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- PDB-6s5o: Non-square conformations of KtrA E125Q mutant rings with bound ADP -

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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: 6s5o
タイトルNon-square conformations of KtrA E125Q mutant rings with bound ADP
要素Ktr system potassium uptake protein A
キーワードTRANSPORT PROTEIN / RCK domain / potassium homeostasis / cation channel / non-square conformation octameric ring / adp
機能・相同性
機能・相同性情報


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
類似検索 - 分子機能
Regulator of K+ conductance, C-terminal domain / : / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain ...Regulator of K+ conductance, C-terminal domain / : / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / Ktr system potassium uptake protein A
類似検索 - 構成要素
生物種Bacillus subtilis (枯草菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.983 Å
データ登録者Teixeira-Duarte, C.M. / Fonseca, F. / Morais-Cabral, J.H.
資金援助 ポルトガル, 2件
組織認可番号
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-BQM/29863/2017 ポルトガル
Fundacao para a Ciencia e a TecnologiaPOCI-01-0145-FEDER-007274 ポルトガル
引用ジャーナル: Elife / : 2019
タイトル: Activation of a nucleotide-dependent RCK domain requires binding of a cation cofactor to a conserved site.
著者: Teixeira-Duarte, C.M. / Fonseca, F. / Morais Cabral, J.H.
履歴
登録2019年7月2日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年1月8日Provider: repository / タイプ: Initial release
改定 1.12024年1月24日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)202,74416
ポリマ-199,3268
非ポリマー3,4188
00
1
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
ヘテロ分子

A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
ヘテロ分子

G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
ヘテロ分子

G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)202,74416
ポリマ-199,3268
非ポリマー3,4188
0
タイプ名称対称操作
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_445x-1/2,y-1/2,z1
crystal symmetry operation8_455x-1/2,-y+1/2,-z1
2
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
ヘテロ分子

C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)202,74416
ポリマ-199,3268
非ポリマー3,4188
0
タイプ名称対称操作
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
単位格子
Length a, b, c (Å)108.203, 155.217, 285.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain G
21chain H
31chain A
41chain B
51chain C
61chain D
71chain E
81chain F

NCSドメイン領域:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNchain GGG8 - 1408 - 140
2ASNASNchain HHH8 - 1408 - 140
3METMETchain AAA8 - 2228 - 222
4METMETchain BBB8 - 2228 - 222
5METMETchain CCC8 - 2228 - 222
6METMETchain DDD8 - 2228 - 222
7METMETchain EEE8 - 2228 - 222
8METMETchain FFF8 - 2228 - 222

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要素

#1: タンパク質
Ktr system potassium uptake protein A / K(+)-uptake protein KtrA


分子量: 24915.775 Da / 分子数: 8 / 変異: E125Q / 由来タイプ: 組換発現
由来: (組換発現) Bacillus subtilis (strain 168) (枯草菌)
: 168 / 遺伝子: ktrA, yuaA, BSU31090 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O32080
#2: 化合物
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 8 / 由来タイプ: 合成 / : C10H15N5O10P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: ADP, エネルギー貯蔵分子*YM
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: 3.01 Å3/Da / 溶媒含有率: 59.16 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法 / 詳細: 100mM ADA pH 6.5, 4% PEG 4000, 20% glycerol

