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- PDB-4dr4: 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: 4dr4
タイトルCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, cognate transfer RNA anticodon stem-loop and multiple copies of paromomycin molecules bound
要素
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
  • 5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3'
  • 5'-R(*UP*UP*U)-3'
キーワードRIBOSOME/ANTIBIOTIC / decoding / Streptomycin / RNA structure / antibiotic resistance / RIBOSOME-ANTIBIOTIC complex
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 / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol
類似検索 - 分子機能
Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A ...Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S14/S29 / 30s Ribosomal Protein S14; Chain N / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S3 C-terminal domain / Helix hairpin bin / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / K homology (KH) domain / Double Stranded RNA Binding Domain - #20 / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / GMP Synthetase; Chain A, domain 3 / Ribosomal Protein S5; domain 2 / Double Stranded RNA Binding Domain / Ribosomal protein S14, type Z / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / 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 S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / 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 / Few Secondary Structures / Irregular / 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 / : / 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 S2, conserved site / Ribosomal protein S5, N-terminal, conserved site
類似検索 - ドメイン・相同性
PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 ...PAROMOMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / 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 uS12 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS19 / 30S ribosomal protein S17 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 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 (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: 3.969 Å
データ登録者Demirci, H. / Murphy IV, F. / Murphy, E. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
引用ジャーナル: Nat Commun / 年: 2013
タイトル: A structural basis for streptomycin-induced misreading of the genetic code.
著者: Demirci, H. / Murphy, F. / Murphy, E. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
履歴
登録2012年2月16日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02012年11月14日Provider: repository / タイプ: Initial release
改定 1.12013年1月23日Group: Database references
改定 1.22013年1月30日Group: Database references

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: 16S 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
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
V: 5'-R(*UP*UP*U)-3'
W: 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)809,514400
ポリマ－789,62523
非ポリマー19,889377
水8,971498
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)400.951, 400.951, 176.675
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 AVW

#1: RNA鎖 16S rRNA


分子量: 494170.781 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: GenBank: M26923.1
#22: RNA鎖 5'-R(*UP*UP*U)-3'


分子量: 873.540 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: mRNA / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8
#23: RNA鎖 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 / 詳細: ASL (Phenylalanine) / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8

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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 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHQ5
#6: タンパク質 30S ribosomal protein S6


分子量: 11988.753 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS
#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 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: F6DEQ7, UniProt: Q5SHN3*PLUS
#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 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: P80377
#14: タンパク質 30S ribosomal protein S14


分子量: 7158.725 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHQ1, UniProt: P0DOY6*PLUS
#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 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB8 / 参照: UniProt: Q5SHP7, UniProt: P0DOY7*PLUS
#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 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (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 / 由来: (天然) Thermus thermophilus (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


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

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非ポリマー , 4種, 875分子

#24: 化合物
ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I, AMMINOSIDIN, CATENULIN, CRESTOMYCIN, MONOMYCIN A, NEOMYCIN E / パロモマイシン


分子量: 615.628 Da / 分子数: 18 / 由来タイプ: 合成 / 式: C23H45N5O14 / コメント: 抗菌剤, 薬剤*YM
#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: 357 / 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: 498 / 由来タイプ: 天然 / 式: H2O

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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: 4.5 Å3/Da / 溶媒含有率: 72.64 %
結晶化温度: 277 K / 手法: ハンギングドロップ法 / pH: 6.5 / 詳細: MPD, pH 6.5, HANGING DROP, temperature 277K

