[日本語] English
- PDB-5zea: Crystal structure of the nucleotide-free mutant A3B3 -

+
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: 5zea
タイトルCrystal structure of the nucleotide-free mutant A3B3
要素
  • V-type sodium ATPase catalytic subunit A
  • V-type sodium ATPase subunit B
キーワードHYDROLASE / V-ATPase / rotary motor
機能・相同性
機能・相同性情報


Na+-transporting two-sector ATPase / sodium-transporting ATPase activity, rotational mechanism / proton motive force-driven plasma membrane ATP synthesis / sodium ion transport / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
類似検索 - 分子機能
Rossmann fold - #12240 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal ...Rossmann fold - #12240 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
V-type sodium ATPase catalytic subunit A / V-type sodium ATPase subunit B
類似検索 - 構成要素
生物種Enterococcus hirae (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.384 Å
データ登録者Maruyama, S. / Suzuki, K. / Mizutani, K. / Saito, Y. / Imai, F.L. / Ishizuka-Katsura, Y. / Shirouzu, M. / Ichiro, Y. / Murata, T.
引用ジャーナル: Sci Adv / : 2019
タイトル: Metastable asymmetrical structure of a shaftless V1motor.
著者: Maruyama, S. / Suzuki, K. / Imamura, M. / Sasaki, H. / Matsunami, H. / Mizutani, K. / Saito, Y. / Imai, F.L. / Ishizuka-Katsura, Y. / Kimura-Someya, T. / Shirouzu, M. / Uchihashi, T. / Ando, ...著者: Maruyama, S. / Suzuki, K. / Imamura, M. / Sasaki, H. / Matsunami, H. / Mizutani, K. / Saito, Y. / Imai, F.L. / Ishizuka-Katsura, Y. / Kimura-Someya, T. / Shirouzu, M. / Uchihashi, T. / Ando, T. / Yamato, I. / Murata, T.
履歴
登録2018年2月27日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02019年2月6日Provider: repository / タイプ: Initial release
改定 1.12019年2月20日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
改定 1.22023年11月22日Group: 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
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: V-type sodium ATPase catalytic subunit A
B: V-type sodium ATPase catalytic subunit A
C: V-type sodium ATPase catalytic subunit A
D: V-type sodium ATPase subunit B
E: V-type sodium ATPase subunit B
F: V-type sodium ATPase subunit B
G: V-type sodium ATPase catalytic subunit A
H: V-type sodium ATPase catalytic subunit A
I: V-type sodium ATPase catalytic subunit A
J: V-type sodium ATPase subunit B
K: V-type sodium ATPase subunit B
L: V-type sodium ATPase subunit B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)704,92629
ポリマ-703,36112
非ポリマー1,56617
1,802100
1
A: V-type sodium ATPase catalytic subunit A
B: V-type sodium ATPase catalytic subunit A
C: V-type sodium ATPase catalytic subunit A
D: V-type sodium ATPase subunit B
E: V-type sodium ATPase subunit B
F: V-type sodium ATPase subunit B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)352,78518
ポリマ-351,6806
非ポリマー1,10512
1086
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area23270 Å2
ΔGint-71 kcal/mol
Surface area118370 Å2
手法PISA
2
G: V-type sodium ATPase catalytic subunit A
H: V-type sodium ATPase catalytic subunit A
I: V-type sodium ATPase catalytic subunit A
J: V-type sodium ATPase subunit B
