[日本語] English
万見
- PDB-6xht: Crystal structure of S. aureus TarI in complex with CDP-ribitol (... -

+
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: 6xht
タイトルCrystal structure of S. aureus TarI in complex with CDP-ribitol (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 / CDP-ribitol / 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: 1.8 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

-
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: 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)176,50719
ポリマ－174,7936
非ポリマー1,71413
水25,7071427
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)59,0347
ポリマ－58,2642
非ポリマー7705
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-33 kcal/mol
Surface area19910 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 area4630 Å2
ΔGint-32 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)58,9766
ポリマ－58,2642
非ポリマー7124
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-28 kcal/mol
Surface area19520 Å2
手法PISA
単位格子
Length a, b, c (Å)49.731, 138.598, 109.532
Angle α, β, γ (deg.)90.000, 96.510, 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 through 11 or resid 18...
21(chain B and (resid 1 through 11 or resid 18...
31(chain C and (resid 1 through 11 or resid 18...
41(chain D and (resid 1 through 11 or resid 18...
51(chain E and (resid 1 through 19 or (resid 20...
61(chain F and (resid 1 through 11 or resid 18...

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
11METMETILEILE(chain A and (resid 1 through 11 or resid 18...AA1 - 111 - 11
12VALVALPROPRO(chain A and (resid 1 through 11 or resid 18...AA18 - 1918 - 19
13LEULEULEULEU(chain A and (resid 1 through 11 or resid 18...AA2020
14METMETGLYGLY(chain A and (resid 1 through 11 or resid 18...AA1 - 2331 - 233
15METMETGLYGLY(chain A and (resid 1 through 11 or resid 18...AA1 - 2331 - 233
16METMETGLYGLY(chain A and (resid 1 through 11 or resid 18...AA1 - 2331 - 233
17METMETGLYGLY(chain A and (resid 1 through 11 or resid 18...AA1 - 2331 - 233
21METMETILEILE(chain B and (resid 1 through 11 or resid 18...BB1 - 111 - 11
22VALVALLEULEU(chain B and (resid 1 through 11 or resid 18...BB18 - 2518 - 25
23ASPASPASPASP(chain B and (resid 1 through 11 or resid 18...BB2626
24METMETALAALA(chain B and (resid 1 through 11 or resid 18...BB1 - 2361 - 236
25METMETALAALA(chain B and (resid 1 through 11 or resid 18...BB1 - 2361 - 236
26METMETALAALA(chain B and (resid 1 through 11 or resid 18...BB1 - 2361 - 236
27METMETALAALA(chain B and (resid 1 through 11 or resid 18...BB1 - 2361 - 236
31METMETILEILE(chain C and (resid 1 through 11 or resid 18...CC1 - 111 - 11
32VALVALPROPRO(chain C and (resid 1 through 11 or resid 18...CC18 - 1918 - 19
33METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
34METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
35METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
36METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
37METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
38METMETALAALA(chain C and (resid 1 through 11 or resid 18...CC1 - 2361 - 236
41METMETILEILE(chain D and (resid 1 through 11 or resid 18...DD1 - 111 - 11
42VALVALPROPRO(chain D and (resid 1 through 11 or resid 18...DD18 - 1918 - 19
43METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
44METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
45METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
46METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
47METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
48METMETALAALA(chain D and (resid 1 through 11 or resid 18...DD1 - 2361 - 236
51METMETPROPRO(chain E and (resid 1 through 19 or (resid 20...EE1 - 191 - 19
52LEULEULEULEU(chain E and (resid 1 through 19 or (resid 20...EE2020
53METMETALAALA(chain E and (resid 1 through 19 or (resid 20...EE1 - 2361 - 236
61METMETILEILE(chain F and (resid 1 through 11 or resid 18...FF1 - 111 - 11
62VALVALPROPRO(chain F and (resid 1 through 11 or resid 18...FF18 - 1918 - 19
63METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236
64METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236
65METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236
66METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236
67METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236
68METMETALAALA(chain F and (resid 1 through 11 or resid 18...FF1 - 2361 - 236

-
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


分子量: 58.082 Da / 分子数: 11 / 由来タイプ: 合成 / 式: CNS
#3: 化合物 ChemComp-V2V / CDP-ribitol / [(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4,5-tetrahydroxypentyl dihydrogen diphosphate


分子量: 537.307 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C14H25N3O15P2 / タイプ: SUBJECT OF INVESTIGATION
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1427 / 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

-
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: 2.15 Å3/Da / 溶媒含有率: 42.68 %
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, 50 mM CTP, 10 mM ribitol-5-phosphate

-
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1月23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: 1.8→50.649 Å / Num. obs: 133473 / % possible obs: 98.16 % / 冗長度: 3.4 % / CC1/2: 0.997 / Rpim(I) all: 0.05645 / Net I/σ(I): 11.92
反射 シェル解像度: 1.8→1.864 Å / 冗長度: 3.5 % / Mean I/σ(I) obs: 1.52 / Num. unique obs: 13181 / CC1/2: 0.602 / Rpim(I) all: 0.5751 / % possible all: 97.64

-
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: 1.8→50.649 Å / SU ML: 0.25 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 23.17 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2167 6771 5.07 %
Rwork0.1697 126679 -
obs0.1715 133450 98.17 %
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: 92.05 Å2 / Biso mean: 32.146 Å2 / Biso min: 11.6 Å2
精密化ステップサイクル: final / 解像度: 1.8→50.649 Å
タンパク質核酸リガンド溶媒全体
原子数10872 0 101 1427 12400
Biso mean--28.14 40.17 -
残基数----1407
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A4080X-RAY DIFFRACTION6.759TORSIONAL
12B4080X-RAY DIFFRACTION6.759TORSIONAL
13C4080X-RAY DIFFRACTION6.759TORSIONAL
14D4080X-RAY DIFFRACTION6.759TORSIONAL
15E4080X-RAY DIFFRACTION6.759TORSIONAL
16F4080X-RAY DIFFRACTION6.759TORSIONAL
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 (%)
1.8-1.82050.37052040.3445418798
1.8205-1.84190.33792210.3317419898
1.8419-1.86430.34732070.3091415898
1.8643-1.88790.31382170.286420197
1.8879-1.91280.32712240.2684422298
1.9128-1.9390.26992260.2402413397
1.939-1.96670.29852040.2326417898
1.9667-1.99610.28032160.2198422498
1.9961-2.02720.25242190.2139421198
