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- PDB-6xhr: Crystal structure of S. aureus TarI (space group P1211) -

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基本情報

登録情報
データベース: PDB / ID: 6xhr
タイトルCrystal structure of S. aureus TarI (space group P1211)
要素Ribitol-5-phosphate cytidylyltransferase 1
キーワードTRANSFERASE / cytidylyltransferase
機能・相同性
機能・相同性情報


D-ribitol-5-phosphate cytidylyltransferase / D-ribitol-5-phosphate cytidylyltransferase activity / poly(ribitol phosphate) teichoic acid biosynthetic process / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isoprenoid biosynthetic process / cell wall organization
類似検索 - 分子機能
Ribitol-5-phosphate cytidylyltransferase / : / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site / Cytidylyltransferase IspD/TarI / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. / Nucleotide-diphospho-sugar transferases
類似検索 - ドメイン・相同性
THIOCYANATE ION / Ribitol-5-phosphate cytidylyltransferase 1
類似検索 - 構成要素
生物種Staphylococcus aureus (黄色ブドウ球菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.1 Å
データ登録者Li, F.K.K. / Strynadka, N.C.J.
資金援助 カナダ, 3件
組織認可番号国
Canadian Institutes of Health Research (CIHR) カナダ
Howard Hughes Medical Institute (HHMI) カナダ
Natural Sciences and Engineering Research Council (NSERC, Canada) カナダ
引用ジャーナル: J.Struct.Biol. / 年: 2021
タイトル: Crystallographic analysis of TarI and TarJ, a cytidylyltransferase and reductase pair for CDP-ribitol synthesis in Staphylococcus aureus wall teichoic acid biogenesis.
著者: Li, F.K.K. / Gale, R.T. / Petrotchenko, E.V. / Borchers, C.H. / Brown, E.D. / Strynadka, N.C.J.
履歴
登録2020年6月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年4月21日Provider: repository / タイプ: Initial release
改定 1.12021年4月28日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume
改定 1.22023年10月18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 / 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: Ribitol-5-phosphate cytidylyltransferase 1
B: Ribitol-5-phosphate cytidylyltransferase 1
C: Ribitol-5-phosphate cytidylyltransferase 1
D: Ribitol-5-phosphate cytidylyltransferase 1
E: Ribitol-5-phosphate cytidylyltransferase 1
F: Ribitol-5-phosphate cytidylyltransferase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)175,25814
ポリマ－174,7936
非ポリマー4658
水6,918384
1
A: Ribitol-5-phosphate cytidylyltransferase 1
B: Ribitol-5-phosphate cytidylyltransferase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)58,3814
ポリマ－58,2642
非ポリマー1162
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-25 kcal/mol
Surface area19790 Å2
手法PISA
2
C: Ribitol-5-phosphate cytidylyltransferase 1
D: Ribitol-5-phosphate cytidylyltransferase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)58,4976
ポリマ－58,2642
非ポリマー2324
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-34 kcal/mol
Surface area20410 Å2
手法PISA
3
E: Ribitol-5-phosphate cytidylyltransferase 1
F: Ribitol-5-phosphate cytidylyltransferase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)58,3814
ポリマ－58,2642
非ポリマー1162
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-27 kcal/mol
Surface area19980 Å2
手法PISA
単位格子
Length a, b, c (Å)50.522, 138.448, 110.114
Angle α, β, γ (deg.)90.000, 96.450, 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
11(chain A and (resid 1 or (resid 2 and (name...
21(chain B and (resid 1 or (resid 2 and (name...
31(chain C and (resid 1 or (resid 2 and (name...
41(chain D and (resid 1 or (resid 2 and (name...
51(chain E and (resid 1 or (resid 2 and (name...
61(chain F and (resid 1 through 9 or resid 21...