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.98 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2008年12月3日
放射モノクロメーター: Kohzu HLD8-24 / 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: 0.98 Å / 相対比: 1
Reflection冗長度: 7.3 % / Av σ(I) over netI: 10.62 / 数: 901205 / Rmerge(I) obs: 0.253 / Χ2: 1.05 / D res high: 3.97 Å / D res low: 50 Å / Num. obs: 123861 / % possible obs: 100
Diffraction reflection shell
最高解像度 (Å)最低解像度 (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
10.745099.810.041.0597.1
8.5410.7410010.0831.0357.1
7.468.5410010.1241.0777.2
6.787.4610010.1641.0727.3
6.36.7810010.2191.0897.4
5.936.310010.2481.0687.4
5.635.9310010.2611.0337.4
5.395.6310010.2741.0287.4
5.185.3910010.3161.0297.5
55.1810010.341.0327.5
4.84510010.3671.0357.5
4.714.8410010.4231.0497.5
4.584.7110010.4641.057.5
4.474.5810010.5111.0547.4
4.374.4710010.5771.0267.4
4.284.3710010.6541.0377.3
4.194.2810010.7411.0427.2
4.114.1910010.8261.0457
4.044.1110010.9171.0286.9
3.974.0410010.9921.0216.7
反射解像度: 3.969→50 Å / Num. all: 123861 / Num. obs: 123861 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / 冗長度: 7.3 % / Rmerge(I) obs: 0.253 / Χ2: 1.046 / Net I/σ(I): 3.9
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.969-4.046.70.99261021.0211100
4.04-4.116.90.91761351.0281100
4.11-4.1970.82661121.0451100
4.19-4.287.20.74161121.0421100
4.28-4.377.30.65461341.0371100
4.37-4.477.40.57761161.0261100
4.47-4.587.40.51161251.0541100
4.58-4.717.50.46461551.051100
4.71-4.847.50.42361471.0491100
4.84-57.50.36761451.0351100
5-5.187.50.3461631.0321100
5.18-5.397.50.31661641.0291100
5.39-5.637.40.27461641.0281100
5.63-5.937.40.26162091.0331100
5.93-6.37.40.24861971.0681100
6.3-6.787.40.21962171.0891100
6.78-7.467.30.16462391.0721100
7.46-8.547.20.12462821.0771100
8.54-10.747.10.08363391.0351100
10.74-507.10.0466041.059199.8