K: V-type sodium ATPase subunit B
L: V-type sodium ATPase subunit B
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)352,14111
ポリマ-351,6806
非ポリマー4605
905
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area21490 Å2
ΔGint-67 kcal/mol
Surface area118440 Å2
手法PISA
単位格子
Length a, b, c (Å)180.840, 107.770, 193.370
Angle α, β, γ (deg.)90.000, 99.390, 90.000
Int Tables number4
Space group name H-MP1211

-
要素

#1: タンパク質
V-type sodium ATPase catalytic subunit A / Na(+)-translocating ATPase subunit A / V-type sodium pump catalytic subunit A


分子量: 65771.211 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258) (バクテリア)
: ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258
遺伝子: ntpA, EHR_08260 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q08636, EC: 3.6.3.15
#2: タンパク質
V-type sodium ATPase subunit B / Na(+)-translocating ATPase subunit B / V-type sodium pump subunit B


分子量: 51455.566 Da / 分子数: 6 / Mutation: L65Y / 由来タイプ: 組換発現
由来: (組換発現) Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258) (バクテリア)
: ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258
遺伝子: ntpB, EHR_08265 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q08637
#3: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 17 / 由来タイプ: 合成 / : C3H8O3
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 100 / 由来タイプ: 天然 / : H2O

-
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: 2.66 Å3/Da / 溶媒含有率: 53.78 %
結晶化温度: 296 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: 28% PEG 3350, 0.1 M Bis-Tris propane pH 6.5, 0.1 M NaCl, 0.1 M Ammonium acetate

-
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: Photon Factory / ビームライン: BL-1A / 波長: 1.1 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2014年12月9日
放射モノクロメーター: Cryo-cooled channel-cut Si(111) / 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: 1.1 Å / 相対比: 1
反射解像度: 3.38→48.199 Å / Num. obs: 101833 / % possible obs: 99 % / 冗長度: 6.716 % / Biso Wilson estimate: 97.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.123 / Χ2: 1.146 / Net I/σ(I): 15.77 / Num. measured all: 683871
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.38-3.596.3730.6742.9155380.8220.73394.2
3.59-3.836.710.4115.1154780.930.44699.9
3.83-4.147.1030.2528.42144410.9770.27299.9
4.14-4.536.9350.13714.76132940.9920.148100
4.53-5.066.5420.09419.93120560.9950.10299.9
5.06-5.837.0740.09919.62106930.9950.106100
5.83-7.126.5920.07723.6990690.9970.08499.9
7.12-9.966.5770.03841.3571110.9990.04199.9
9.96-48.1996.0580.03149.4341530.9990.03398.4

-
位相決定

位相決定手法: 分子置換
Phasing MRR rigid body: 0.422
最高解像度最低解像度
Rotation48.73 Å3.66 Å

-
解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
MOLREP位相決定
PHENIX1.12_2829精密化
PDB_EXTRACT3.24データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 3VR2
解像度: 3.384→48.199 Å / SU ML: 0.44 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 26.34
Rfactor反射数%反射
Rfree0.2575 5084 4.99 %
Rwork0.2151 --
obs0.2172 101796 99.01 %
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: 324.78 Å2 / Biso mean: 108.6861 Å2 / Biso min: 24.89 Å2
精密化ステップサイクル: final / 解像度: 3.384→48.199 Å
タンパク質核酸リガンド溶媒全体