2.0272-2.06050.23922390.2011417698
2.0605-2.0960.26042100.1997419597
2.096-2.13410.25272330.1944419598
2.1341-2.17520.23912300.192419998
2.1752-2.21960.24642490.1739416998
2.2196-2.26780.21122450.1664423398
2.2678-2.32060.20012220.1622418798
2.3206-2.37860.22022210.1685426299
2.3786-2.44290.2252460.172419998
2.4429-2.51480.21912320.1687428099
2.5148-2.5960.24392330.1694424399
2.596-2.68880.22622040.1806428099
2.6888-2.79640.22852290.1772425399
2.7964-2.92370.24722290.1775430599
2.9237-3.07780.23362250.1677423699
3.0778-3.27060.22772210.1599428999
3.2706-3.52310.19052080.1546424798
3.5231-3.87750.17262400.1396426699
3.8775-4.43830.17062350.127421598
4.4383-5.59060.16332380.1238426798
5.5906-50.6490.18132440.1467427198
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)
11.50420.3589-0.10022.29050.00992.70910.0652-0.1107-0.04910.128-0.0387-0.2366-0.05010.36910.00130.0926-0.00930.00060.1538-0.00550.1867.90590.874132.29
22.38370.334-0.19182.1107-0.59544.5384-0.05280.02290.2483-0.02390.0298-0.1407-0.410.27910.01350.1596-0.0227-0.00820.119-0.00140.20514.99519.967430.6183
37.3682-4.85814.87954.7907-5.96748.0394-0.01970.07240.02210.5994-0.11820.1395-0.4149-0.09090.12480.13690.0110.00020.137-0.02050.1197-8.12415.839127.8632
43.5482-1.67461.11722.3263-0.30962.26030.06290.11560.1594-0.3444-0.0886-0.134-0.12940.07950.02220.1755-0.0340.02740.12850.01120.14291.27650.059417.1417
50.4927-0.49010.23163.7193-1.6751.095-0.0497-0.0833-0.0429-0.11920.0275-0.00880.0421-0.05350.01850.1272-0.00210.00440.1917-0.00580.19610.8485-21.70725.2221
65.9340.3434-2.42236.2735-1.39595.53060.03840.10690.0904-0.0246-0.03950.6395-0.1193-0.55930.01150.13790.0028-0.04070.1783-0.04070.1694-11.6444-1.163721.097
74.64791.1692-6.64062.8248-1.28949.76850.1705-0.9934-0.30020.4284-0.19170.28610.1112-0.0899-0.04340.2376-0.060.02480.36720.02980.3095-12.9917-8.998928.6452
84.6015-0.39412.71312.49910.65554.51480.00750.026-0.0102-0.09180.038-0.04830.05420.0336-0.06050.1205-0.0110.02620.05460.01960.16622.7175-10.188121.1515
97.44055.2654-0.70598.3441-5.20924.7996-0.6525-0.0132-0.9925-0.2457-0.3757-2.28210.04860.29030.8810.2042-0.01410.0070.1979-0.00030.630219.1706-8.867631.5678
104.49341.9089-2.59746.4758-4.02638.89520.07580.5760.5352-0.7899-0.0738-0.2364-0.46260.36260.16260.30280.01780.05120.27730.09330.320821.167-34.72621.0822
113.40150.1966-0.02852.58980.16812.45460.05350.14290.3478-0.1494-0.0534-0.7097-0.01670.4412-0.00470.13280.01150.03950.27760.04120.414227.5767-35.453728.3871
124.3451.17410.52991.50880.44461.8340.04140.09770.0144-0.0987-0.2362-0.50550.16160.3820.10530.17710.03860.0330.2040.03830.320627.0387-41.239427.9325
138.5474-6.46636.02885.4834-6.22088.33070.32850.2782-0.2438-0.6429-0.2880.06680.82030.1141-0.03980.18110.00460.05110.1716-0.01060.178615.2924-46.980725.4137
140.5508-0.56520.31962.6416-0.43081.0012-0.0328-0.05140.04560.09670.0041-0.1161-0.02860.04920.00850.0864-0.00860.03250.14350.0070.13259.7581-32.727534.2476
154.8481-5.26414.78876.5606-5.04864.71030.0022-0.0788-0.1137-0.10550.09770.1404-0.0129-0.0977-0.04010.1441-0.02190.02080.1458-0.0090.1792-0.7911-20.901526.3779
161.28720.12460.17472.46830.27781.78710.04630.0267-0.0232-0.1439-0.0480.13180.1163-0.16790.01150.12480.00410.01660.17080.02570.18195.4711-36.858527.8913