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
11METMETMETMET(chain A and (resid 1 or (resid 2 and (name...AA11
12LYSLYSLYSLYS(chain A and (resid 1 or (resid 2 and (name...AA22
13METMETALAALA(chain A and (resid 1 or (resid 2 and (name...AA1 - 2361 - 236
14METMETALAALA(chain A and (resid 1 or (resid 2 and (name...AA1 - 2361 - 236
15METMETALAALA(chain A and (resid 1 or (resid 2 and (name...AA1 - 2361 - 236
16METMETALAALA(chain A and (resid 1 or (resid 2 and (name...AA1 - 2361 - 236
21METMETMETMET(chain B and (resid 1 or (resid 2 and (name...BB11
22LYSLYSLYSLYS(chain B and (resid 1 or (resid 2 and (name...BB22
23METMETGLYGLY(chain B and (resid 1 or (resid 2 and (name...BB1 - 2331 - 233
24METMETGLYGLY(chain B and (resid 1 or (resid 2 and (name...BB1 - 2331 - 233
25METMETGLYGLY(chain B and (resid 1 or (resid 2 and (name...BB1 - 2331 - 233
26METMETGLYGLY(chain B and (resid 1 or (resid 2 and (name...BB1 - 2331 - 233
31METMETMETMET(chain C and (resid 1 or (resid 2 and (name...CC11
32LYSLYSLYSLYS(chain C and (resid 1 or (resid 2 and (name...CC22
33METMETALAALA(chain C and (resid 1 or (resid 2 and (name...CC1 - 2361 - 236
34METMETALAALA(chain C and (resid 1 or (resid 2 and (name...CC1 - 2361 - 236
35METMETALAALA(chain C and (resid 1 or (resid 2 and (name...CC1 - 2361 - 236
36METMETALAALA(chain C and (resid 1 or (resid 2 and (name...CC1 - 2361 - 236
41METMETMETMET(chain D and (resid 1 or (resid 2 and (name...DD11
42LYSLYSLYSLYS(chain D and (resid 1 or (resid 2 and (name...DD22
43METMETALAALA(chain D and (resid 1 or (resid 2 and (name...DD1 - 2361 - 236
44METMETALAALA(chain D and (resid 1 or (resid 2 and (name...DD1 - 2361 - 236
45METMETALAALA(chain D and (resid 1 or (resid 2 and (name...DD1 - 2361 - 236
46METMETALAALA(chain D and (resid 1 or (resid 2 and (name...DD1 - 2361 - 236
51METMETMETMET(chain E and (resid 1 or (resid 2 and (name...EE11
52LYSLYSLYSLYS(chain E and (resid 1 or (resid 2 and (name...EE22
53METMETGLYGLY(chain E and (resid 1 or (resid 2 and (name...EE1 - 2331 - 233
54METMETGLYGLY(chain E and (resid 1 or (resid 2 and (name...EE1 - 2331 - 233
55METMETGLYGLY(chain E and (resid 1 or (resid 2 and (name...EE1 - 2331 - 233
56METMETGLYGLY(chain E and (resid 1 or (resid 2 and (name...EE1 - 2331 - 233
61METMETGLYGLY(chain F and (resid 1 through 9 or resid 21...FF1 - 91 - 9
62PROPROPROPRO(chain F and (resid 1 through 9 or resid 21...FF2121
63LYSLYSLYSLYS(chain F and (resid 1 through 9 or resid 21...FF2222
64METMETGLYGLY(chain F and (resid 1 through 9 or resid 21...FF1 - 2331 - 233
65METMETGLYGLY(chain F and (resid 1 through 9 or resid 21...FF1 - 2331 - 233
66METMETGLYGLY(chain F and (resid 1 through 9 or resid 21...FF1 - 2331 - 233
67METMETGLYGLY(chain F and (resid 1 through 9 or resid 21...FF1 - 2331 - 233

