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- PDB-7duj: Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal... -

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基本情報

登録情報
データベース: PDB / ID: 7duj
タイトルCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1,3''Bz bound
要素
  • (30S ribosomal protein ...) x 20
  • 30S Ribosomal RNA rRNA
  • RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')
  • RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
キーワードRIBOSOME / 30S ribosomal subunit / Sisomicin / RNA structure / Thermus thermophilus / Antibiotic resistance / Decoding
機能・相同性
機能・相同性情報


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
類似検索 - 分子機能
Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Ribosomal protein S11/S14 / Helix hairpin bin / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Double Stranded RNA Binding Domain - #20 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx ...Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Ribosomal protein S11/S14 / Helix hairpin bin / RNA-binding S4 domain / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Double Stranded RNA Binding Domain - #20 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal Protein S5; domain 2 / Ribosomal protein S14, type Z / Double Stranded RNA Binding Domain / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Nucleotidyltransferase; domain 5 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / : / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Helix Hairpins / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S14
類似検索 - ドメイン・相同性
Chem-SIS / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS17 ...Chem-SIS / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18
類似検索 - 構成要素
生物種Thermus thermophilus HB8 (バクテリア)
Thermus thermophilus (バクテリア)
手法X線回折 / シンクロトロン / フーリエ合成 / 解像度: 3.75 Å
データ登録者DeMirci, H. / Destan, E.
資金援助 米国, トルコ, 2件
組織認可番号国
National Science Foundation (NSF, United States)1231306 米国
Other government118C270 トルコ
引用ジャーナル: to be published
タイトル: Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1,3''Bz bound
著者: Demirci, H.
履歴
登録2021年1月9日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年1月12日Provider: repository / タイプ: Initial release
改定 1.12025年2月12日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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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: 30S Ribosomal RNA rRNA
B: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein Thx
Y: RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')
W: RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)797,173275
ポリマ－790,54323
非ポリマー6,630252
水4,306239
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: native gel electrophoresis
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area102830 Å2
ΔGint-769 kcal/mol
Surface area278070 Å2
単位格子
Length a, b, c (Å)400.000, 400.000, 173.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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要素

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RNA鎖 , 3種, 3分子 AYW

#1: RNA鎖 30S Ribosomal RNA rRNA


分子量: 494169.781 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8
#22: RNA鎖 RNA (5'-R(*UP*UP*UP*UP*UP*U)-3')


分子量: 1792.037 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア)
#23: RNA鎖 RNA (5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3')


分子量: 4815.937 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア)

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30S ribosomal protein ... , 20種, 20分子 BCDEFGHIJKLMNOPQRSTU

#2: タンパク質 30S ribosomal protein S2


分子量: 29317.703 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: P80371
#3: タンパク質 30S ribosomal protein S3


分子量: 26751.076 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: P80372
#4: タンパク質 30S ribosomal protein S4


分子量: 24373.447 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: P80373
#5: タンパク質 30S ribosomal protein S5


分子量: 17583.416 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHQ5
#6: タンパク質 30S ribosomal protein S6 / TS9


分子量: 11988.753 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: Q5SLP8
#7: タンパク質 30S ribosomal protein S7


分子量: 18050.973 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: P17291
#8: タンパク質 30S ribosomal protein S8


分子量: 15868.570 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: P0DOY9
#9: タンパク質 30S ribosomal protein S9


分子量: 14410.614 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: P80374
#10: タンパク質 30S ribosomal protein S10


分子量: 11954.968 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHN7
#11: タンパク質 30S ribosomal protein S11


分子量: 13737.868 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: P80376
#12: タンパク質 30S ribosomal protein S12


分子量: 14966.846 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: A0A3P4AU90
#13: タンパク質 30S ribosomal protein S13


分子量: 14338.861 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: P80377
#14: タンパク質 30S ribosomal protein S14 type Z


分子量: 7158.725 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: P0DOY6
#15: タンパク質 30S ribosomal protein S15


分子量: 10578.407 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: Q5SJ76
#16: タンパク質 30S ribosomal protein S16


分子量: 10409.983 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: Q5SJH3
#17: タンパク質 30S ribosomal protein S17


分子量: 12324.670 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: P24321
#18: タンパク質 30S ribosomal protein S18


分子量: 10258.299 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: Q5SLQ0
#19: タンパク質 30S ribosomal protein S19


分子量: 10605.464 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHP2
#20: タンパク質 30S ribosomal protein S20