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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: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.97857 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年12月6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: 0.97857 Å / 相対比: 1
反射解像度: 3.98→48.07 Å / Num. obs: 20970 / % possible obs: 99.4 % / 冗長度: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.033 / Rrim(I) all: 0.117 / Net I/σ(I): 12
反射 シェル解像度: 3.98→4.36 Å / 冗長度: 13 % / Rmerge(I) obs: 1.326 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4853 / CC1/2: 0.771 / Rpim(I) all: 0.379 / % possible all: 97.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.8.2_1309精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4j90
解像度: 3.983→47.66 Å / SU ML: 0.71 / 交差検証法: FREE R-VALUE / σ(F): 1.42 / 位相誤差: 34.9
Rfactor反射数%反射
Rfree0.2862 3992 10.11 %
Rwork0.2496 --
obs0.2535 20970 99.32 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 297.9 Å2 / Biso min: 43.28 Å2
精密化ステップサイクル: final / 解像度: 3.983→47.66 Å
タンパク質核酸リガンド溶媒全体
原子数12210 0 216 0 12426
Biso mean--120.01 --
残基数----1556
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00312632
X-RAY DIFFRACTIONf_angle_d0.79117118
X-RAY DIFFRACTIONf_chiral_restr0.0311984
X-RAY DIFFRACTIONf_plane_restr0.0032150
X-RAY DIFFRACTIONf_dihedral_angle_d15.2744688
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsタイプ
11G7545X-RAY DIFFRACTION3.909TORSIONAL
12H7545X-RAY DIFFRACTION3.909TORSIONAL
13A7545X-RAY DIFFRACTION3.909TORSIONAL
14B7545X-RAY DIFFRACTION3.909TORSIONAL
15C7545X-RAY DIFFRACTION3.909TORSIONAL
16D7545X-RAY DIFFRACTION3.909TORSIONAL
17E7545X-RAY DIFFRACTION3.909TORSIONAL
18F7545X-RAY DIFFRACTION3.909TORSIONAL
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 (%)
3.9833-4.03010.47561030.4084102483
4.0301-4.07930.42731480.37991242100
4.0793-4.13090.37391410.36451235100
4.1309-4.18520.37761150.35561232100
4.1852-4.24250.39851230.351227100
4.2425-4.30310.42671260.3281298100
4.3031-4.36720.36041570.3161166100
4.3672-4.43540.34031290.32211246100
4.4354-4.50810.36261660.31481261100
4.5081-4.58580.27721460.29271166100
4.5858-4.66910.34311260.29391243100
4.6691-4.75880.36041460.29271251100
4.7588-4.85590.34151140.28661250100
4.8559-4.96130.32871620.29291224100
4.9613-5.07660.33941400.28471184100
5.0766-5.20340.3391460.2781253100
5.2034-5.34390.31461230.29631249100
5.3439-5.5010.36661490.30111206100
5.501-5.67830.40741310.3021246100
5.6783-5.88090.34371350.29451238100
5.8809-6.11590.35551530.28751218100
6.1159-6.39360.34111320.27861251100
6.3936-6.72980.29781370.26851242100
6.7298-7.15010.3241390.2531225100
7.1501-7.70010.2721520.21951215100
7.7001-8.47110.22841270.21041244100
8.4711-9.68790.21931390.15811230100
9.6879-12.1720.17051490.17161222100
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)
14.48130.5656-0.24913.1307-0.87511.2894-0.44470.70710.94390.84610.40470.8178-0.8549-0.1194-0.11812.0316-0.27630.5521.23630.12241.181-20.93240.2244-26.0024
22.79010.4193-0.83982.91521.85451.5934-0.0702-0.48850.14140.41640.2630.51060.34750.2382-0.09681.9395-0.80261.92560.52770.81950.9597-22.9655-11.4506-16.9733