原子数47785 0 102 100 47987
Biso mean--101.58 53.43 -
残基数----6235
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00248700
X-RAY DIFFRACTIONf_angle_d0.43565993
X-RAY DIFFRACTIONf_chiral_restr0.0417480
X-RAY DIFFRACTIONf_plane_restr0.0038676
X-RAY DIFFRACTIONf_dihedral_angle_d15.48929511
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3839-3.42240.33851200.36052328244872
3.4224-3.46260.32891530.296432833436100
3.4626-3.50480.35471520.290532403392100
3.5048-3.54920.32371670.282332243391100
3.5492-3.59590.31291910.272632303421100
3.5959-3.64510.31651440.264832413385100
3.6451-3.69720.27241660.248532603426100
3.6972-3.75230.28441630.248632433406100
3.7523-3.81090.31611800.243432553435100
3.8109-3.87340.28341760.254231813357100
3.8734-3.94010.30311800.241632193399100
3.9401-4.01180.26241790.237732833462100
4.0118-4.08890.25981600.240632163376100
4.0889-4.17230.29541600.22232563416100
4.1723-4.2630.2311650.210532633428100
4.263-4.36210.24231740.201832143388100
4.3621-4.47110.22231720.186832623434100
4.4711-4.59190.23491820.184932483430100
4.5919-4.72690.22981840.189932153399100
4.7269-4.87930.23691790.194532493428100
4.8793-5.05350.25261610.195432393400100
5.0535-5.25560.25131810.211432673448100
5.2556-5.49450.27761750.217332543429100
5.4945-5.78370.28131570.230732773434100
5.7837-6.14540.30321860.239432503436100
6.1454-6.61880.25341710.225632883459100
6.6188-7.28290.29241640.217832983462100
7.2829-8.3320.23581800.199932783458100
8.332-10.47970.18481680.14733123480100
10.4797-48.20380.23091940.19733339353399
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)
19.1629-6.3332-5.32468.80451.66034.990.06610.0406-0.1685-0.47640.08760.2813-0.0865-0.272-0.16140.4946-0.014-0.17180.468-0.01150.4099-9.9788-37.16101.2442
21.52470.4744-0.1591.72320.14891.362-0.0118-0.08110.03770.09850.03310.01270.1806-0.0537-0.02280.44930.0104-0.05320.37790.01460.3842-10.2599-17.843781.058
33.28182.5139-0.49586.7899-1.29133.30240.2119-0.07870.07890.2966-0.2051-0.6205-0.27560.6199-0.01350.39320.07160.06820.5421-0.05040.555814.0295-3.986673.4034
48.38222.3189-1.20046.5149-2.68165.44790.36150.03251.104-0.0037-0.1072-0.3076-0.95350.3974-0.23270.7371-0.01850.19850.4268-0.05110.638613.535215.390764.0364
58.2232-2.71960.71763.7951-0.39119.86160.18320.1381-0.573-0.0317-0.2153-0.42330.37720.58670.030.50210.0453-0.03670.44670.00310.799821.3455-62.605892.0453
61.21681.01990.27181.4195-1.23934.28290.10610.3145-0.3462-0.2026-0.12930.11260.38570.91480.03190.82910.2213-0.04680.8737-0.07050.946335.6761-62.636378.0495
70.20570.59360.62842.91320.30461.84710.0539-0.249-0.6684-0.02240.0373-0.85691.15110.8336-0.05791.0370.51780.09211.30250.16751.492551.4706-76.522685.7504
82.0226-1.09792.20183.2326-1.26442.83390.09480.039-0.2729-0.2905-0.0837-0.596-0.02451.21890.0230.68260.04950.18151.39680.02140.96954.6236-48.701280.7329
93.59910.2637-2.27684.882.16066.1732-0.3089-0.5414-0.12380.16350.0123-0.03440.04470.99890.34690.55730.0836-0.16240.85130.09510.771640.5763-49.560990.3578
102.71783.089-2.3395.5179-1.50682.52480.2013-0.41280.50060.2393-0.2244-0.3178-0.15771.035-0.02810.6717-0.0556-0.09711.4630.02140.864458.3881-41.045189.7071