分子量: 11736.143 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: P80380
#21: タンパク質・ペプチド 30S ribosomal protein Thx / S31


分子量: 3350.030 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: cell / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / 株: HB8 / 参照: UniProt: Q5SIH3

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非ポリマー , 4種, 491分子

#24: 化合物...
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 249 / 由来タイプ: 合成 / 式: Mg
#25: 化合物 ChemComp-SIS / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / Sisomicin / シソマイシン


分子量: 447.526 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C19H37N5O7 / タイプ: SUBJECT OF INVESTIGATION / コメント: 抗生剤*YM
#26: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
#27: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 239 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

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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: 3

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試料調製

結晶マシュー密度: 4.46 Å3/Da / 溶媒含有率: 72.44 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 / 詳細: 17% MPD

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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: SSRL / ビームライン: BL12-2 / 波長: 0.9898 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2016年6月19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: 0.9898 Å / 相対比: 1
反射解像度: 2.91→39.801 Å / Num. obs: 292041 / % possible obs: 96.6 % / 冗長度: 70.208 % / Biso Wilson estimate: 119.05 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 1.212 / Rrim(I) all: 1.221 / Χ2: 0.893 / Net I/σ(I): 4.38 / Num. measured all: 20503703 / Scaling rejects: 30262
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Num. unique obsCC1/2% possible allRmerge(I) obsMean I/σ(I) obsRrim(I) all
2.91-2.9918.281160660.3272.3
2.99-3.0729.6892080296.45.250.685.339
3.07-3.1636.17204060.3297.1
3.16-3.2638.3481980497.1312.95
3.26-3.3640.2281920196.90.0442.604
3.36-3.4840.839184510.3296.1
3.48-3.6153.6051831398.90.1638.209
3.61-3.7679.748178160.15699.80.3817.305
3.76-3.9390.612171020.32599.60.5214.111
3.93-4.1294.456163810.40999.99.6640.829.715
4.12-4.3495.814155630.59299.97.0441.237.08
4.34-4.6196.89146680.72599.34.4971.864.52
4.61-4.92108.444139040.87499.92.5443.342.555
4.92-5.32108.927129410.92999.71.7774.881.785
5.32-5.83103.326119380.95299.71.3256.71.332
5.83-6.51108.809108790.97699.90.9079.740.911
6.51-7.52109.33496610.9931000.50317.430.505
7.52-9.2198.52981650.99799.50.29626.70.297
9.21-13.03100.70764420.9991000.13947.860.14
13.03-39.80188.4793538194.70.07162.960.071