175.14930.97595.35545.14581.27685.7286-0.4174-0.45880.2658-0.0438-0.217-0.5915-0.73410.0310.66910.1987-0.0219-0.0240.27810.06310.44623.6515-16.972829.4777
182.0865-0.0944-0.91111.7335-0.11854.580.04190.12850.0730.3361-0.03920.0753-0.50830.1167-0.05720.22170.01830.01270.139-0.0160.14375.0231-37.842656.6793
195.59541.4254-0.68536.8981-1.93688.4289-0.2573-0.0941-0.01660.16040.1028-1.02610.12760.85630.13920.19020.057-0.04370.226-0.05590.288817.5315-37.966862.9631
201.97880.03840.47992.4364-0.76765.21660.0089-0.1132-0.13430.36960.2681-0.17880.48630.3128-0.28010.32280.0778-0.02050.1654-0.03070.196612.2247-47.336461.6065
212.81370.7285-0.64683.6435-0.09333.9908-0.0185-0.2246-0.37580.3340.2806-0.34240.47730.5497-0.2690.32320.1061-0.00950.2308-0.06060.189910.982-48.992462.3696
224.8269-1.89090.47953.0623-4.87479.4137-0.14890.0708-0.40230.1760.04110.80590.2256-0.10570.0960.1965-0.01420.06120.1529-0.01960.2-2.3311-48.075461.7127
231.27960.6304-0.23871.69441.03982.0083-0.0401-0.2013-0.11540.62120.00940.09620.37850.02920.00070.38380.06360.04350.16530.03230.18172.5702-40.080773.7374
241.0011-1.16541.74895.7231-5.40015.654-0.32360.05320.21560.49170.27820.3594-0.4351-0.18680.0430.364-0.01010.02040.21320.0110.332-3.8039-19.577664.9229
254.9732.5711.19365.3711-0.32825.17180.065-0.1015-0.13040.6153-0.1590.85910.4466-0.36920.11030.33530.01010.15120.16660.00110.3617-9.2279-42.906167.6596
269.09564.27865.98624.41513.67246.7769-0.22531.40031.1478-0.15450.04820.9979-0.12590.31380.17580.33390.0431-0.00430.39770.1090.4822-11.3482-35.228160.426
276.50022.5587-1.5455.09970.85441.4725-0.0459-0.0530.18950.23750.08580.2809-0.0271-0.0334-0.0510.3160.0490.00130.12250.06460.19121.4362-29.782669.9709
282.7173-1.87661.09817.0565-3.12767.0679-0.8411-0.29180.9239-0.0018-0.1291-1.9731-0.27230.61280.96490.34170.0264-0.09130.31790.02560.650118.9044-25.359564.4558
291.61530.49370.44371.9715-0.4153.48740.0354-0.0448-0.15520.16070.0076-0.1886-0.05950.0141-0.03010.2784-0.0105-0.03160.1284-0.00190.154813.0148-2.627769.3943
302.82480.5280.14231.82250.30973.1066-0.07960.11580.1940.03510.1053-0.1349-0.42080.0144-0.02920.3672-0.0402-0.04420.13560.01550.207514.21167.198267.821
315.59913.4903-0.51347.9598-3.8297.1359-0.3304-0.30120.34590.530.19870.2345-0.7706-0.67790.13780.46960.1112-0.0390.2602-0.06580.18450.52089.474266.5059
322.4102-0.69121.14151.79520.72263.3680.00620.01080.0496-0.01450.0364-0.0032-0.1962-0.1913-0.06370.2531-0.03070.0040.14370.01210.1445.22890.620154.9178
331.44630.904-2.41323.851-5.39538.1933-0.12590.0602-0.25520.30160.04920.260.22990.08490.14530.2832-0.0037-0.01160.1629-0.00380.2801-2.1857-17.372362.5623
343.96494.9993-2.15928.8986-3.31573.2657-0.35110.36330.0081-0.20520.55890.64480.2957-0.1729-0.17330.25040.05920.00370.16890.02320.3101-4.6446-20.651564.1674
352.2701-0.56651.57943.0427-0.24563.0418-0.1765-0.4844-0.17260.50830.1730.56380.0269-0.6628-0.01240.30040.0050.05910.28040.02940.2201-4.0508-2.771261.8093
365.13114.5424-4.78886.9663-4.16914.5867-0.6260.4383-1.01520.17680.1677-0.99990.55610.18780.55730.3607-0.0232-0.03170.2943-0.04320.458119.2887-15.798965.1708
376.8458-2.54043.26757.0504-3.5487.6309-0.095-0.3549-0.35670.32230.1058-0.10530.19050.2427-0.01970.3227-0.0133-0.04410.1809-0.0410.191918.7793-2.733104.8646