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解析

ソフトウェア
名称バージョン分類NB
DENZOデータ削減
SCALEPACKデータスケーリング
PHENIXdev_978精密化
PDB_EXTRACT3.1データ抽出
HKL-2000データ収集
PHENIXdev_978位相決定
精密化構造決定の手法: フーリエ合成 / 解像度: 3.969→49.732 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8763 / SU ML: 0.4 / σ(F): 1.34 / 位相誤差: 19.25 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2124 6187 5 %FROM PDB ENTRY 2VQE
Rwork0.1531 ---
obs0.1561 123736 99.94 %-
all-123736 --
溶媒の処理減衰半径: 0.86 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 34.759 Å2 / ksol: 0.247 e/Å3
原子変位パラメータBiso max: 523.53 Å2 / Biso mean: 101.1617 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--12.2147 Å2-0 Å20 Å2
2---12.2147 Å20 Å2
3---2.7328 Å2
精密化ステップサイクル: LAST / 解像度: 3.969→49.732 Å
タンパク質核酸リガンド溶媒全体
原子数19152 32880 1115 498 53645
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01357582
X-RAY DIFFRACTIONf_angle_d1.52785403
X-RAY DIFFRACTIONf_chiral_restr0.08310823
X-RAY DIFFRACTIONf_plane_restr0.0084917
X-RAY DIFFRACTIONf_dihedral_angle_d26.09827930
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.969-4.01440.30262210.224538674088100
4.0144-4.06160.30672260.214238254051100
4.0616-4.11110.26912150.205338624077100
4.1111-4.16320.24141870.18238664053100
4.1632-4.21790.25092010.173539134114100
4.2179-4.27570.2482020.167838654067100
4.2757-4.33670.25222130.172938874100100
4.3367-4.40140.23642270.174438524079100
4.4014-4.47010.2352120.15138554067100
4.4701-4.54340.22152130.157538954108100
4.5434-4.62170.2231910.148238884079100
4.6217-4.70560.18441850.14238924077100
4.7056-4.79610.22311930.140139104103100
4.7961-4.89390.22011920.138839154107100
4.8939-5.00020.19512190.126538684087100
5.0002-5.11640.18651920.127639084100100
5.1164-5.24420.18942020.123939144116100
5.2442-5.38590.17241990.116139114110100
5.3859-5.54410.18592110.109439244135100
5.5441-5.72280.17462090.111438914100100
5.7228-5.92710.19031950.115539364131100
5.9271-6.1640.19071970.116639304127100
6.164-6.44390.16731920.116939474139100
6.4439-6.78290.19692190.118639264145100
6.7829-7.20670.17772010.110939384139100
7.2067-7.76120.16432020.117839864188100
7.7612-8.53870.18482090.130139764185100
8.5387-9.76610.2052300.146139884218100
9.7661-12.27360.19832040.16214023422799
12.2736-49.73570.25542280.25944191441999
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)
10.26440.0648-0.10830.1787-0.00140.09510.03620.05820.03910.09210.04920.05840.08740.0417-00.51340.0310.04170.4824-0.00990.4948144.114983.887-12.2861
20.2398-0.0750.03340.03230.0950.02350.0846-0.18880.16-0.01850.00970.05710.00070.06940.01670.3617-0.17060.10230.812-0.29450.5125222.7266129.68929.2771
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900.01160.0036-0.00650.01280.01080.0215-0.14090.0969-0.04890.1107-0.0151-0.0055-0.0543-0.062300.75610.16380.13980.46090.18880.6113103.509581.75659.4743
910.0159-0.003-0.00740.0079-0.0220.0772-0.0333-0.0886-0.0773-0.0751-0.2560.0679-0.00370.0815-0.0010.6696-0.2240.1360.3906-0.05750.7248102.185775.476316.7563
920.00860.00010.00390.0008-0.00210.005-0.0806-0.0360.078-0.03540.0268-0.0226-0.048-0.00550.00060.4615-0.16760.02610.85270.19780.7067119.188985.8673-33.7382
930.0299-0.0051-0.00750.0274-0.02180.0179-0.0794-0.12030.00630.0341-0.0529-0.0069-0.01530.0183-0.00030.8805-0.29390.03980.95990.06380.662124.839683.9198-37.1628