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要素

#1: タンパク質
Ribitol-5-phosphate cytidylyltransferase 1


分子量: 29132.209 Da / 分子数: 6 / 由来タイプ: 組換発現
由来: (組換発現) Staphylococcus aureus (黄色ブドウ球菌)
遺伝子: tarI, SAOUHSC_00225 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: Q2G1C0, D-ribitol-5-phosphate cytidylyltransferase
#2: 化合物
ChemComp-SCN / THIOCYANATE ION / チオシアン酸アニオン


分子量: 58.082 Da / 分子数: 8 / 由来タイプ: 合成 / 式: CNS
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 384 / 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N

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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: 2.19 Å3/Da / 溶媒含有率: 43.82 %
結晶化温度: 298 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.25 M sodium thiocyanate, 22.5% PEG3350

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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: CLSI / ビームライン: 08ID-1 / 波長: 0.97949 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2018年2月10日
放射モノクロメーター: double crystal 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: 0.97949 Å / 相対比: 1
反射解像度: 2.1→47.71 Å / Num. obs: 85407 / % possible obs: 97.26 % / 冗長度: 3 % / CC1/2: 0.999 / Rpim(I) all: 0.03396 / Net I/σ(I): 13.23
反射 シェル解像度: 2.1→2.175 Å / 冗長度: 2.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8348 / CC1/2: 0.695 / Rpim(I) all: 0.487 / % possible all: 96.45

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
PDB_EXTRACT3.25データ抽出
XDSデータ削減
Aimless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: PDB entry 4JIS