386.4775-1.81531.37318.6739-5.04093.2435-0.0269-0.0853-0.39670.39010.072-0.49710.05730.6662-0.10460.28590.0149-0.08980.2384-0.04850.289825.0807-10.8394102.5411
394.6871-0.22170.79094.23080.75762.4587-0.13650.02110.14910.22050.0238-0.3239-0.22010.38870.12280.3012-0.0606-0.07660.1930.00570.234825.0946-0.1005103.8063
407.27751.3521-3.70324.45160.48047.08730.0782-0.13090.25760.17730.0937-0.507-0.7390.6084-0.18330.305-0.0424-0.13410.25150.04260.202224.77991.3158103.1089
419.24036.3436-5.36866.5371-5.07296.9345-0.0145-0.41280.93040.5024-0.08850.5107-0.83590.15320.08090.51590.0487-0.12460.2225-0.06350.289912.92827.0114104.4488
421.738-0.09520.37094.6101-0.09931.467-0.14420.03870.316-0.13310.0702-0.0133-0.51220.16420.05080.3399-0.0387-0.07460.1621-0.00270.192714.2272-0.588996.2783
434.8955-3.1426-0.13167.741-0.29651.0446-0.12560.23020.1339-0.231-0.00370.0158-0.18830.0050.18050.2731-0.0452-0.01960.23450.01770.140210.5271-3.709587.1517
440.36980.47660.23941.6317-1.4322.76120.1774-0.03650.14630.7501-0.04010.8095-0.1758-0.138-0.11810.30680.01090.11810.1764-0.01080.2766-0.5057-15.8186100.1353
457.47384.0635-4.3854.9791-3.38255.23910.02160.33650.51190.39440.28211.10590.098-0.4192-0.19230.27740.00380.07170.14950.02790.3639-3.876-17.9284101.5857
465.2596-1.3518-3.32473.99642.8474.577-0.3335-0.48090.51091.00510.3980.2261-0.8957-0.1675-0.07170.54280.1167-0.04060.22940.00240.26384.076.053898.8639
473.5954-1.35110.72943.9181-0.80362.7022-0.1909-0.31320.22670.65690.20980.397-0.3994-0.3959-0.0410.31270.02310.03630.21010.0180.22732.9375-5.5443100.9994
483.90634.0806-3.63116.813-4.85053.9291-0.02010.3191-0.907-0.1142-0.4065-0.99640.32060.17480.42430.27080.03550.00650.30780.01320.395519.8488-22.8321102.217
491.72990.0037-0.86393.08070.09894.54980.03250.0531-0.0144-0.20920.0271-0.3139-0.09460.1313-0.02740.1887-0.01890.0080.1267-0.0280.19793.7977-39.781796.9774
501.82790.3028-0.04872.37750.95747.2771-0.0137-0.0434-0.24380.15820.0929-0.07860.3517-0.0386-0.08610.2163-0.0204-0.01020.12520.00320.22120.2827-49.161398.6523
517.86492.7205-2.20063.5204-5.60369.77280.04650.2502-0.14230.1208-0.19490.34010.3116-0.77260.14110.2861-0.01410.02750.3242-0.08360.2348-12.7002-44.9745100.4584
526.69910.9748-3.24481.6883-0.98424.13730.1636-0.2612-0.25710.3815-0.1219-0.027-0.1457-0.0698-0.05920.2628-0.00550.00690.10880.0090.1623-4.1011-38.2011111.592
530.37592.3748-0.9268.1655-4.72772.69170.00520.12550.11310.36440.12130.3735-0.1531-0.2321-0.14030.20930.03730.04780.2225-0.0010.2372-2.5961-17.145102.9108
547.23690.01093.7318.9865-2.93965.98850.1890.3421-0.4537-0.22940.04320.7853-0.0759-0.7394-0.23130.22240.04470.04160.3543-0.03870.2483-16.8409-37.0488106.1488
557.4427-1.54626.17678.7517-3.80697.06580.1241.83530.8424-0.9454-0.08030.5673-0.5002-0.127-0.13330.44270.1025-0.02020.70650.11540.419-16.0077-29.316998.4982
566.31660.4676-2.75973.36380.32622.88070.16480.08080.2520.15670.02420.2399-0.348-0.1832-0.17840.25420.00980.02490.12260.02670.2055-1.835-28.5861107.4138
575.0003-6.42384.61929.6479-6.04314.422-0.5215-0.1499-0.01810.383-0.0014-1.1834-0.19140.13740.4370.27650.0054-0.00350.28640.01640.440615.9669-31.527100.7252
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 183 )A170 - 183
7X-RAY DIFFRACTION7chain 'A' and (resid 184 through 201 )A184 - 201
8X-RAY DIFFRACTION8chain 'A' and (resid 202 through 220 )A202 - 220