940.00550.0054-0.00430.022-0.03180.04110.002-0.0750.0606-0.19510.0232-0.07750.2105-0.01610.00050.7779-0.1718-0.10090.85840.10280.7609131.076290.8494-28.9343
950.02880.00510.01210.01210.00590.01310.00010.00090.041-0.02090.01860.016-0.0355-0.0927-0.00020.8708-0.2375-0.20310.9570.24850.8289116.6681.496-38.1323
960.0005-0.0006-0.00090.00080.00290.0085-0.0437-0.0269-0.0059-0.03630.02290.10160.03740.088101.1272-0.25950.05211.34080.16240.7497135.172887.3127-44.9934
970.00010.0007-0.00010.00360.00050.00030.01260.007-0.0102-0.02230.0046-0.0016-0.0015-0.01370.00041.1229-0.04140.08340.9435-0.09941.1378152.091180.0026-42.069
980.0090.0038-0.02060.0022-0.00770.0485-0.0053-0.00440.00040.00140.01030.0138-0.0053-0.00650.00031.82350.1169-0.02141.75340.04181.6703185.3697140.4413-57.777
990.0052-0.0048-0.00260.01590.0090.0040.02430.03470.0837-0.0818-0.07290.047-0.0902-0.1409-0.00010.8174-0.02410.0361.04860.19961.0421176.682133.4761-74.1485
1000.0169-0.0176-0.00140.020.0010.00910.0068-0.00060.04220.05960.0597-0.1581-0.0923-0.02480.00130.7609-0.08190.17921.37640.03771.1959182.7926130.9444-63.8718
1010.0188-0.0153-0.01050.0315-0.00320.0130.07260.0596-0.02430.19850.1514-0.1116-0.0661-0.1283-0.00030.80060.09620.15951.08240.08480.6912182.7454124.8359-70.4971
1020.0035-0.0059-0.0010.01870.00630.0022-0.040.0071-0.1736-0.04080.04690.04110.08810.0557-0.00020.88640.0486-0.13611.1196-0.10351.1006251.9016113.490827.4211
1030.00280.0016-0.00380.0024-0.00180.00520.0003-0.0207-0.02150.0187-0.0181-0.0032-0.04350.027-0.00031.36430.1897-0.04121.7995-0.0171.0041250.8084100.458942.3201
1040.0024-0.0035-0.00240.00440.00360.00240.0091-0.005-0.0022-0.01320.0343-0.01970.01150.00980.00011.49970.04850.12491.41330.05661.7144251.945988.96140.4484
1050.07630.00390.05110.03850.01290.04230.0015-0.0284-0.10020.00070.0205-0.0598-0.04130.0566-0.01820.7019-0.1095-0.41021.3649-0.17360.7497248.8821100.665232.8863
1060.0090.00190.01240.00840.00890.0217-0.1432-0.1355-0.01620.1815-0.1376-0.05010.02330.11940.00031.0048-0.0276-0.18081.17890.04480.8365245.303396.842624.4855
1070.0133-0.00310.0227-0.0083-0.00480.016-0.18480.13130.0148-0.16480.0342-0.00280.1518-0.056-0.00041.0129-0.2090.07210.63420.1290.657113.331142.1714-14.2617
1080.02320.0163-0.0090.0126-0.00840.00490.1449-0.274-0.15340.1002-0.12430.2124-0.04920.1713-0.00010.9702-0.00590.02220.66890.32510.743398.006343.7127-27.625
1090.00330.0023-0.00160.01070.00070.0026-0.0236-0.0525-0.0327-0.0090-0.01210.03170.049100.8307-0.209-0.12080.72170.07320.7458106.947453.063-14.7618
1100.0261-0.0594-0.06620.13730.14980.1702-0.11150.08860.0484-0.0672-0.2962-0.0393-0.1326-0.0377-0.02180.9113-0.3435-0.12380.83630.31980.880298.806251.2-33.8297
1110.00470.00280.00470.0055-0.00110.01090.0002-0.00180.00120.01250.05520.00430.01970.0214-00.80730.0126-0.141.2041-0.27391.1716251.6042124.31182.2472
1120.0056-0.0013-0.00410.0035-0.0030.0062-0.0164-0.06930.03970.0187-0.0045-0.0001-0.00520.0693-01.3551-0.18480.0051.4471-0.48081.3693251.4003131.687.2625
1130.00050.0057-0.00430.1101-0.08560.0670.0256-0.0355-0.0087-0.0080.0035-0.03050.06350.0804-0.00330.9172-0.4772-0.14021.6843-0.29460.8892195.313798.84-3.4411
1140.0304-0.01450.00260.0097-0.00630.00460.03040.06520.07880.1097-0.3524-0.04980.17470.1731-0.0041.2270.2147-0.1852.2147-0.37441.2999206.49893.25556.5706