113.21950.17451.98880.96741.182.1821-0.0782-0.07830.4821-0.3170.6218-0.619-0.47591.5031-0.52590.97-0.23480.25292.0717-0.09421.452572.0451-26.470482.1023
122.91171.43120.21981.5001-0.58070.6285-0.68260.2856-0.2908-0.88120.3996-1.4812-0.08330.63470.13060.94520.02510.14591.97270.19431.433582.7952-26.787473.513
131.48121.8390.27553.43251.94971.71010.0379-0.6719-0.41070.5682-0.1536-0.43050.40620.29370.07721.0049-0.0042-0.28250.840.2440.767520.2122-43.5525135.7828
142.0413-0.8112-1.01213.70662.23083.1761-0.0708-0.8179-0.11670.9739-0.19750.01050.49070.37630.21611.1513-0.1816-0.29191.40750.26710.675722.6364-28.1477155.3026
152.59881.6446-1.46812.9529-1.14825.07530.4455-1.175-0.26530.3197-0.5458-0.09010.21630.32030.10660.8274-0.1277-0.27920.97090.06250.681820.3442-19.013145.801
163.5215-0.5476-1.6445.2090.94153.89810.2027-0.8057-0.3354-0.1935-0.0634-0.4748-0.11410.5767-0.20720.822-0.0317-0.22130.78920.13060.642929.1812-23.7975134.7195
176.31044.12640.7044.5239-0.98151.5086-0.0867-0.3129-0.3097-0.4947-0.2334-0.3505-0.2873-0.03190.230.93690.0882-0.22290.71770.0360.502323.823-13.4118131.1911
185.65511.4822-0.68075.68780.34293.37320.2282-0.2490.7718-0.5883-0.1116-0.3339-0.83390.7347-0.12611.1738-0.1380.01530.8822-0.03590.909338.61677.1375128.8936
195.7549-0.58490.50659.0142-1.36130.7685-0.00610.0102-0.41920.3199-0.83520.5481-0.16590.44610.88921.0545-0.26840.13641.4479-0.12621.214548.370118.3268135.4322
207.2633-3.1683-0.21916.4391-3.26682.51120.0752-1.3297-0.07720.88910.02860.36720.12440.44210.01670.8204-0.0929-0.14840.7470.05860.6697-4.6984-37.0872126.1608
214.3482-5.2984.61526.7967-5.30734.5519-0.1742-0.3854-0.03930.79260.2221-0.0429-0.10750.11540.13050.8836-0.0552-0.16640.69350.08880.5672-2.7533-34.7073124.8854
225.09943.2759-0.45684.86511.16160.90310.4015-0.44120.00780.5673-0.25250.36450.1338-0.0742-0.11590.69010.1122-0.08440.4109-0.01120.4094-1.8542-2.593116.3103
233.90090.34450.60542.8971-0.56761.979-0.0374-0.2483-0.20240.29760.0678-0.35240.42270.1021-0.0320.66360.0801-0.10190.3819-0.06820.4276.2646-8.5854114.9193
245.04031.307-1.24715.9575-1.19543.91060.02420.25220.6365-0.3045-0.109-0.5093-0.41630.29530.0890.6476-0.01720.00770.36450.01230.525916.751817.1813103.3442
256.0955-3.5632-2.93983.0051.57092.4739-0.24220.2832-0.7922-0.50370.16190.06110.542-0.13390.0470.6717-0.01680.01050.4622-0.03540.67680.741-50.796484.1936
266.1021-2.7479-2.74567.0752-1.82418.0846-0.15461.362-0.6056-0.6781-0.44941.0015-0.0407-1.18490.70690.75820.0815-0.12440.9235-0.24260.73079.2263-43.548860.6073
274.5298-0.3602-0.25865.3457-0.60664.11430.17210.49570.1034-0.3636-0.2876-0.6402-0.24850.5490.08540.51380.05920.03410.5803-0.01930.577525.3493-33.267768.4362
283.5371-1.417-3.3840.51971.10546.7639-0.0073-0.17290.9399-0.0957-0.1026-0.36-0.94410.93970.02561.4295-0.38740.07961.53490.4391.962745.61-9.777665.5241
291.9439-1.25971.23941.7351-1.01824.43520.67972.60412.91050.3603-0.5833-0.6486-0.60420.60310.01521.07840.09370.42971.43080.47431.635343.0743-16.909454.6535
