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- PDB-7dug: 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: 7dug
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''TFMS 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(UPUPUPUPUPU)-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-HJR / 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-HJR / 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''TFMS 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(UPUPUPUPUPU)-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)797,276275
ポリマ－790,54323
非ポリマー6,733252
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 area102840 Å2
ΔGint-775 kcal/mol
Surface area278170 Å2
単位格子
Length a, b, c (Å)400.000, 400.000, 173.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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(UPUPUPUPUPU)-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-HJR / N-[(1R,2R,3R,4S,5R)-4-[(2R,6S)-6-(aminomethyl)oxan-2-yl]oxy-5-azanyl-2-[(2R,4S,5R}-5-methyl-4-(methylamino)-5-oxidanyl-oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-1,1,1-tris(fluoranyl)methanesulfonamide


分子量: 550.590 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C20H37F3N4O8S
#25: 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
#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→39.779 Å / Num. obs: 287028 / % possible obs: 94.5 % / 冗長度: 84.9 % / Biso Wilson estimate: 100.3 Å2 / Rmerge(I) obs: 0.91 / Net I/σ(I): 6.58
反射 シェル解像度: 2.92→2.98 Å / 冗長度: 36.31 % / Rmerge(I) obs: 9.901 / Mean I/σ(I) obs: 0.51 / % possible all: 53.8

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解析

ソフトウェア
名称バージョン分類
PHENIXDEV-3318精密化
XDSデータ削減
XSCALEデータスケーリング
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→39.78 Å / SU ML: 0.48 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 26.08 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.225 979 0.7 %
Rwork0.186 --
obs0.186 140493 98.4 %
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 mean: 165 Å2
精密化ステップサイクル: LAST / 解像度: 3.75→39.78 Å
タンパク質核酸リガンド溶媒全体
原子数19088 32943 287 239 52557
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.75-3.94750.35021390.318419844X-RAY DIFFRACTION99
3.9475-4.19460.33851400.274819901X-RAY DIFFRACTION99
4.1946-4.51810.30451350.257419228X-RAY DIFFRACTION96
4.5181-4.9720.23891390.201519924X-RAY DIFFRACTION99
4.972-5.68960.21411410.177720021X-RAY DIFFRACTION99
5.6896-7.16150.23711400.17520024X-RAY DIFFRACTION98
7.1615-39.40.17051450.141620572X-RAY DIFFRACTION98
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)
10.44030.1472-0.14680.472-0.04670.3012-0.0120.0409-0.02250.16140.09380.1280.1116-0.0077-0.08541.21360.12510.11121.0754-0.0421.6218143.484783.2735-12.829
21.039-0.25990.21530.6997-0.14850.28240.0626-0.59180.29910.28370.0261-0.1369-0.20560.0948-0.07471.2522-0.21140.14531.8179-0.57961.6844221.8786129.0989.0846