4jis


解像度: 2.1→47.706 Å / SU ML: 0.29 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 28.34 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2415 4253 5 %
Rwork0.1977 80831 -
obs0.1995 85084 97.27 %
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: 152.43 Å2 / Biso mean: 61.0383 Å2 / Biso min: 25.9 Å2
精密化ステップサイクル: final / 解像度: 2.1→47.706 Å
タンパク質核酸リガンド溶媒全体
原子数10596 0 24 384 11004
Biso mean--59.4 51.86 -
残基数----1389
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A3726X-RAY DIFFRACTION5.974TORSIONAL
12B3726X-RAY DIFFRACTION5.974TORSIONAL
13C3726X-RAY DIFFRACTION5.974TORSIONAL
14D3726X-RAY DIFFRACTION5.974TORSIONAL
15E3726X-RAY DIFFRACTION5.974TORSIONAL
16F3726X-RAY DIFFRACTION5.974TORSIONAL
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 (%)
2.1-2.12390.3511380.3159262996
2.1239-2.14890.30821390.3045264397
2.1489-2.17510.37041400.2979265396
2.1751-2.20260.29021440.2773272797
2.2026-2.23160.34271380.3179262396
2.2316-2.26220.45131180.3887226983
2.2622-2.29450.40261370.3315264394
2.2945-2.32870.30241390.2645264597
2.3287-2.36510.30751410.2503267197
2.3651-2.40390.30031450.2345275497
2.4039-2.44530.27281390.2267264798
2.4453-2.48980.28581420.2331268897
2.4898-2.53770.2641440.2231274298
2.5377-2.58950.30551420.231269698
2.5895-2.64580.27341440.2338273899
2.6458-2.70730.27771420.2331269998
2.7073-2.7750.27711450.2274275499
2.775-2.850.29531440.2369272899
2.85-2.93390.28011430.2335270898
2.9339-3.02860.23621410.2317269698
3.0286-3.13680.25481460.2111276498
3.1368-3.26240.25891400.2247266098
3.2624-3.41080.29841450.2213274998
3.4108-3.59060.23251440.2006273998
3.5906-3.81540.22431410.1812267097
3.8154-4.10990.20841450.1608275299
4.1099-4.52320.16881450.1392275999
4.5232-5.1770.18641460.1322768100
5.177-6.51990.2311470.17342790100
6.5199-47.7060.18861490.1495282799
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)
11.8013-0.53151.96582.6676-0.48536.0368-0.1475-0.13540.1450.42060.0181-0.4692-0.26440.07970.14920.2117-0.0303-0.05040.2958-0.0080.3367.91351.138732.093
23.9261-0.3835-0.44174.5438-1.09268.2466-0.1703-0.04570.49910.37170.1153-0.1956-0.8841-0.0391-0.0030.32730.0134-0.0660.18040.01330.33554.606610.063330.4507
37.4576-1.61791.90593.6015-5.24887.9374-0.3414-0.0455-0.07030.10350.2415-0.0584-0.3663-0.40860.0410.28150.0524-0.01250.4990.00820.268-8.46225.615928.0481
43.0386-1.46210.16194.59970.71572.20160.10880.19680.0973-0.5934-0.0425-0.2078-0.17720.1079-0.07790.2268-0.05520.03660.32940.03340.23020.79060.165917.0449
51.2766-1.06861.47526.1642-5.10645.9617-0.0597-0.0308-0.328-0.12270.11490.32550.55-0.2038-0.0550.3167-0.0160.04590.3693-0.00740.36451.0779-21.628324.947
65.7751.1627-2.76397.15850.24992.912-0.2303-0.4831-0.65250.21010.10990.70360.2221-0.55510.10640.2438-0.0183-0.03640.52570.05160.383-12.6116-5.844825.2671
78.7695-1.23535.67313.1329-0.74674.5451-0.12330.2576-0.3878-0.07320.0969-0.32090.01580.11660.03310.2316-0.01660.04080.2132-0.00130.256810.1209-9.246224.4565
85.46813.6613-3.10685.0245-5.49338.6467-0.60560.445-0.1117-1.3623-0.1103-2.03791.13890.21210.64590.69870.12850.2430.4640.00090.822525.9446-32.562227.9267
97.6679-0.5985-1.81775.36492.29694.6967-0.290.06540.0633-0.28680.0538-1.23390.50240.36740.25960.59170.06470.11110.32540.07210.704627.9499-37.137129.2186