303.12960.92860.25040.90630.10862.2014-0.469-0.3694-0.49270.5784-0.2326-0.05740.7366-0.29570.54981.0101-0.0514-0.07460.75280.20170.964325.6954-62.7306116.0965
319.2357-1.3943-3.46393.25155.13048.04820.0522-0.4713-1.87760.6817-0.17410.05580.29010.66520.15750.9353-0.0025-0.15320.58170.17011.271430.5488-61.5712114.6242
322.68140.76341.38081.51422.69885.3225-0.0355-0.4126-0.38570.14360.4487-0.8221-0.09811.1078-0.39310.80860.026-0.28580.97470.15631.362546.9223-51.2338123.0443
332.98240.1594-1.77197.1792.90567.38720.3676-0.4705-0.76430.07540.1486-0.7101-0.23121.8353-0.67880.6953-0.1356-0.25561.4559-0.0121.160958.6486-41.8273116.7974
340.81020.0795-0.91733.626-1.18843.93690.42690.0935-0.54950.19170.0546-0.27260.13220.877-0.50.5622-0.0624-0.22710.9460.02591.097846.1182-44.4608119.7772
350.5378-0.2409-1.75263.40461.39086.4382-0.47040.38650.4839-0.3952-0.43850.9854-0.66870.02920.85650.7647-0.0099-0.16740.83260.02081.650938.4803-37.5642120.9118
364.8846-0.63291.80181.51961.85493.37770.11190.07870.7183-0.5363-0.02660.0022-1.8276-0.1908-0.14421.407-0.118-0.1251.0412-0.04181.474445.6543-30.2035114.8723
374.8470.8027-1.41443.3191-0.77522.9837-0.14250.07890.5649-0.41030.3683-0.5504-2.08550.89-0.06291.8388-0.69880.1221.2598-0.19321.693960.7749-19.1661116.4578
389.04173.7711.93465.03013.95773.3199-0.1432-1.7010.2914-1.34320.01350.3972-1.2519-0.29890.79212.9505-0.70180.35871.8131-0.05571.58269.4248-8.8426108.0002
394.3897-1.63041.31632.34882.6675.91320.47420.20750.51960.22920.7703-1.3255-1.1411.1793-1.11081.6688-0.69170.20321.8433-0.14081.58771.2948-18.0706121.868
407.78740.35960.95362.2867-6.99435.0834-0.3530.03-0.0660.26730.1572-0.2852-0.570.41130.13760.645-0.0551-0.02470.4862-0.14990.490483.585815.7928-3.8974
410.83332.50762.30716.48665.73236.750.16180.15230.1798-0.17130.398-0.9417-0.34580.3849-0.59710.4477-0.0291-0.04940.5376-0.10780.666691.929129.9926.1407
422.0779-1.97321.97313.7989-2.65545.66380.3002-0.3350.27560.02690.0423-0.49420.3040.2943-0.29950.522-0.1188-0.0960.5993-0.19610.8061100.382133.92877.7038
433.3816-1.722-2.03054.08210.03952.3396-0.1145-0.38830.4510.27590.1715-0.6294-0.01890.4758-0.05470.6877-0.0466-0.25940.5881-0.23260.8415102.567226.816119.7931
442.0733-0.03470.27343.10361.25522.8347-0.2693-0.1420.63860.66560.09840.1155-0.44510.12980.20340.6118-0.0198-0.06250.4794-0.15010.715382.816943.790917.9906
458.29821.1445-0.19496.4763.23642.35730.050.6365-0.5983-0.48320.41710.40151.0347-0.3897-0.4920.642-0.0912-0.08310.6145-0.05670.681469.438227.48910.3429
464.4775-4.2378-1.41369.2597-0.04160.7929-0.13-0.65440.18110.03930.20380.60210.0936-0.3796-0.04970.7155-0.10580.03690.4877-0.08340.488275.699736.196124.041
472.3368-0.4434-0.86182.7440.38123.7007-0.1017-0.6190.75631.26910.38260.3372-0.8294-0.213-0.30741.28140.21620.14010.8849-0.29291.035267.693657.41935.8905
488.7936-8.2754-7.00358.18626.62835.32710.3542-0.94570.3358-0.27530.5048-0.6815-1.32010.5403-1.10611.57270.1889-0.10811.1988-0.40271.191472.588671.835942.4385
495.2747-1.54481.66963.4814-2.62017.5746-0.3243-0.0464-0.4376-0.27090.14020.6140.836-0.44220.13890.6737-0.09340.09490.5375-0.16261.054455.5309-9.70112.9475