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
XSCALEデータスケーリング
PHENIXDEV-3318精密化
PDB_EXTRACT3.27データ抽出
PHENIX位相決定
精密化構造決定の手法: フーリエ合成 / 解像度: 3.75→39.801 Å / SU ML: 0.64 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 30.5 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2349 973 0.69 %
Rwork0.189 140754 -
obs0.1893 141727 99.27 %
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: 399.28 Å2 / Biso mean: 181.2395 Å2 / Biso min: 60.03 Å2
精密化ステップサイクル: final / 解像度: 3.75→39.801 Å
タンパク質核酸リガンド溶媒全体
原子数19088 32943 521 0 52552
Biso mean--161.87 --
残基数----3910
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 (%)
3.75-3.94750.42391350.37061944397
3.9475-4.19460.37251390.314920001100
4.1946-4.51810.31391370.28311987199
4.5181-4.9720.26851390.219320087100
4.972-5.68970.22081390.17820192100
5.6897-7.16150.21711400.176620324100
7.1615-39.40.18361440.133820836100
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)
10.4430.1541-0.14780.4691-0.05350.3334-0.02240.007-0.05020.16440.10520.11360.10580.0157-0.07661.40780.14070.10141.2632-0.0511.69143.50683.2758-12.7867
21.1715-0.30760.240.7461-0.17950.33210.0443-0.60370.31770.34390.0331-0.1439-0.26010.0039-0.05311.3647-0.19180.12811.8501-0.60321.6484221.9645129.08919.1389
32.4630.8966-0.82930.5296-0.38610.2195-0.4009-0.1548-0.7147-0.41070.3093-0.73940.21260.15320.11061.54530.21040.00121.6208-0.12461.7323164.351869.8347-26.3165
45.0975-4.7336.39894.4838-6.05818.3063-0.901-2.4816-1.28330.84182.40231.5076-1.13350.2794-1.70832.8595-0.40960.63464.30140.26553.0295203.2395111.8532-33.4857
51.3772-2.149-2.64394.37415.70287.4239-0.0015-0.2022-1.0099-3.48430.2785-0.5818-0.77571.0818-0.22592.0641-0.18130.28911.28270.06051.7493155.2818157.8297-34.9209
66.9816-1.2474-0.78366.44994.77283.77550.55220.08440.2806-1.8487-0.19531.1029-0.662-1.5677-0.23181.83260.34210.29520.92710.25422.1541149.2271155.9461-27.7678
79.8609-3.0573-4.11654.1132-0.64012.9696-0.737-0.46881.70970.3883-0.29450.1061-0.88810.8631.07291.586-0.07480.13221.2921-0.10172.1177166.3311162.5735-19.3532
86.04434.41941.26267.3871-1.71912.62620.4183-0.87970.8827-0.1552-0.15191.0412-1.06260.1042-0.26851.53650.09580.44351.3342-0.49871.9561173.3834157.4483-7.1767
98.0233-4.8504-0.39389.1617-4.51733.6384-0.6001-0.97211.58780.52651.3201-0.4657-1.11041.3604-0.57992.0447-0.24050.24021.3116-0.73152.4837189.4546162.6758-5.1463
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947.01346.22856.89575.51856.11226.7666-1.19270.57483.212-0.3569-0.0910.8836-4.42761.77171.27772.2927-0.27180.87491.11920.00922.408109.963986.482320.5316
954.99926.41813.64438.26614.70042.6718-0.69990.26531.0022-1.6964-0.60150.5354-2.9328-0.53961.13711.87510.44010.10791.57550.81652.3841100.917479.3335.6894
968.8913-4.156-2.06555.44934.0993.2859-0.2857-1.1583-2.78771.3139-0.97441.02930.57730.03961.29881.6077-0.22170.61091.03150.28212.0715101.431874.869716.4881
979.43397.09361.3188.1758-0.43590.8985-0.22780.56920.2517-0.67060.6341-0.04970.0938-0.0213-0.37180.75390.05840.00671.17830.48871.9056119.549780.775-38.4556
980.9647-1.1820.70761.86230.30073.79020.20390.14-0.55420.15010.22690.80870.2757-0.1124-0.35580.8842-0.12530.13331.26090.21441.4012121.571584.6338-35.7099
995.3719-0.13544.8853.2573-4.52912.01151.20932.2848-0.0601-0.5708-1.3738-0.3456-0.59421.28450.17421.6059-0.20460.05531.9871-0.09581.2904137.668585.6928-44.8334