31.97780.5338-0.68180.2795-0.37250.2308-0.2727-0.1427-0.5055-0.21390.2693-0.47680.22320.14460.00461.3320.17150.01641.3809-0.14991.6693164.342169.8228-26.3647
44.11140.17233.99513.5782-2.89146.5037-0.2461-1.8467-0.41190.32822.17071.4373-1.35150.4064-2.0432.6956-0.36740.9283.71680.41893.0027203.2217111.7867-33.506
51.8194-2.0743-1.92454.35315.0556.0975-0.15280.0078-0.4882-2.42190.5220.0173-0.57931.0561-0.32171.7552-0.05220.30881.12790.26571.9007155.0918157.7037-34.9888
66.1297-0.48651.95318.85562.88495.40710.8562-0.26720.6765-1.5948-0.4930.9905-0.4376-1.4843-0.31511.43870.31040.42160.80460.21192.2871149.112155.8326-27.8303
74.458-1.4586-0.5858.07192.0829.92310.451-0.24912.2006-0.0863-0.2865-0.1994-2.35441.5773-0.27691.6095-0.16890.29051.0844-0.02492.0252166.1586162.5218-19.4611
85.40133.18171.5777.6179-1.96331.96070.1232-0.84870.2365-0.07720.03990.6778-1.0548-0.2411-0.17981.17640.00790.49271.0854-0.54161.8624173.3084157.4767-7.3102
98.8538-4.13170.08344.5103-4.13366.5331-0.7567-0.84671.42950.17551.1093-0.7987-1.5591.9635-0.21361.8041-0.37430.34871.4175-0.64722.3148189.3292162.7491-5.3289
103.21180.51362.15354.1363-2.79243.9977-0.1481-0.08960.2672-0.82170.1794-0.9057-0.07740.15160.00231.57080.09470.65750.7352-0.25632.1687159.3644156.3301-18.8305
115.76285.8548-3.35436.4526-3.98782.61860.9504-0.4312.01690.42430.59170.7735-2.2658-0.4851-1.5143.69290.06050.06390.97050.42093.0952162.0487174.8052-23.7344
123.5103-1.3802-2.09451.8776-0.06081.9994-0.2371-0.76490.66750.83670.2363-0.2469-0.3292-0.26670.01641.7179-0.11460.05091.9867-0.7721.4588204.5861141.605533.1787
131.6356-2.28881.92939.0761-0.66682.898-0.18-0.92460.18970.09580.35640.17690.0539-0.969-0.25221.0457-0.12970.43062.3905-0.50421.6084189.2529133.431217.2882
149.333-4.7103-3.08588.8781-0.5977.7265-0.39090.8886-1.15310.60551.45031.21571.3351-0.7019-0.97271.1173-0.14620.00820.9084-0.21111.5588154.3717110.676437.1774
156.87061.58341.43916.2224-3.33382.73570.8582-0.55410.90590.3457-0.3459-0.5968-0.53160.7311-0.41921.5917-0.01340.10121.1778-0.33221.364160.5734112.801224.8573
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1008.0036-5.526-1.44517.9199-2.17366.3039-0.992-2.44216.28850.24730.7328-0.394-4.065-0.09660.41942.2621-0.03350.61920.9885-0.46962.3235179.893140.2267-63.9666
1016.2062-5.44160.17885.5481-0.59372.8757-2.1325-2.54687.94870.5568-0.11141.3633-5.4174-1.91442.24013.010.56630.58191.431-0.13782.6569174.5948141.83-71.652
1029.7032-7.2472-6.36838.57534.50624.1914-0.1569-0.5055-0.0635-0.1746-0.9244-1.6216-0.02970.64061.06391.03590.1543-0.00242.16640.42291.5368172.0334129.232-76.9236
1034.23093.7021.29514.1749-0.45023.09160.65251.42822.5484-2.4974-0.7014-2.2162-2.8876-0.1425-0.06061.21110.27490.60831.17150.54381.939181.124133.1861-74.7283