105.81913.1625-4.54587.9319-0.98974.01440.09490.2493-0.4434-1.0899-0.2917-1.64090.51130.19350.31510.59170.13830.13880.33310.08230.748928.0031-41.018627.7669
112.6636-2.0827-2.0225.0074-1.7524.8702-0.23690.588-0.4624-2.2993-0.2366-0.51641.5477-1.13040.07111.4381-0.16060.2480.4818-0.0480.498116.2225-46.817125.2047
121.6838-1.1771-0.32457.1639-0.74971.8452-0.2545-0.01-0.21970.09320.0862-0.20360.91880.01970.18030.6437-0.0029-0.00360.3008-0.00910.30414.8362-37.584837.3828
135.4492-6.23216.61647.41-6.38868.6986-0.26890.0277-0.12910.18070.1030.1855-0.084-0.10550.12290.3996-0.1420.06130.35-0.00130.41231.07-22.19726.5963
143.17211.97213.30186.56593.18764.1386-0.20870.3941-0.3031-0.667-0.02361.02891.2762-0.08740.19140.9222-0.18420.01430.3768-0.01410.58036.7708-45.780629.6485
157.5011-2.51914.88592.7152-3.67885.4113-0.84861.95130.3068-1.98960.17150.5808-0.15910.91320.62241.3511-0.4149-0.08010.85730.03940.56183.0461-39.744221.658
167.40913.2137-2.18375.3756-4.04315.7076-0.24050.1966-0.125-0.71860.0749-0.02450.5103-0.27570.12050.44180.05480.04510.23090.04850.36399.8716-28.995632.5041
174.9484-2.00645.06432.3408-1.42322.0107-0.3227-0.17450.9811-1.3439-0.7659-2.5987-0.9599-0.0930.78670.67190.09060.15320.49450.22551.109323.9498-16.573628.0041
183.15892.298-4.03182.9115-4.8258.9493-0.08390.4932-0.06980.4470.3320.31670.2549-0.8023-0.18851.1135-0.0690.06390.3573-0.00260.37216.1572-38.385356.9411
196.83315.487-6.41796.9831-3.21758.1395-0.4313-0.4579-0.5388-0.1904-0.196-0.69330.74490.84920.6320.69930.159-0.02850.39340.0390.431518.453-37.546162.9392
201.7616-0.0713-0.95942.0903-0.7124.1878-0.425-0.0227-0.4975-0.25310.1054-0.03191.7165-0.06050.31651.3167-0.03710.06550.390.00190.44668.9172-47.833661.5571
211.0119-0.0166-0.2592.57061.40441.1053-0.516-0.158-0.17140.00710.154-0.06311.0972-0.21890.29570.8363-0.06840.03880.35540.03810.33363.4759-40.155873.6762
223.8164-3.75423.27746.6418-6.82228.2934-0.40470.44540.289-0.23780.2671-0.16340.0757-0.12070.20870.5249-0.11230.0050.43310.01350.4483-1.878-21.498665.9915
233.2865-4.17724.13946.1433-6.13216.0588-0.2911-0.0534-0.03460.23250.27740.4884-0.2675-0.57810.00220.5863-0.0475-0.04350.44370.03180.4706-4.1346-18.253664.3554
244.36970.1785-1.05515.4394-0.80970.3759-0.4510.48440.2515-0.2740.05350.62121.2748-1.41570.09981.0166-0.52340.03750.8455-0.02710.5339-9.5284-39.195263.6508
256.03152.9229-3.36744.407-1.27093.12030.07170.06740.1618-0.30040.00220.0504-0.0976-0.2403-0.03910.7140.0298-0.04530.30750.01440.33483.0083-29.451370.0647
266.7605-4.18815.76853.4008-4.38345.7515-0.0705-0.70351.9952-0.0977-0.7895-1.11110.7312-0.04570.86740.80540.0451-0.04430.51080.03590.819119.6206-24.958264.6577
271.78381.8641-0.35223.4398-1.47855.2223-0.0345-0.1226-0.20110.4847-0.2722-0.3905-0.9622-0.08620.27320.67560.0177-0.14820.3058-0.01370.341613.7352-2.193569.202
283.2132-0.1222-0.24632.19672.5943.0853-0.38920.10650.73860.7631-0.1316-0.4424-1.67540.01980.22741.272-0.0865-0.23340.2410.01090.442914.74536.944467.8836
291.2368-1.54721.56692.48-1.73694.6868-0.24920.17670.90650.6121-0.0138-0.3814-1.60170.0280.29521.1804-0.0857-0.21530.30990.01750.485714.07678.113967.1736
301.8439-0.28640.83233.01680.45893.3171-0.3213-0.14040.34060.53630.2255-0.0688-1.1594-0.86120.03970.80040.1717-0.04340.43550.00260.3074.18783.422558.5477