502.95280.0516-0.49472.18430.95072.6261-0.22290.2009-1.46350.1452-0.16230.36071.0881-0.44680.30871.0309-0.20270.25980.6691-0.1721.32633.3164-18.807328.0106
515.07030.674-2.28372.1654-0.94733.1702-0.25190.647-0.4197-0.08360.08930.06970.1344-0.4390.17030.55520.02420.06290.5913-0.06110.557429.57753.130325.5149
524.9412-1.346-1.62632.73171.68155.10180.2220.73020.9549-0.27820.10.0936-0.9035-1.0664-0.33190.93710.26350.1510.95780.30260.722915.998224.088426.975
538.6889-5.4293-0.56616.20491.6262.81510.14170.12310.63630.5437-0.20680.5234-0.2537-0.7675-0.04580.98170.22520.36451.04620.14430.87613.302123.847641.393
54-0.1982-0.5287-0.07961.3123-0.6810.5458-0.00090.0928-0.0118-0.3367-0.00460.08190.2192-0.5506-0.02080.7953-0.1398-0.15681.1222-0.12820.755944.583118.0939-39.3519
551.2380.1709-0.25872.05360.11392.9850.12780.08270.4673-0.025-0.0540.83420.0933-1.2239-0.04610.6678-0.0586-0.07311.4479-0.05470.920731.96535.7395-29.179
562.37881.8654-2.41616.0306-2.61432.94970.1164-0.03850.01870.55980.01220.1105-0.2936-0.7828-0.16940.7105-0.0916-0.1751.2041-0.13890.799443.860532.6903-21.4615
57-0.5754-0.68250.43494.56071.15711.45710.0437-0.23760.9240.3786-0.10920.0383-0.5178-0.83220.06561.11250.2299-0.06511.4489-0.23641.86324.868161.7963-19.3774
583.95313.828-0.62873.65351.24562.7782-0.15610.9366-0.255-0.79160.339-0.03520.2723-0.6-0.05820.7149-0.1282-0.1650.8631-0.06070.655971.651619.933-25.4893
593.3179-2.9594-0.42725.24231.05421.91260.25860.20590.2605-0.5064-0.0973-0.1845-0.1611-0.1726-0.13340.4773-0.13070.0110.5130.0540.618169.932350.8106-15.4635
606.8323.12630.06587.95271.36423.11380.11750.0509-0.17720.3488-0.17130.38420.547-0.47370.04170.59770.0346-0.00470.52940.01360.474666.50641.6746-15.1323
613.8535-0.7436-1.46656.08080.70883.34140.0609-0.2650.4750.71880.01140.9509-0.2683-0.8671-0.04060.59930.04740.04810.7686-0.01540.699857.04164.0019-0.1137
623.712.5624-5.21399.2607-4.11258.0648-0.2399-0.2605-0.38960.26340.4157-0.18210.40080.2416-0.01810.560.0539-0.05060.5249-0.06840.636577.62741.793215.1896
630.75141.2684-0.37437.0351.82792.3418-0.3539-0.625-0.49320.59810.2422-0.25550.53730.4596-0.00530.69680.18770.00780.86620.09240.458864.01589.369741.117
649.43631.0227-2.77864.7768-0.18589.68350.1626-0.9531-0.04921.0547-0.209-0.18440.02350.52320.00460.54320.0257-0.00890.5548-0.03790.425556.410424.17644.0992
652.91691.3952-2.5563.4787-0.44555.42530.1352-0.05490.13090.09020.070.1671-0.5231-0.0481-0.16610.52040.0814-0.00930.4818-0.01230.488258.880319.68734.7789
667.5604-0.3719-2.89567.9661.57482.30980.26280.60641.0118-0.1705-0.18130.8659-1.0537-0.5875-0.14261.25290.19090.2740.8007-0.04670.940440.943444.514844.1038
677.1845-1.8445-1.1683.59742.9674.61760.3414-0.81621.06030.04660.0550.11280.0742-0.0138-0.44771.019-0.03910.21140.6901-0.04640.832644.655535.823455.3792
683.94450.576-0.10414.7289-5.27795.8969-0.28380.8302-0.7681-0.59670.19110.38311.1283-0.36950.00170.8052-0.16190.14641.0725-0.49620.968642.2712-11.3965-7.6544
697.7013-2.46843.31593.7811-1.93592.8634-0.64251.0477-0.3741-0.8060.25360.04220.9511-0.56310.34430.8226-0.40540.13281.212-0.24580.903537.2121-7.7894-8.0738