33.7119-0.4774-0.21723.9081-1.79393.9338-0.32240.1836-0.5374-0.42910.00620.74170.5582-0.410.16011.1758-0.83390.83890.143-0.21460.9514-15.2273-13.3446-23.4734
40.2775-0.8189-0.01512.4098-0.3323.54-0.2676-0.0241-0.04230.3569-0.51470.01640.02590.88510.58412.1367-0.25610.1381.30770.13430.4153-6.9027-13.3558-28.0931
52.39093.8296-2.29596.1336-3.69572.2177-0.01480.2449-0.2621-0.13920.34040.28850.5338-0.4-0.05852.6476-0.270.42420.9389-0.06090.84980.8614.0532-36.5792
64.114-0.7092-0.69062.8173-2.98043.75360.6397-0.2936-0.04160.6907-0.5381-0.14730.54790.480.01372.6635-0.6179-0.19121.31810.31641.1945-0.16075.369-49.2205
71.38471.56020.27652.02830.030.33920.03520.45620.5658-0.6319-0.89660.5864-0.3705-0.26760.21212.6558-0.46390.89311.2829-0.00220.1564-2.81215.1028-60.1888
80.3201-0.6119-0.53221.22871.02920.8505-0.36110.54180.1856-1.01230.3253-0.5121-1.3361.6497-0.0512.8774-0.85920.42222.3834-0.75091.646-6.933818.4676-60.7787
99.8733-0.04752.26426.60390.10894.29050.54580.2785-1.3077-0.08630.02450.3959-0.39460.4695-0.30271.4896-0.42040.0781.3337-0.55771.09714.72138.7889-55.4363
104.6453-0.64480.24296.42910.62328.09410.10160.4355-0.33510.22790.0108-0.07080.64580.1158-0.05911.3093-0.35610.00221.22820.06741.14218.70724.5126-33.2093
110.3282-0.63720.89121.2991-1.85672.63190.0555-0.1734-0.470.91490.0251-0.93360.67750.7969-0.10041.5932-0.0339-0.54951.76210.05631.923115.18313.2089-27.5911
122.2844-1.3711-1.35930.83410.82591.95740.2488-0.70480.18790.10860.3301-1.22360.02620.5683-0.44640.8706-0.7279-0.07562.467-0.04112.016216.621414.9222-21.5105
131.3296-1.89281.03863.088-0.1167.16540.29820.36690.7175-0.1556-0.2974-1.4341-0.68911.8171-0.00870.3466-1.45920.29481.63110.25250.82369.566114.9822-29.1059
141.8695-0.02070.37282.11010.33493.0274-0.9792-0.07630.2685-0.5112-0.3057-0.4068-0.68280.62490.77612.483-0.5092-0.09390.953-0.08930.00143.87518.2713-25.3245
15-0.07710.44060.02511.79450.0966-0.0020.5997-0.4766-0.1230.25530.3544-0.293-1.0621-0.2658-0.16972.1695-0.71270.46171.9367-0.4059-0.7097-7.879810.832-30.1098
164.64270.10291.74118.1358-2.1847.470.2713-1.22530.4220.68220.09250.5052-0.9105-0.8179-0.34041.1591-0.43920.42851.1499-0.24141.1748-13.89380.5586-48.08
173.06862.2313-4.56881.7434-2.40742.00140.04930.306-0.0933-0.15760.43430.2552-0.3687-0.283-0.16290.4813-0.18991.78760.5698-1.4498-0.6387-16.0134-14.1321-59.2417
184.47381.6382-1.76664.48270.7312.3314-0.10230.9013-0.1533-0.69280.2121-0.28520.1494-0.8363-0.0570.749-0.2452-0.08311.306-0.23040.7102-10.0425-6.0253-58.8859
192.6957-1.13683.08621.12020.77382.00890.3522-0.22250.0923-0.78520.0814-0.32090.22320.5129-0.13040.8619-0.6023-0.08180.941-1.62980.6436-8.285-12.5166-60.3031
203.68210.8863-1.34440.2839-0.56581.29190.4831-0.16820.66020.50250.1330.8284-0.6222-0.584-0.30710.9426-0.13050.42231.1767-0.76261.7542-19.4074-3.2621-53.1943
212.90550.1116-0.60972.49050.16532.0879-0.0181-0.4243-1.0471-1.6218-0.80720.25670.8157-0.92630.6620.28990.23450.71390.9974-0.40340.838237.831823.4514-68.8989
221.2072-0.3220.6173.2826-2.80643.39490.5318-0.36550.35241.4167-1.0958-0.25460.10950.34140.60951.2568-0.26450.15081.3811-0.12340.690327.584335.4894-33.6919