9X-RAY DIFFRACTION9chain 'A' and (resid 221 through 234 )A221 - 234
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 21 )B1 - 21
11X-RAY DIFFRACTION11chain 'B' and (resid 22 through 67 )B22 - 67
12X-RAY DIFFRACTION12chain 'B' and (resid 68 through 83 )B68 - 83
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 99 )B84 - 99
14X-RAY DIFFRACTION14chain 'B' and (resid 100 through 150 )B100 - 150
15X-RAY DIFFRACTION15chain 'B' and (resid 151 through 169 )B151 - 169
16X-RAY DIFFRACTION16chain 'B' and (resid 170 through 220 )B170 - 220
17X-RAY DIFFRACTION17chain 'B' and (resid 221 through 236 )B221 - 236
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 67 )C42 - 67
21X-RAY DIFFRACTION21chain 'C' and (resid 68 through 83 )C68 - 83
22X-RAY DIFFRACTION22chain 'C' and (resid 84 through 98 )C84 - 98
23X-RAY DIFFRACTION23chain 'C' and (resid 99 through 132 )C99 - 132
24X-RAY DIFFRACTION24chain 'C' and (resid 133 through 169 )C133 - 169
25X-RAY DIFFRACTION25chain 'C' and (resid 170 through 183 )C170 - 183
26X-RAY DIFFRACTION26chain 'C' and (resid 184 through 201 )C184 - 201
27X-RAY DIFFRACTION27chain 'C' and (resid 202 through 220 )C202 - 220
28X-RAY DIFFRACTION28chain 'C' and (resid 221 through 236 )C221 - 236
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 41 )D1 - 41
30X-RAY DIFFRACTION30chain 'D' and (resid 42 through 83 )D42 - 83
31X-RAY DIFFRACTION31chain 'D' and (resid 84 through 98 )D84 - 98
32X-RAY DIFFRACTION32chain 'D' and (resid 99 through 132 )D99 - 132
33X-RAY DIFFRACTION33chain 'D' and (resid 133 through 150 )D133 - 150
34X-RAY DIFFRACTION34chain 'D' and (resid 151 through 169 )D151 - 169
35X-RAY DIFFRACTION35chain 'D' and (resid 170 through 220 )D170 - 220
36X-RAY DIFFRACTION36chain 'D' and (resid 221 through 236 )D221 - 236
37X-RAY DIFFRACTION37chain 'E' and (resid 1 through 21 )E1 - 21
38X-RAY DIFFRACTION38chain 'E' and (resid 22 through 41 )E22 - 41
39X-RAY DIFFRACTION39chain 'E' and (resid 42 through 67 )E42 - 67
40X-RAY DIFFRACTION40chain 'E' and (resid 68 through 83 )E68 - 83
41X-RAY DIFFRACTION41chain 'E' and (resid 84 through 98 )E84 - 98
42X-RAY DIFFRACTION42chain 'E' and (resid 99 through 118 )E99 - 118
43X-RAY DIFFRACTION43chain 'E' and (resid 119 through 132 )E119 - 132
44X-RAY DIFFRACTION44chain 'E' and (resid 133 through 150 )E133 - 150
45X-RAY DIFFRACTION45chain 'E' and (resid 151 through 169 )E151 - 169
46X-RAY DIFFRACTION46chain 'E' and (resid 170 through 183 )E170 - 183
47X-RAY DIFFRACTION47chain 'E' and (resid 184 through 220 )E184 - 220
48X-RAY DIFFRACTION48chain 'E' and (resid 221 through 236 )E221 - 236
49X-RAY DIFFRACTION49chain 'F' and (resid 1 through 41 )F1 - 41
50X-RAY DIFFRACTION50chain 'F' and (resid 42 through 83 )F42 - 83
51X-RAY DIFFRACTION51chain 'F' and (resid 84 through 99 )F84 - 99
52X-RAY DIFFRACTION52chain 'F' and (resid 100 through 132 )F100 - 132
53X-RAY DIFFRACTION53chain 'F' and (resid 133 through 169 )F133 - 169
54X-RAY DIFFRACTION54chain 'F' and (resid 170 through 183 )F170 - 183
55X-RAY DIFFRACTION55chain 'F' and (resid 184 through 201 )F184 - 201
56X-RAY DIFFRACTION56chain 'F' and (resid 202 through 220 )F202 - 220
57X-RAY DIFFRACTION57chain 'F' and (resid 221 through 236 )F221 - 236

+
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