701.88920.01290.52871.49420.49694.9039-0.3199-0.39820.2337-0.4094-0.08870.7612-0.0847-1.9140.32750.6049-0.0772-0.12512.0591-0.39061.039616.666311.0193-10.3974
717.1127-7.29342.89498.4431-5.45916.67810.7996-0.6716-0.9569-0.13320.57491.47040.8204-1.1088-0.99090.5173-0.2210.10242.4427-0.24610.999410.52899.1153-1.051
724.07750.89080.85793.75830.4422.30010.1014-0.55470.0743-0.1042-0.09850.32240.1792-0.7596-0.00450.5091-0.07410.04911.2862-0.16750.638525.28969.5699-7.9807
733.8002-0.4087-3.53236.1912-0.48523.6223-0.4109-1.23981.16430.55850.69970.2133-1.2617-0.7352-0.33290.91790.3454-0.01221.6868-0.3511.017417.888826.2037-3.1086
740.79780.92320.56991.82650.07630.50650.56650.03060.1966-0.0702-0.6397-0.4035-1.1314-1.4850.18942.06870.55820.21421.6023-0.12541.50199.42742.49976.7722
750.6028-1.92841.80917.7815-6.06464.7963-0.8086-0.20050.12221.71990.86040.8318-1.4629-0.2578-0.43081.39030.11370.01681.95360.31471.5645-0.291934.2785-2.866
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 62 )A1 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 380 )A63 - 380
3X-RAY DIFFRACTION3chain 'A' and (resid 381 through 477 )A381 - 477
4X-RAY DIFFRACTION4chain 'A' and (resid 478 through 587 )A478 - 587
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 62 )B1 - 62
6X-RAY DIFFRACTION6chain 'B' and (resid 63 through 107 )B63 - 107
7X-RAY DIFFRACTION7chain 'B' and (resid 108 through 192 )B108 - 192
8X-RAY DIFFRACTION8chain 'B' and (resid 193 through 292 )B193 - 292
9X-RAY DIFFRACTION9chain 'B' and (resid 293 through 368 )B293 - 368
10X-RAY DIFFRACTION10chain 'B' and (resid 369 through 452 )B369 - 452
11X-RAY DIFFRACTION11chain 'B' and (resid 453 through 537 )B453 - 537
12X-RAY DIFFRACTION12chain 'B' and (resid 538 through 586 )B538 - 586
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 97 )C1 - 97
14X-RAY DIFFRACTION14chain 'C' and (resid 98 through 150 )C98 - 150
15X-RAY DIFFRACTION15chain 'C' and (resid 151 through 247 )C151 - 247
16X-RAY DIFFRACTION16chain 'C' and (resid 248 through 366 )C248 - 366
17X-RAY DIFFRACTION17chain 'C' and (resid 367 through 416 )C367 - 416
18X-RAY DIFFRACTION18chain 'C' and (resid 417 through 536 )C417 - 536
19X-RAY DIFFRACTION19chain 'C' and (resid 537 through 584 )C537 - 584
20X-RAY DIFFRACTION20chain 'D' and (resid 2 through 38 )D2 - 38
21X-RAY DIFFRACTION21chain 'D' and (resid 39 through 77 )D39 - 77
22X-RAY DIFFRACTION22chain 'D' and (resid 78 through 175 )D78 - 175
23X-RAY DIFFRACTION23chain 'D' and (resid 176 through 346 )D176 - 346
24X-RAY DIFFRACTION24chain 'D' and (resid 347 through 455 )D347 - 455
25X-RAY DIFFRACTION25chain 'E' and (resid 2 through 77 )E2 - 77
26X-RAY DIFFRACTION26chain 'E' and (resid 78 through 106 )E78 - 106
27X-RAY DIFFRACTION27chain 'E' and (resid 107 through 362 )E107 - 362
28X-RAY DIFFRACTION28chain 'E' and (resid 363 through 408 )E363 - 408
29X-RAY DIFFRACTION29chain 'E' and (resid 409 through 453 )E409 - 453
30X-RAY DIFFRACTION30chain 'F' and (resid 3 through 28 )F3 - 28
31X-RAY DIFFRACTION31chain 'F' and (resid 29 through 56 )F29 - 56