234.04830.3213-0.57512.88620.31793.77620.8259-1.6772-0.09521.0868-1.261-1.7589-1.11730.82360.12881.1184-0.2449-0.0781.00020.04191.468349.707514.0363-41.9982
241.7069-0.5012-0.03884.7141-2.20051.8913-0.3703-0.51620.45861.1796-0.00830.311-0.2541-0.60890.32680.7302-0.0959-0.05780.5092-0.40840.869835.446411.0133-46.8848
252.7437-0.4559-0.433.9655-1.5513.08251.0473-0.32690.77520.0658-0.90350.83370.4243-0.6334-0.13560.8537-0.17820.02860.8772-0.20741.082926.968445.4757-53.1554
263.8348-0.0374-1.03754.01251.36325.48330.26150.53770.1968-0.24160.0894-0.0603-0.3871-0.5036-0.2950.6284-0.0669-0.08230.35860.05710.747424.5394-11.2451-61.2651
272-6.16782.03153.8496-0.54760.78310.1102-0.6664-2.01360.3423-0.0768-0.08230.80030.6818-0.24420.25020.1486-0.40011.27690.23711.972139.7606-25.7436-49.849
282.57421.3133-0.25665.99390.72954.2133-0.544-0.5270.47590.7431-0.2626-1.74060.38250.5370.35291.1380.37750.04681.0997-0.42821.774134.5106-34.7679-42.1582
296.5994-3.534-7.00371.88333.74077.4016-0.52710.3519-0.68630.3933-0.0513-0.03360.8622-0.42340.47192.19930.3835-0.49710.6662-0.47813.460639.1721-52.7158-39.4199
302.0412-1.2282.1916.6843-2.23421.04440.2267-0.8472-1.29121.1071-0.32230.30710.76660.0017-0.00441.46810.2174-0.37761.25260.1751.26530.8386-47.4755-42.1165
311.67970.0921-0.62074.2344-0.29880.7236-0.1048-1.13050.1171.1397-0.1477-0.68340.80710.42380.17551.7760.2834-0.63461.2438-0.66242.091835.7773-45.175-39.5001
322.0057-7.47680.83218.7452.93362.706-0.2129-1.1707-0.24461.3860.2831-0.1876-0.3756-0.4469-0.13791.5194-0.32890.91711.9827-0.12551.738147.2065-22.8422-47.9014
332.7344-5.25971.28551.998-1.61741.36970.1464-2.0683-0.13511.23320.1394-0.7442-0.35730.6533-0.14321.9537-0.4062-0.42121.96740.21311.61253.4686-17.0685-46.4316
341.0371-1.1642-3.65471.38944.24742.0067-0.186-0.6513-0.50920.06-0.0326-1.20180.9712.18160.21732.0529-0.55320.60673.2374-0.12551.291562.7715-20.1613-55.4466
356.73631.0009-2.06761.40991.69663.7895-0.29840.1213-0.10490.4225-0.4016-1.3605-0.4673-0.09710.32521.1820.81981.13050.00060.35241.911855.4035-26.6765-55.0585
362.10880.9543-1.69464.1273-1.30334.4016-0.1290.511-0.0255-1.1373-1.083-0.2698-0.19050.44960.4452.03152.19780.88270.72770.32961.301453.5266-27.037-62.5283
377.9025-4.9823-0.56143.64631.29481.99320.31010.6845-0.9211-0.72920.3665-2.16040.87551.2842-0.17231.21990.60960.11890.4211-0.45441.811438.8135-26.9546-63.2222
385.33541.0082-3.58288.74443.07037.690.43870.97360.2022-0.6475-0.3548-0.0384-0.1068-0.40730.0021.71020.51380.40180.76050.17750.991322.6812-33.3761-50.214
393.802-3.222.16942.7267-1.86111.2493-0.3993-0.3395-0.02520.4296-0.32990.04730.29840.27210.34350.9977-0.09711.98251.6331.47130.90736.7697-33.5135-40.2913
403.4781.24360.30965.34371.91574.92470.25460.64010.23851.3739-0.07821.25890.8618-0.255-0.03831.04450.15980.22791.58240.28050.830414.7664-35.7038-42.2514
410.41630.3962-0.83920.3732-0.78631.6980.25440.6760.3059-0.09540.1474-0.7885-0.7171-0.0508-0.51741.22310.73170.07531.5593-0.23061.855164.34249.992-7.2746
425.1101-6.27274.87667.704-5.98864.6505-0.2518-0.8096-0.43170.46150.2263-0.640.50570.6412-0.03220.5661.02750.0032.2470.06141.440867.592443.6816-2.6621