1002.5891-0.67581.96762.1009-0.29882.0095-1.1419-1.62226.8486-0.06370.7923-0.061-4.13640.13710.38292.6655-0.1290.34941.0781-0.3082.2011179.8776140.3099-63.8224
1015.73013.4925.74952.15363.55695.8753-2.4835-2.10578.20370.66340.17910.8883-5.4843-1.29372.35593.37890.41730.70231.696-0.23463.1992174.5229141.8274-71.4793
1024.5946-3.9653-5.05756.38373.38415.8886-0.2141-0.4596-0.1781-0.0389-1.1537-1.0779-0.00490.03591.32071.32540.19810.03792.2070.3511.3112172.0337129.254-76.7549
1035.8975.1991.1874.59710.86842.14130.56551.58172.1871-2.5379-0.1463-2.079-3.1010.5823-0.46771.54720.17450.52651.23810.60471.7306181.0751133.2848-74.552
1045.7971-3.8532-2.2655.5673-1.54473.97360.3737-0.92672.54311.38490.5878-3.9646-1.39523.5693-0.89860.7994-0.3148-0.2372.4144-0.54021.4153186.1524128.7237-66.3076
1055.2097-4.7003-4.85364.22864.32544.82011.4446-1.34190.84330.10890.5372-0.7714-0.2778-1.271-1.67031.290.01560.24771.41280.18850.9385175.5019127.2144-67.1909
1069.19051.60210.37284.6262-0.56680.1320.08380.4886-0.71550.3863-0.1065-1.11630.27140.3453-0.01861.75230.39480.19011.3920.13061.4656192.7134126.0896-70.8674
1074.37775.2822-5.20946.3872-6.13826.8461-1.27782.9546-0.4052-1.63050.50552.28912.3528-3.96950.61621.65580.0734-0.48962.5117-1.12142.4817251.2025112.277128.0148
1084.2342-3.64724.32763.5517-4.03724.6479-3.3839-4.33161.3115.5112.074-0.0987-2.3248-0.15831.2271.94820.379-0.21342.6636-0.40971.1745250.260499.100842.1547
1095.5787-5.90875.71366.2463-6.04175.8353-1.07180.41010.49021.13980.178-0.6624-0.5111-1.45290.81521.1960.0529-0.55252.4096-0.24031.8571245.771192.622336.8919
1109.87315.06581.67936.6175.49685.626-1.1316-5.8114.94590.651-0.56250.8803-1.6417-2.09651.70051.4532-0.2023-0.19912.9854-0.23441.9398245.9741104.263628.8414
1114.50872.41876.23364.73271.70979.4404-0.8169-0.5068-0.26850.06270.8601-0.2558-0.48510.2690.04171.55350.0366-0.02741.8181-0.00581.8865248.962895.467228.8643
1124.4756-3.18865.67457.1688-3.75937.1583-1.21671.5477-1.1974-0.57370.3747-1.67980.16592.37110.62011.35260.04680.34252.5499-0.20821.8516240.572196.222217.7672
1133.484-1.68155.55821.6673-2.31519.74230.4193-0.0982-0.8883-0.07480.56290.5321-0.4706-0.2707-0.94481.3306-0.0540.38760.82530.16811.7125107.710241.9054-20.2297
1143.16053.951-2.87836.7626-5.7355.18491.38340.40660.08451.46361.28193.54681.3648-0.1593-2.57621.5189-0.1422-0.20411.70020.29481.5452105.431851.8845-14.9268
1154.39572.92723.88824.07082.55253.4278-0.24860.89350.6232-0.1104-0.3795-0.1756-1.41481.85350.34961.4166-0.46580.29491.6140.75962.2601102.878152.3631-31.6927
1163.121-0.82273.19236.1663.88537.01820.3924-0.2171-0.3209-1.6952-3.10212.4028-0.3526-2.21662.38481.6506-0.0451-0.17711.9405-0.15521.765692.261848.007-39.7251
1176.0148-7.01580.14198.2808-0.30650.3970.473-0.4495-0.9161.6371-0.13322.5516-0.65630.2588-0.39941.4840.01630.19281.8037-1.0692.8554250.7176123.99422.1601
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:920)A5 - 920
2X-RAY DIFFRACTION2chain 'A' and (resseq 921:1400)A921 - 1400
3X-RAY DIFFRACTION3chain 'A' and (resseq 1401:1532)A1401 - 1532
4X-RAY DIFFRACTION4chain 'A' and (resseq 1533:1541)A1533 - 1541
5X-RAY DIFFRACTION5chain 'B' and (resseq 7:25)B7 - 25
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:64)B26 - 64
7X-RAY DIFFRACTION7chain 'B' and (resseq 65:86)B65 - 86
8X-RAY DIFFRACTION8chain 'B' and (resseq 87:122)B87 - 122