32X-RAY DIFFRACTION32chain 'F' and (resid 57 through 138 )F57 - 138
33X-RAY DIFFRACTION33chain 'F' and (resid 139 through 217 )F139 - 217
34X-RAY DIFFRACTION34chain 'F' and (resid 218 through 263 )F218 - 263
35X-RAY DIFFRACTION35chain 'F' and (resid 264 through 296 )F264 - 296
36X-RAY DIFFRACTION36chain 'F' and (resid 297 through 325 )F297 - 325
37X-RAY DIFFRACTION37chain 'F' and (resid 326 through 388 )F326 - 388
38X-RAY DIFFRACTION38chain 'F' and (resid 389 through 411 )F389 - 411
39X-RAY DIFFRACTION39chain 'F' and (resid 412 through 453 )F412 - 453
40X-RAY DIFFRACTION40chain 'G' and (resid 1 through 62 )G1 - 62
41X-RAY DIFFRACTION41chain 'G' and (resid 63 through 90 )G63 - 90
42X-RAY DIFFRACTION42chain 'G' and (resid 91 through 134 )G91 - 134
43X-RAY DIFFRACTION43chain 'G' and (resid 135 through 202 )G135 - 202
44X-RAY DIFFRACTION44chain 'G' and (resid 203 through 330 )G203 - 330
45X-RAY DIFFRACTION45chain 'G' and (resid 331 through 366 )G331 - 366
46X-RAY DIFFRACTION46chain 'G' and (resid 367 through 416 )G367 - 416
47X-RAY DIFFRACTION47chain 'G' and (resid 417 through 538 )G417 - 538
48X-RAY DIFFRACTION48chain 'G' and (resid 539 through 587 )G539 - 587
49X-RAY DIFFRACTION49chain 'H' and (resid 1 through 62 )H1 - 62
50X-RAY DIFFRACTION50chain 'H' and (resid 63 through 192 )H63 - 192
51X-RAY DIFFRACTION51chain 'H' and (resid 193 through 390 )H193 - 390
52X-RAY DIFFRACTION52chain 'H' and (resid 391 through 499 )H391 - 499
53X-RAY DIFFRACTION53chain 'H' and (resid 500 through 586 )H500 - 586
54X-RAY DIFFRACTION54chain 'I' and (resid 1 through 202 )I1 - 202
55X-RAY DIFFRACTION55chain 'I' and (resid 203 through 320 )I203 - 320
56X-RAY DIFFRACTION56chain 'I' and (resid 321 through 408 )I321 - 408
57X-RAY DIFFRACTION57chain 'I' and (resid 409 through 584 )I409 - 584
58X-RAY DIFFRACTION58chain 'J' and (resid 1 through 85 )J1 - 85
59X-RAY DIFFRACTION59chain 'J' and (resid 86 through 187 )J86 - 187
60X-RAY DIFFRACTION60chain 'J' and (resid 188 through 296 )J188 - 296
61X-RAY DIFFRACTION61chain 'J' and (resid 297 through 455 )J297 - 455
62X-RAY DIFFRACTION62chain 'K' and (resid 2 through 77 )K2 - 77
63X-RAY DIFFRACTION63chain 'K' and (resid 78 through 136 )K78 - 136
64X-RAY DIFFRACTION64chain 'K' and (resid 137 through 175 )K137 - 175
65X-RAY DIFFRACTION65chain 'K' and (resid 176 through 364 )K176 - 364
66X-RAY DIFFRACTION66chain 'K' and (resid 365 through 410 )K365 - 410
67X-RAY DIFFRACTION67chain 'K' and (resid 411 through 455 )K411 - 455
68X-RAY DIFFRACTION68chain 'L' and (resid 1 through 38 )L1 - 38
69X-RAY DIFFRACTION69chain 'L' and (resid 39 through 85 )L39 - 85
70X-RAY DIFFRACTION70chain 'L' and (resid 86 through 157 )L86 - 157
71X-RAY DIFFRACTION71chain 'L' and (resid 158 through 200 )L158 - 200
72X-RAY DIFFRACTION72chain 'L' and (resid 201 through 297 )L201 - 297
73X-RAY DIFFRACTION73chain 'L' and (resid 298 through 366 )L298 - 366
74X-RAY DIFFRACTION74chain 'L' and (resid 367 through 411 )L367 - 411
75X-RAY DIFFRACTION75chain 'L' and (resid 412 through 453 )L412 - 453

+
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