431.26890.32770.24112.00180.57630.0893-0.0491-0.2811-0.00030.57920.0672-1.09340.51311.0326-0.16651.80160.36070.49311.65910.10180.319170.302451.8494-7.3181
445.8741.1738-1.05220.7691-1.73254.5143-0.0132-0.6105-0.43131.1708-0.1556-0.26250.55070.09120.19881.1531-0.5489-0.2441.3788-0.22981.628971.597654.96460.0292
455.42150.8246-2.04092.94872.14742.91480.51040.98980.4011-0.2608-0.2247-0.35420.00350.1013-0.16980.6967-0.14540.23651.73240.37321.753470.04960.833-14.2984
460.01720.008-0.01680.0037-0.01230.01170.01480.908-0.1116-0.9479-0.1822-1.79-0.16931.30510.12831.2646-0.70941.22251.89790.3130.803265.096251.9029-14.9367
474.6068-4.05541.18462.00323.73213.54180.15860.4028-0.1165-0.1417-0.5366-0.99070.28090.24520.25241.23460.20040.47531.17380.25450.497958.396558.324-18.4405
482.8638-0.02192.05034.9133-0.90331.6249-0.33790.11220.0373-0.8876-0.4338-0.8449-0.00580.24130.39611.56560.57380.30731.4480.43870.290858.549950.1681-16.3479
492.39062.82991.03428.2603-6.32222.01331.16270.004-0.632-0.03380.31050.63970.1314-0.8595-1.23031.88130.2958-0.12771.03860.18590.77350.139150.6639-16.8836
504.4713.0202-0.89988.73660.45710.3480.7107-0.2976-0.28220.42810.0322-0.57760.11630.1318-0.51540.9386-0.31140.08642.0603-0.25241.530546.90337.25171.5741
512.706-0.70491.55140.99311.09383.7672-1.0617-0.0209-0.78630.8801-0.49410.67011.7571-0.57540.96981.3532-0.25360.56091.596-0.3761.25339.263241.65661.4953
520.382-0.3143-0.20742.51010.20040.67310.03620.10180.1920.6209-0.35480.1805-0.6313-0.08930.08772.8752-0.31430.46022.23330.73391.541932.513347.94252.5457
536.94821.87350.33522.7081-1.54321.23680.6841-0.006-0.040.8069-1.00390.25651.295-1.21680.39510.9604-0.19230.13210.87750.15672.598931.677648.35645.2022
543.10980.88216.11790.24651.72991.99870.3359-0.4953-0.23271.1148-0.19720.14320.6717-0.0894-0.10872.66310.64921.11871.56710.41791.313131.026851.068117.5907
551.95350.2230.91390.20160.31480.70840.3369-1.5267-0.71181.54470.54551.46610.5102-1.0628-0.22011.3490.16461.38041.33040.19010.029939.169444.773512.4518
561.6907-0.09682.03355.8061.83923.16080.30920.3469-0.057-0.14760.52050.2740.1458-0.3907-0.28632.0360.36790.98160.4683-0.29120.217548.598448.55914.791
573.486-0.3563-2.95481.89552.08827.6229-0.0166-0.4908-0.41580.4083-0.3546-0.02330.48910.20750.20871.82310.5569-0.14063.1422-0.61671.300559.949540.5602-6.5349
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 50 )A8 - 50
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 66 )A51 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 94 )A67 - 94
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 123 )A95 - 123
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 137 )A124 - 137
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 157 )A138 - 157
7X-RAY DIFFRACTION7chain 'A' and (resid 158 through 191 )A158 - 191
8X-RAY DIFFRACTION8chain 'A' and (resid 192 through 203 )A192 - 203
9X-RAY DIFFRACTION9chain 'A' and (resid 204 through 222 )A204 - 222
10X-RAY DIFFRACTION10chain 'B' and (resid 8 through 28 )B8 - 28
11X-RAY DIFFRACTION11chain 'B' and (resid 29 through 50 )B29 - 50
12X-RAY DIFFRACTION12chain 'B' and (resid 51 through 66 )B51 - 66