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:148)B123 - 148
10X-RAY DIFFRACTION10chain 'B' and (resseq 149:226)B149 - 226
11X-RAY DIFFRACTION11chain 'B' and (resseq 227:240)B227 - 240
12X-RAY DIFFRACTION12chain 'C' and (resseq 2:112)C2 - 112
13X-RAY DIFFRACTION13chain 'C' and (resseq 113:207)C113 - 207
14X-RAY DIFFRACTION14chain 'D' and (resseq 2:34)D2 - 34
15X-RAY DIFFRACTION15chain 'D' and (resseq 35:67)D35 - 67
16X-RAY DIFFRACTION16chain 'D' and (resseq 68:148)D68 - 148
17X-RAY DIFFRACTION17chain 'D' and (resseq 149:181)D149 - 181
18X-RAY DIFFRACTION18chain 'D' and (resseq 182:209)D182 - 209
19X-RAY DIFFRACTION19chain 'E' and (resseq 5:14)E5 - 14
20X-RAY DIFFRACTION20chain 'E' and (resseq 15:27)E15 - 27
21X-RAY DIFFRACTION21chain 'E' and (resseq 28:50)E28 - 50
22X-RAY DIFFRACTION22chain 'E' and (resseq 51:63)E51 - 63
23X-RAY DIFFRACTION23chain 'E' and (resseq 64:79)E64 - 79
24X-RAY DIFFRACTION24chain 'E' and (resseq 80:86)E80 - 86
25X-RAY DIFFRACTION25chain 'E' and (resseq 87:103)E87 - 103
26X-RAY DIFFRACTION26chain 'E' and (resseq 104:140)E104 - 140
27X-RAY DIFFRACTION27chain 'E' and (resseq 141:154)E141 - 154
28X-RAY DIFFRACTION28chain 'F' and (resseq 1:32)F1 - 32
29X-RAY DIFFRACTION29chain 'F' and (resseq 33:92)F33 - 92
30X-RAY DIFFRACTION30chain 'F' and (resseq 93:101)F93 - 101
31X-RAY DIFFRACTION31chain 'G' and (resseq 2:11)G2 - 11
32X-RAY DIFFRACTION32chain 'G' and (resseq 12:20)G12 - 20
33X-RAY DIFFRACTION33chain 'G' and (resseq 21:52)G21 - 52
34X-RAY DIFFRACTION34chain 'G' and (resseq 53:57)G53 - 57
35X-RAY DIFFRACTION35chain 'G' and (resseq 58:79)G58 - 79
36X-RAY DIFFRACTION36chain 'G' and (resseq 80:92)G80 - 92
37X-RAY DIFFRACTION37chain 'G' and (resseq 93:109)G93 - 109
38X-RAY DIFFRACTION38chain 'G' and (resseq 110:129)G110 - 129
39X-RAY DIFFRACTION39chain 'G' and (resseq 130:144)G130 - 144
40X-RAY DIFFRACTION40chain 'G' and (resseq 145:156)G145 - 156
41X-RAY DIFFRACTION41chain 'H' and (resseq 1:18)H1 - 18
42X-RAY DIFFRACTION42chain 'H' and (resseq 19:29)H19 - 29
43X-RAY DIFFRACTION43chain 'H' and (resseq 30:41)H30 - 41
44X-RAY DIFFRACTION44chain 'H' and (resseq 42:53)H42 - 53
45X-RAY DIFFRACTION45chain 'H' and (resseq 54:62)H54 - 62
46X-RAY DIFFRACTION46chain 'H' and (resseq 63:72)H63 - 72
47X-RAY DIFFRACTION47chain 'H' and (resseq 73:85)H73 - 85
48X-RAY DIFFRACTION48chain 'H' and (resseq 86:95)H86 - 95
49X-RAY DIFFRACTION49chain 'H' and (resseq 96:100)H96 - 100
50X-RAY DIFFRACTION50chain 'H' and (resseq 101:106)H101 - 106
51X-RAY DIFFRACTION51chain 'H' and (resseq 107:116)H107 - 116
52X-RAY DIFFRACTION52chain 'H' and (resseq 117:127)H117 - 127
53X-RAY DIFFRACTION53chain 'H' and (resseq 128:138)H128 - 138
54X-RAY DIFFRACTION54chain 'I' and (resseq 2:25)I2 - 25
55X-RAY DIFFRACTION55chain 'I' and (resseq 26:32)I26 - 32
56X-RAY DIFFRACTION56chain 'I' and (resseq 33:53)I33 - 53
57X-RAY DIFFRACTION57chain 'I' and (resseq 54:88)I54 - 88
58X-RAY DIFFRACTION58chain 'I' and (resseq 89:97)I89 - 97
59X-RAY DIFFRACTION59chain 'I' and (resseq 98:117)I98 - 117
60X-RAY DIFFRACTION60chain 'I' and (resseq 118:128)I118 - 128
61X-RAY DIFFRACTION61chain 'J' and (resseq 3:29)J3 - 29
62X-RAY DIFFRACTION62chain 'J' and (resseq 30:42)J30 - 42
63X-RAY DIFFRACTION63chain 'J' and (resseq 43:47)J43 - 47
64X-RAY DIFFRACTION64chain 'J' and (resseq 48:70)J48 - 70