1045.1002-5.5408-4.32797.14282.17339.28890.7749-0.09341.66021.34180.5353-3.8231-0.73763.754-1.18880.8165-0.084-0.28692.119-0.55341.2732186.1696128.6392-66.3673
1055.2152-4.8328-4.60414.46764.22254.34361.2681-1.1280.8712-0.15160.6062-0.7532-0.5653-0.7747-1.64311.05170.05650.21131.25860.15071.1441175.4984127.1299-67.2923
1061.354-1.3856-0.36622.8951-0.7340.9236-0.08370.1598-0.44430.2984-0.0007-0.84820.17680.36810.04381.69440.46750.19961.5951-0.05551.4231192.6782125.9485-70.9976
1070.74152.4777-2.22038.35-6.82328.5356-1.12823.6463-0.5988-2.30080.42711.72062.8842-3.70050.54441.4883-0.0438-0.42723.0224-0.98491.785251.0995112.286927.9792
1086.1254-1.56033.87895.3386-3.94195.2349-3.3085-4.81050.92945.83461.9214-0.2699-2.3782-0.23351.21692.00840.3002-0.24412.4909-0.21591.1528250.078599.21142.2133
1092.0394-3.12773.83115.4547-7.03539.2432-1.18620.29290.49890.97190.1654-0.5554-0.3137-1.37940.89621.09090.0492-0.54542.2784-0.27141.8692245.551492.672436.9801
1103.29543.62224.3744.59055.35536.29850.039-6.9382.35410.9095-1.42050.6541-2.0926-1.89521.39331.8025-0.1321-0.19852.7838-0.1121.9173245.7519104.2428.837
1118.88634.76257.11986.12983.45569.669-0.4658-0.8199-1.2618-0.16930.7197-0.9923-0.32350.4419-0.17561.3730.08240.0271.43980.07621.6518248.813995.53428.8944
1124.44290.29196.29372.3618-0.78319.5612-0.80531.7736-1.5372-0.53540.2965-1.77820.25851.70650.33381.43950.27520.21862.2105-0.16781.7397240.467496.257117.8574
1132.4826-1.26034.26581.2344-2.25898.26920.3442-0.18-0.40210.00950.22550.56190.1679-0.4038-0.65161.1667-0.04710.34050.82180.16981.8043107.822341.8232-20.3347
1144.01824.5308-4.51196.3971-7.31829.65471.62311.32881.57370.82281.02232.94420.2184-0.0052-2.56321.2033-0.1923-0.15141.85110.39731.6101105.497651.8145-14.9996
1152.35252.25644.25842.15434.01059.0546-0.24150.60160.7596-0.2079-0.4204-0.3068-2.07592.44160.46341.2487-0.39850.24061.45420.69172.2633103.007152.3189-31.7763
1164.8731-4.59580.51654.88730.70242.5796-0.031-0.1606-0.7066-1.0439-2.57842.86560.4055-3.1612.31661.3186-0.1843-0.15151.7984-0.18021.690192.41347.9465-39.9097
1172.30161.89361.01521.90261.29321.05420.486-0.1422-0.59821.5973-0.07752.1236-0.78350.841-0.3441.3616-0.04640.23031.4066-0.83542.4904250.6082123.97572.1256
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESSEQ 5:920)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESSEQ 921:1400)
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESSEQ 1401:1532)
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESSEQ 1533:1541)
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESSEQ 7:25)
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESSEQ 26:64)
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESSEQ 65:86)
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESSEQ 87:122)
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESSEQ 123:148)
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESSEQ 149:226)