13X-RAY DIFFRACTION13chain 'B' and (resid 67 through 81 )B67 - 81
14X-RAY DIFFRACTION14chain 'B' and (resid 82 through 106 )B82 - 106
15X-RAY DIFFRACTION15chain 'B' and (resid 107 through 137 )B107 - 137
16X-RAY DIFFRACTION16chain 'B' and (resid 138 through 157 )B138 - 157
17X-RAY DIFFRACTION17chain 'B' and (resid 158 through 171 )B158 - 171
18X-RAY DIFFRACTION18chain 'B' and (resid 172 through 191 )B172 - 191
19X-RAY DIFFRACTION19chain 'B' and (resid 192 through 203 )B192 - 203
20X-RAY DIFFRACTION20chain 'B' and (resid 204 through 222 )B204 - 222
21X-RAY DIFFRACTION21chain 'C' and (resid 8 through 137 )C8 - 137
22X-RAY DIFFRACTION22chain 'C' and (resid 138 through 222 )C138 - 222
23X-RAY DIFFRACTION23chain 'D' and (resid 8 through 66 )D8 - 66
24X-RAY DIFFRACTION24chain 'D' and (resid 67 through 137 )D67 - 137
25X-RAY DIFFRACTION25chain 'D' and (resid 138 through 222 )D138 - 222
26X-RAY DIFFRACTION26chain 'E' and (resid 8 through 123 )E8 - 123
27X-RAY DIFFRACTION27chain 'E' and (resid 124 through 137 )E124 - 137
28X-RAY DIFFRACTION28chain 'E' and (resid 138 through 157 )E138 - 157
29X-RAY DIFFRACTION29chain 'E' and (resid 158 through 171 )E158 - 171
30X-RAY DIFFRACTION30chain 'E' and (resid 172 through 191 )E172 - 191
31X-RAY DIFFRACTION31chain 'E' and (resid 192 through 222 )E192 - 222
32X-RAY DIFFRACTION32chain 'F' and (resid 8 through 28 )F8 - 28
33X-RAY DIFFRACTION33chain 'F' and (resid 29 through 50 )F29 - 50
34X-RAY DIFFRACTION34chain 'F' and (resid 51 through 65 )F51 - 65
35X-RAY DIFFRACTION35chain 'F' and (resid 66 through 81 )F66 - 81
36X-RAY DIFFRACTION36chain 'F' and (resid 82 through 106 )F82 - 106
37X-RAY DIFFRACTION37chain 'F' and (resid 107 through 137 )F107 - 137
38X-RAY DIFFRACTION38chain 'F' and (resid 138 through 157 )F138 - 157
39X-RAY DIFFRACTION39chain 'F' and (resid 158 through 171 )F158 - 171
40X-RAY DIFFRACTION40chain 'F' and (resid 172 through 222 )F172 - 222
41X-RAY DIFFRACTION41chain 'G' and (resid 8 through 17 )G8 - 17
42X-RAY DIFFRACTION42chain 'G' and (resid 18 through 28 )G18 - 28
43X-RAY DIFFRACTION43chain 'G' and (resid 29 through 38 )G29 - 38
44X-RAY DIFFRACTION44chain 'G' and (resid 39 through 50 )G39 - 50
45X-RAY DIFFRACTION45chain 'G' and (resid 51 through 66 )G51 - 66
46X-RAY DIFFRACTION46chain 'G' and (resid 67 through 81 )G67 - 81
47X-RAY DIFFRACTION47chain 'G' and (resid 82 through 94 )G82 - 94
48X-RAY DIFFRACTION48chain 'G' and (resid 95 through 106 )G95 - 106
49X-RAY DIFFRACTION49chain 'G' and (resid 107 through 123 )G107 - 123
50X-RAY DIFFRACTION50chain 'G' and (resid 124 through 140 )G124 - 140
51X-RAY DIFFRACTION51chain 'H' and (resid 8 through 28 )H8 - 28
52X-RAY DIFFRACTION52chain 'H' and (resid 29 through 44 )H29 - 44
53X-RAY DIFFRACTION53chain 'H' and (resid 45 through 59 )H45 - 59
54X-RAY DIFFRACTION54chain 'H' and (resid 60 through 66 )H60 - 66
55X-RAY DIFFRACTION55chain 'H' and (resid 67 through 81 )H67 - 81
56X-RAY DIFFRACTION56chain 'H' and (resid 82 through 123 )H82 - 123
57X-RAY DIFFRACTION57chain 'H' and (resid 124 through 140 )H124 - 140

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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