11(chain A and resid 310:350)A310 - 350
12X-RAY DIFFRACTION12(chain A and resid 351:369)A351 - 369
13X-RAY DIFFRACTION13(chain A and resid 370:412)A370 - 412
14X-RAY DIFFRACTION14(chain A and resid 413:423)A413 - 423
15X-RAY DIFFRACTION15(chain A and resid 424:457)A424 - 457
16X-RAY DIFFRACTION16(chain A and resid 458:466)A458 - 466
17X-RAY DIFFRACTION17(chain B and resid 24:79)B24 - 79
18X-RAY DIFFRACTION18(chain B and resid 80:94)B80 - 94
19X-RAY DIFFRACTION19(chain B and resid 95:136)B95 - 136
20X-RAY DIFFRACTION20(chain B and resid 137:146)B137 - 146
21X-RAY DIFFRACTION21(chain B and resid 147:211)B147 - 211
22X-RAY DIFFRACTION22(chain B and resid 212:234)B212 - 234
23X-RAY DIFFRACTION23(chain B and resid 235:272)B235 - 272
24X-RAY DIFFRACTION24(chain B and resid 273:293)B273 - 293
25X-RAY DIFFRACTION25(chain B and resid 294:310)B294 - 310
26X-RAY DIFFRACTION26(chain B and resid 311:340)B311 - 340
27X-RAY DIFFRACTION27(chain B and resid 341:365)B341 - 365
28X-RAY DIFFRACTION28(chain B and resid 366:372)B366 - 372
29X-RAY DIFFRACTION29(chain B and resid 373:384)B373 - 384
30X-RAY DIFFRACTION30(chain B and resid 385:412)B385 - 412
31X-RAY DIFFRACTION31(chain B and resid 413:444)B413 - 444
32X-RAY DIFFRACTION32(chain B and resid 445:466)B445 - 466
33X-RAY DIFFRACTION33(chain C and resid 24:82)C24 - 82
34X-RAY DIFFRACTION34(chain C and resid 83:120)C83 - 120
35X-RAY DIFFRACTION35(chain C and resid 121:141)C121 - 141
36X-RAY DIFFRACTION36(chain C and resid 142:146)C142 - 146
37X-RAY DIFFRACTION37(chain C and resid 147:249)C147 - 249
38X-RAY DIFFRACTION38(chain C and resid 250:258)C250 - 258
39X-RAY DIFFRACTION39(chain C and resid 259:287)C259 - 287
40X-RAY DIFFRACTION40(chain C and resid 288:312)C288 - 312
41X-RAY DIFFRACTION41(chain C and resid 313:318)C313 - 318
42X-RAY DIFFRACTION42(chain C and resid 319:329)C319 - 329
43X-RAY DIFFRACTION43(chain C and resid 330:358)C330 - 358
44X-RAY DIFFRACTION44(chain C and resid 361:369)C361 - 369
45X-RAY DIFFRACTION45(chain C and resid 370:412)C370 - 412
46X-RAY DIFFRACTION46(chain C and resid 413:429)C413 - 429
47X-RAY DIFFRACTION47(chain C and resid 430:461)C430 - 461
48X-RAY DIFFRACTION48(chain C and resid 462:466)C462 - 466
49X-RAY DIFFRACTION49(chain D and resid 24:34)D24 - 34
50X-RAY DIFFRACTION50(chain D and resid 35:84)D35 - 84
51X-RAY DIFFRACTION51(chain D and resid 85:94)D85 - 94
52X-RAY DIFFRACTION52(chain D and resid 95:140)D95 - 140
53X-RAY DIFFRACTION53(chain D and resid 141:147)D141 - 147
54X-RAY DIFFRACTION54(chain D and resid 148:209)D148 - 209
55X-RAY DIFFRACTION55(chain D and resid 210:246)D210 - 246
56X-RAY DIFFRACTION56(chain D and resid 247:253)D247 - 253
57X-RAY DIFFRACTION57(chain D and resid 254:288)D254 - 288
58X-RAY DIFFRACTION58(chain D and resid 289:310)D289 - 310
59X-RAY DIFFRACTION59(chain D and resid 311:340)D311 - 340
60X-RAY DIFFRACTION60(chain D and resid 341:364)D341 - 364
61X-RAY DIFFRACTION61(chain D and resid 365:369)D365 - 369
62X-RAY DIFFRACTION62(chain D and resid 370:378)D370 - 378
63X-RAY DIFFRACTION63(chain D and resid 379:384)D379 - 384
64X-RAY DIFFRACTION64(chain D and resid 385:466)D385 - 466

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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