65X-RAY DIFFRACTION65chain 'J' and (resseq 71:78)J71 - 78
66X-RAY DIFFRACTION66chain 'J' and (resseq 79:85)J79 - 85
67X-RAY DIFFRACTION67chain 'J' and (resseq 86:93)J86 - 93
68X-RAY DIFFRACTION68chain 'J' and (resseq 94:100)J94 - 100
69X-RAY DIFFRACTION69chain 'K' and (resseq 11:34)K11 - 34
70X-RAY DIFFRACTION70chain 'K' and (resseq 35:57)K35 - 57
71X-RAY DIFFRACTION71chain 'K' and (resseq 58:75)K58 - 75
72X-RAY DIFFRACTION72chain 'K' and (resseq 76:100)K76 - 100
73X-RAY DIFFRACTION73chain 'K' and (resseq 101:110)K101 - 110
74X-RAY DIFFRACTION74chain 'K' and (resseq 111:126)K111 - 126
75X-RAY DIFFRACTION75chain 'L' and (resseq 5:32)L5 - 32
76X-RAY DIFFRACTION76chain 'L' and (resseq 33:128)L33 - 128
77X-RAY DIFFRACTION77chain 'M' and (resseq 2:14)M2 - 14
78X-RAY DIFFRACTION78chain 'M' and (resseq 15:21)M15 - 21
79X-RAY DIFFRACTION79chain 'M' and (resseq 22:61)M22 - 61
80X-RAY DIFFRACTION80chain 'M' and (resseq 62:83)M62 - 83
81X-RAY DIFFRACTION81chain 'M' and (resseq 84:93)M84 - 93
82X-RAY DIFFRACTION82chain 'M' and (resseq 94:119)M94 - 119
83X-RAY DIFFRACTION83chain 'N' and (resseq 2:11)N2 - 11
84X-RAY DIFFRACTION84chain 'N' and (resseq 12:16)N12 - 16
85X-RAY DIFFRACTION85chain 'N' and (resseq 17:24)N17 - 24
86X-RAY DIFFRACTION86chain 'N' and (resseq 25:29)N25 - 29
87X-RAY DIFFRACTION87chain 'N' and (resseq 30:61)N30 - 61
88X-RAY DIFFRACTION88chain 'O' and (resseq 2:15)O2 - 15
89X-RAY DIFFRACTION89chain 'O' and (resseq 16:49)O16 - 49
90X-RAY DIFFRACTION90chain 'O' and (resseq 50:73)O50 - 73
91X-RAY DIFFRACTION91chain 'O' and (resseq 74:88)O74 - 88
92X-RAY DIFFRACTION92chain 'P' and (resseq 1:19)P1 - 19
93X-RAY DIFFRACTION93chain 'P' and (resseq 20:43)P20 - 43
94X-RAY DIFFRACTION94chain 'P' and (resseq 44:52)P44 - 52
95X-RAY DIFFRACTION95chain 'P' and (resseq 53:62)P53 - 62
96X-RAY DIFFRACTION96chain 'P' and (resseq 63:83)P63 - 83
97X-RAY DIFFRACTION97chain 'Q' and (resseq 2:17)Q2 - 17
98X-RAY DIFFRACTION98chain 'Q' and (resseq 18:82)Q18 - 82
99X-RAY DIFFRACTION99chain 'Q' and (resseq 83:100)Q83 - 100
100X-RAY DIFFRACTION100chain 'R' and (resseq 19:23)R19 - 23
101X-RAY DIFFRACTION101chain 'R' and (resseq 24:28)R24 - 28
102X-RAY DIFFRACTION102chain 'R' and (resseq 29:36)R29 - 36
103X-RAY DIFFRACTION103chain 'R' and (resseq 37:43)R37 - 43
104X-RAY DIFFRACTION104chain 'R' and (resseq 44:52)R44 - 52
105X-RAY DIFFRACTION105chain 'R' and (resseq 53:76)R53 - 76
106X-RAY DIFFRACTION106chain 'R' and (resseq 77:88)R77 - 88
107X-RAY DIFFRACTION107chain 'S' and (resseq 2:12)S2 - 12
108X-RAY DIFFRACTION108chain 'S' and (resseq 13:25)S13 - 25
109X-RAY DIFFRACTION109chain 'S' and (resseq 26:35)S26 - 35
110X-RAY DIFFRACTION110chain 'S' and (resseq 36:40)S36 - 40
111X-RAY DIFFRACTION111chain 'S' and (resseq 41:70)S41 - 70
112X-RAY DIFFRACTION112chain 'S' and (resseq 71:81)S71 - 81
113X-RAY DIFFRACTION113chain 'T' and (resseq 8:66)T8 - 66
114X-RAY DIFFRACTION114chain 'T' and (resseq 67:75)T67 - 75
115X-RAY DIFFRACTION115chain 'T' and (resseq 76:91)T76 - 91
116X-RAY DIFFRACTION116chain 'T' and (resseq 92:106)T92 - 106
117X-RAY DIFFRACTION117chain 'U' and (resseq 2:8)U2 - 8

+
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

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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

+
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