313.40181.0262-2.86894.7699-6.35678.8943-0.0422-0.0012-0.54020.024-0.05530.22280.3095-0.52550.15650.4366-0.0096-0.10330.3821-0.01230.3439-1.6554-17.42962.5343
328.4496.871-6.6545.7886-6.04736.4683-0.44120.7858-0.1016-0.26030.43520.5860.2657-0.627-0.18080.54890.0014-0.0360.3624-0.01520.4659-4.0677-20.704664.0179
330.9939-1.0517-1.60033.63814.27595.2058-0.4817-0.3451-0.3941.09290.38920.8331-0.3817-1.91570.0660.81090.39050.12071.13470.1590.5078-8.0281.445263.9754
346.0756-0.75652.55512.7853-2.63988.04070.00950.0290.03430.07230.0634-0.03870.3102-0.6714-0.03010.458-0.0241-0.0480.2942-0.00360.30943.9342-9.899558.7833
354.10264.3473-6.0314.6965-6.53929.0916-0.76390.2503-0.9767-0.16680.0038-1.71310.19520.28410.77520.7514-0.040.02030.40690.00980.825319.8909-15.743365.5193
364.46311.09491.39072.8524.0525.792-0.3251-0.4666-0.34941.26070.179-0.38030.11540.2580.12280.76540.1478-0.16410.5734-0.05480.446123.0638-7.2342103.7681
373.4363-0.15362.31472.1369-0.35485.1278-0.1568-0.09090.2155-0.00290.0097-0.1709-0.69870.19830.16130.66180.012-0.10990.4384-0.02860.363519.14770.666899.6434
382.06481.3741-0.05875.29260.66890.98080.0083-0.26830.36290.8871-0.10640.734-0.2511-0.41550.10870.80590.1644-0.020.5394-0.07130.4490.0512-6.3418101.9035
397.4535-3.49483.87515.0397-3.69627.8371-0.0329-0.3368-0.29310.171-0.0717-0.29590.3654-0.1190.12560.5140.0089-0.09980.3146-0.03270.3612.2966-15.017299.3681
405.20920.4411-0.6769.0092-1.15893.2926-0.0773-0.0931-0.15561.150.1143-0.75-0.01560.2139-0.02150.65560.0325-0.03930.382-0.07190.4494.2649-39.810496.6626
415.04560.53350.35011.8186-0.61937.0904-0.2065-0.4651-0.40581.57310.14740.05820.3325-0.31970.03970.87320.01130.0170.3580.02940.45560.9369-48.50998.1727
428.50413.2364-3.69495.69081.17267.7588-0.3577-0.3495-0.43521.60730.1487-0.39260.7727-0.71910.13510.953-0.0684-0.04350.3112-0.03090.4591-0.4836-49.585899.0451
438.80462.0655-0.71325.205-6.5848.7799-0.1779-0.1506-0.88651.8474-0.80722.03610.5581-1.51820.58770.9549-0.12020.45240.8763-0.12640.9393-12.3432-44.983999.5928
442.2789-0.6024-0.13570.29940.27672.5918-0.1509-0.3506-0.48692.53390.0540.41590.2733-0.59350.02171.66580.06690.40960.71550.12570.6487-4.1915-38.2008110.7436
450.32580.6079-0.20447.1336-2.21850.6262-0.3305-0.09-0.06861.57490.16880.45040.0765-0.31920.24360.99040.15540.06230.5536-0.0950.4568-2.6733-17.1218102.7191
465.58272.11670.16448.7455-1.38698.61960.2181-0.36570.03481.15080.32822.1368-0.0449-1.6358-0.43050.8551-0.00060.43921.01050.06331.0145-16.4218-37.2183105.0412
472.0253-0.79192.13241.9805-3.30289.6082-1.67450.2841-0.24470.40420.97610.9693-0.8871-1.37950.80351.0170.03320.05631.15980.01890.9456-15.6182-29.622197.5585
488.07440.5655-4.6396.57161.60493.92860.4577-0.09740.41451.25720.18750.2595-0.8822-0.636-0.52481.13830.22620.04720.58370.13770.4158-1.2814-28.6661106.5688
496.6918-0.2558-0.89932.747-4.91769.0901-1.0670.27980.14061.9147-0.4304-3.4655-0.84350.44711.36080.93380.0386-0.36480.4599-0.0021.041815.6448-30.782499.9853
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 41 )A1 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 83 )A42 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 98 )A84 - 98
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 132 )A99 - 132