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESSEQ 227:240)
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESSEQ 2:112)
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESSEQ 113:207)
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESSEQ 2:34)
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESSEQ 35:67)
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESSEQ 68:148)
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESSEQ 149:181)
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESSEQ 182:209)
19X-RAY DIFFRACTION19CHAIN 'E' AND (RESSEQ 5:14)
20X-RAY DIFFRACTION20CHAIN 'E' AND (RESSEQ 15:27)
21X-RAY DIFFRACTION21CHAIN 'E' AND (RESSEQ 28:50)
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESSEQ 51:63)
23X-RAY DIFFRACTION23CHAIN 'E' AND (RESSEQ 64:79)
24X-RAY DIFFRACTION24CHAIN 'E' AND (RESSEQ 80:86)
25X-RAY DIFFRACTION25CHAIN 'E' AND (RESSEQ 87:103)
26X-RAY DIFFRACTION26CHAIN 'E' AND (RESSEQ 104:140)
27X-RAY DIFFRACTION27CHAIN 'E' AND (RESSEQ 141:154)
28X-RAY DIFFRACTION28CHAIN 'F' AND (RESSEQ 1:32)
29X-RAY DIFFRACTION29CHAIN 'F' AND (RESSEQ 33:92)
30X-RAY DIFFRACTION30CHAIN 'F' AND (RESSEQ 93:101)
31X-RAY DIFFRACTION31CHAIN 'G' AND (RESSEQ 2:11)
32X-RAY DIFFRACTION32CHAIN 'G' AND (RESSEQ 12:20)
33X-RAY DIFFRACTION33CHAIN 'G' AND (RESSEQ 21:52)
34X-RAY DIFFRACTION34CHAIN 'G' AND (RESSEQ 53:57)
35X-RAY DIFFRACTION35CHAIN 'G' AND (RESSEQ 58:79)
36X-RAY DIFFRACTION36CHAIN 'G' AND (RESSEQ 80:92)
37X-RAY DIFFRACTION37CHAIN 'G' AND (RESSEQ 93:109)
38X-RAY DIFFRACTION38CHAIN 'G' AND (RESSEQ 110:129)
39X-RAY DIFFRACTION39CHAIN 'G' AND (RESSEQ 130:144)
40X-RAY DIFFRACTION40CHAIN 'G' AND (RESSEQ 145:156)
41X-RAY DIFFRACTION41CHAIN 'H' AND (RESSEQ 1:18)
42X-RAY DIFFRACTION42CHAIN 'H' AND (RESSEQ 19:29)
43X-RAY DIFFRACTION43CHAIN 'H' AND (RESSEQ 30:41)
44X-RAY DIFFRACTION44CHAIN 'H' AND (RESSEQ 42:53)
45X-RAY DIFFRACTION45CHAIN 'H' AND (RESSEQ 54:62)
46X-RAY DIFFRACTION46CHAIN 'H' AND (RESSEQ 63:72)
47X-RAY DIFFRACTION47CHAIN 'H' AND (RESSEQ 73:85)
48X-RAY DIFFRACTION48CHAIN 'H' AND (RESSEQ 86:95)
49X-RAY DIFFRACTION49CHAIN 'H' AND (RESSEQ 96:100)
50X-RAY DIFFRACTION50CHAIN 'H' AND (RESSEQ 101:106)
51X-RAY DIFFRACTION51CHAIN 'H' AND (RESSEQ 107:116)
52X-RAY DIFFRACTION52CHAIN 'H' AND (RESSEQ 117:127)
53X-RAY DIFFRACTION53CHAIN 'H' AND (RESSEQ 128:138)
54X-RAY DIFFRACTION54CHAIN 'I' AND (RESSEQ 2:25)
55X-RAY DIFFRACTION55CHAIN 'I' AND (RESSEQ 26:32)
56X-RAY DIFFRACTION56CHAIN 'I' AND (RESSEQ 33:53)
57X-RAY DIFFRACTION57CHAIN 'I' AND (RESSEQ 54:88)
58X-RAY DIFFRACTION58CHAIN 'I' AND (RESSEQ 89:97)
59X-RAY DIFFRACTION59CHAIN 'I' AND (RESSEQ 98:117)
60X-RAY DIFFRACTION60CHAIN 'I' AND (RESSEQ 118:128)
61X-RAY DIFFRACTION61CHAIN 'J' AND (RESSEQ 3:29)
62X-RAY DIFFRACTION62CHAIN 'J' AND (RESSEQ 30:42)
63X-RAY DIFFRACTION63CHAIN 'J' AND (RESSEQ 43:47)
64X-RAY DIFFRACTION64CHAIN 'J' AND (RESSEQ 48:70)
65X-RAY DIFFRACTION65CHAIN 'J' AND (RESSEQ 71:78)
66X-RAY DIFFRACTION66CHAIN 'J' AND (RESSEQ 79:85)
67X-RAY DIFFRACTION67CHAIN 'J' AND (RESSEQ 86:93)
68X-RAY DIFFRACTION68CHAIN 'J' AND (RESSEQ 94:100)
69X-RAY DIFFRACTION69CHAIN 'K' AND (RESSEQ 11:34)
70X-RAY DIFFRACTION70CHAIN 'K' AND (RESSEQ 35:57)
71X-RAY DIFFRACTION71CHAIN 'K' AND (RESSEQ 58:75)
72X-RAY DIFFRACTION72CHAIN 'K' AND (RESSEQ 76:100)
73X-RAY DIFFRACTION73CHAIN 'K' AND (RESSEQ 101:110)
74X-RAY DIFFRACTION74CHAIN 'K' AND (RESSEQ 111:126)
75X-RAY DIFFRACTION75CHAIN 'L' AND (RESSEQ 5:32)
76X-RAY DIFFRACTION76CHAIN 'L' AND (RESSEQ 33:128)
77X-RAY DIFFRACTION77CHAIN 'M' AND (RESSEQ 2:14)
78X-RAY DIFFRACTION78CHAIN 'M' AND (RESSEQ 15:21)
79X-RAY DIFFRACTION79CHAIN 'M' AND (RESSEQ 22:61)
80X-RAY DIFFRACTION80CHAIN 'M' AND (RESSEQ 62:83)
81X-RAY DIFFRACTION81CHAIN 'M' AND (RESSEQ 84:93)
82X-RAY DIFFRACTION82CHAIN 'M' AND (RESSEQ 94:119)
83X-RAY DIFFRACTION83CHAIN 'N' AND (RESSEQ 2:11)
84X-RAY DIFFRACTION84CHAIN 'N' AND (RESSEQ 12:16)
85X-RAY DIFFRACTION85CHAIN 'N' AND (RESSEQ 17:24)
86X-RAY DIFFRACTION86CHAIN 'N' AND (RESSEQ 25:29)
87X-RAY DIFFRACTION87CHAIN 'N' AND (RESSEQ 30:61)
88X-RAY DIFFRACTION88CHAIN 'O' AND (RESSEQ 2:15)
89X-RAY DIFFRACTION89CHAIN 'O' AND (RESSEQ 16:49)
90X-RAY DIFFRACTION90CHAIN 'O' AND (RESSEQ 50:73)
91X-RAY DIFFRACTION91CHAIN 'O' AND (RESSEQ 74:88)
92X-RAY DIFFRACTION92CHAIN 'P' AND (RESSEQ 1:19)
93X-RAY DIFFRACTION93CHAIN 'P' AND (RESSEQ 20:43)
94X-RAY DIFFRACTION94CHAIN 'P' AND (RESSEQ 44:52)
95X-RAY DIFFRACTION95CHAIN 'P' AND (RESSEQ 53:62)
96X-RAY DIFFRACTION96CHAIN 'P' AND (RESSEQ 63:83)
97X-RAY DIFFRACTION97CHAIN 'Q' AND (RESSEQ 2:17)
98X-RAY DIFFRACTION98CHAIN 'Q' AND (RESSEQ 18:82)
99X-RAY DIFFRACTION99CHAIN 'Q' AND (RESSEQ 83:100)
100X-RAY DIFFRACTION100CHAIN 'R' AND (RESSEQ 19:23)
101X-RAY DIFFRACTION101CHAIN 'R' AND (RESSEQ 24:28)
102X-RAY DIFFRACTION102CHAIN 'R' AND (RESSEQ 29:36)
103X-RAY DIFFRACTION103CHAIN 'R' AND (RESSEQ 37:43)
104X-RAY DIFFRACTION104CHAIN 'R' AND (RESSEQ 44:52)
105X-RAY DIFFRACTION105CHAIN 'R' AND (RESSEQ 53:76)
106X-RAY DIFFRACTION106CHAIN 'R' AND (RESSEQ 77:88)
107X-RAY DIFFRACTION107CHAIN 'S' AND (RESSEQ 2:12)
108X-RAY DIFFRACTION108CHAIN 'S' AND (RESSEQ 13:25)
109X-RAY DIFFRACTION109CHAIN 'S' AND (RESSEQ 26:35)
110X-RAY DIFFRACTION110CHAIN 'S' AND (RESSEQ 36:40)
111X-RAY DIFFRACTION111CHAIN 'S' AND (RESSEQ 41:70)
112X-RAY DIFFRACTION112CHAIN 'S' AND (RESSEQ 71:81)
113X-RAY DIFFRACTION113CHAIN 'T' AND (RESSEQ 8:66)
114X-RAY DIFFRACTION114CHAIN 'T' AND (RESSEQ 67:75)
115X-RAY DIFFRACTION115CHAIN 'T' AND (RESSEQ 76:91)
116X-RAY DIFFRACTION116CHAIN 'T' AND (RESSEQ 92:106)
117X-RAY DIFFRACTION117CHAIN 'U' AND (RESSEQ 2:8)

+
万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
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