5X-RAY DIFFRACTION5chain 'A' and (resid 133 through 169 )A133 - 169
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 201 )A170 - 201
7X-RAY DIFFRACTION7chain 'A' and (resid 202 through 236 )A202 - 236
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 31 )B1 - 31
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 67 )B32 - 67
10X-RAY DIFFRACTION10chain 'B' and (resid 68 through 83 )B68 - 83
11X-RAY DIFFRACTION11chain 'B' and (resid 84 through 98 )B84 - 98
12X-RAY DIFFRACTION12chain 'B' and (resid 99 through 132 )B99 - 132
13X-RAY DIFFRACTION13chain 'B' and (resid 133 through 169 )B133 - 169
14X-RAY DIFFRACTION14chain 'B' and (resid 170 through 183 )B170 - 183
15X-RAY DIFFRACTION15chain 'B' and (resid 184 through 201 )B184 - 201
16X-RAY DIFFRACTION16chain 'B' and (resid 202 through 220 )B202 - 220
17X-RAY DIFFRACTION17chain 'B' and (resid 221 through 233 )B221 - 233
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 21 )C1 - 21
19X-RAY DIFFRACTION19chain 'C' and (resid 22 through 41 )C22 - 41
20X-RAY DIFFRACTION20chain 'C' and (resid 42 through 98 )C42 - 98
21X-RAY DIFFRACTION21chain 'C' and (resid 99 through 132 )C99 - 132
22X-RAY DIFFRACTION22chain 'C' and (resid 133 through 150 )C133 - 150
23X-RAY DIFFRACTION23chain 'C' and (resid 151 through 169 )C151 - 169
24X-RAY DIFFRACTION24chain 'C' and (resid 170 through 202 )C170 - 202
25X-RAY DIFFRACTION25chain 'C' and (resid 203 through 220 )C203 - 220
26X-RAY DIFFRACTION26chain 'C' and (resid 221 through 236 )C221 - 236
27X-RAY DIFFRACTION27chain 'D' and (resid 1 through 41 )D1 - 41
28X-RAY DIFFRACTION28chain 'D' and (resid 42 through 67 )D42 - 67
29X-RAY DIFFRACTION29chain 'D' and (resid 68 through 83 )D68 - 83
30X-RAY DIFFRACTION30chain 'D' and (resid 84 through 132 )D84 - 132
31X-RAY DIFFRACTION31chain 'D' and (resid 133 through 150 )D133 - 150
32X-RAY DIFFRACTION32chain 'D' and (resid 151 through 169 )D151 - 169
33X-RAY DIFFRACTION33chain 'D' and (resid 170 through 202 )D170 - 202
34X-RAY DIFFRACTION34chain 'D' and (resid 203 through 220 )D203 - 220
35X-RAY DIFFRACTION35chain 'D' and (resid 221 through 236 )D221 - 236
36X-RAY DIFFRACTION36chain 'E' and (resid 1 through 41 )E1 - 41
37X-RAY DIFFRACTION37chain 'E' and (resid 42 through 132 )E42 - 132
38X-RAY DIFFRACTION38chain 'E' and (resid 133 through 201 )E133 - 201
39X-RAY DIFFRACTION39chain 'E' and (resid 202 through 233 )E202 - 233
40X-RAY DIFFRACTION40chain 'F' and (resid 1 through 41 )F1 - 41
41X-RAY DIFFRACTION41chain 'F' and (resid 42 through 67 )F42 - 67
42X-RAY DIFFRACTION42chain 'F' and (resid 68 through 83 )F68 - 83
43X-RAY DIFFRACTION43chain 'F' and (resid 84 through 99 )F84 - 99
44X-RAY DIFFRACTION44chain 'F' and (resid 100 through 132 )F100 - 132
45X-RAY DIFFRACTION45chain 'F' and (resid 133 through 169 )F133 - 169
46X-RAY DIFFRACTION46chain 'F' and (resid 170 through 183 )F170 - 183
47X-RAY DIFFRACTION47chain 'F' and (resid 184 through 201 )F184 - 201
48X-RAY DIFFRACTION48chain 'F' and (resid 202 through 220 )F202 - 220
49X-RAY DIFFRACTION49chain 'F' and (resid 221 through 234 )F221 - 234

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万見について

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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