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 1401:1544)A0
4X-RAY DIFFRACTION4chain 'B' and (resseq 6:63)B6 - 63
5X-RAY DIFFRACTION5chain 'B' and (resseq 64:104)B64 - 104
6X-RAY DIFFRACTION6chain 'B' and (resseq 105:148)B105 - 148
7X-RAY DIFFRACTION7chain 'B' and (resseq 149:241)B149 - 241
8X-RAY DIFFRACTION8chain 'C' and (resseq 2:112)C2 - 112
9X-RAY DIFFRACTION9chain 'C' and (resseq 113:143)C113 - 143
10X-RAY DIFFRACTION10chain 'C' and (resseq 144:208)C144 - 208
11X-RAY DIFFRACTION11chain 'D' and (resseq 2:14)D2 - 14
12X-RAY DIFFRACTION12chain 'D' and (resseq 15:34)D15 - 34
13X-RAY DIFFRACTION13chain 'D' and (resseq 35:52)D35 - 52
14X-RAY DIFFRACTION14chain 'D' and (resseq 53:99)D53 - 99
15X-RAY DIFFRACTION15chain 'D' and (resseq 100:148)D100 - 148
16X-RAY DIFFRACTION16chain 'D' and (resseq 149:164)D149 - 164
17X-RAY DIFFRACTION17chain 'D' and (resseq 165:181)D165 - 181
18X-RAY DIFFRACTION18chain 'D' and (resseq 182:209)D182 - 209
19X-RAY DIFFRACTION19chain 'E' and (resseq 5:20)E5 - 20
20X-RAY DIFFRACTION20chain 'E' and (resseq 21:35)E21 - 35
21X-RAY DIFFRACTION21chain 'E' and (resseq 36:50)E36 - 50
22X-RAY DIFFRACTION22chain 'E' and (resseq 51:64)E51 - 64
23X-RAY DIFFRACTION23chain 'E' and (resseq 65:79)E65 - 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 141:155)E141 - 155
28X-RAY DIFFRACTION28chain 'F' and (resseq 1:15)F1 - 15
29X-RAY DIFFRACTION29chain 'F' and (resseq 16:32)F16 - 32
30X-RAY DIFFRACTION30chain 'F' and (resseq 33:42)F33 - 42
31X-RAY DIFFRACTION31chain 'F' and (resseq 43:47)F43 - 47
32X-RAY DIFFRACTION32chain 'F' and (resseq 48:68)F48 - 68
33X-RAY DIFFRACTION33chain 'F' and (resseq 69:81)F69 - 81
34X-RAY DIFFRACTION34chain 'F' and (resseq 82:92)F82 - 92
35X-RAY DIFFRACTION35chain 'F' and (resseq 93:101)F93 - 101
36X-RAY DIFFRACTION36chain 'G' and (resseq 2:11)G2 - 11
37X-RAY DIFFRACTION37chain 'G' and (resseq 12:128)G12 - 128
38X-RAY DIFFRACTION38chain 'G' and (resseq 129:156)G129 - 156
39X-RAY DIFFRACTION39chain 'H' and (resseq 1:18)H1 - 18
40X-RAY DIFFRACTION40chain 'H' and (resseq 19:29)H19 - 29
41X-RAY DIFFRACTION41chain 'H' and (resseq 30:41)H30 - 41
42X-RAY DIFFRACTION42chain 'H' and (resseq 42:62)H42 - 62
43X-RAY DIFFRACTION43chain 'H' and (resseq 63:72)H63 - 72
44X-RAY DIFFRACTION44chain 'H' and (resseq 73:85)H73 - 85
45X-RAY DIFFRACTION45chain 'H' and (resseq 86:95)H86 - 95
46X-RAY DIFFRACTION46chain 'H' and (resseq 96:114)H96 - 114
47X-RAY DIFFRACTION47chain 'H' and (resseq 115:138)H115 - 138
48X-RAY DIFFRACTION48chain 'I' and (resseq 2:21)I2 - 21
49X-RAY DIFFRACTION49chain 'I' and (resseq 22:32)I22 - 32
50X-RAY DIFFRACTION50chain 'I' and (resseq 33:40)I33 - 40
51X-RAY DIFFRACTION51chain 'I' and (resseq 41:69)I41 - 69
52X-RAY DIFFRACTION52chain 'I' and (resseq 70:88)I70 - 88
53X-RAY DIFFRACTION53chain 'I' and (resseq 89:119)I89 - 119
54X-RAY DIFFRACTION54chain 'I' and (resseq 120:128)I120 - 128
55X-RAY DIFFRACTION55chain 'J' and (resseq 3:10)J3 - 10
56X-RAY DIFFRACTION56chain 'J' and (resseq 11:28)J11 - 28
57X-RAY DIFFRACTION57chain 'J' and (resseq 29:80)J29 - 80
58X-RAY DIFFRACTION58chain 'J' and (resseq 81:93)J81 - 93
59X-RAY DIFFRACTION59chain 'J' and (resseq 94:101)J94 - 101
60X-RAY DIFFRACTION60chain 'K' and (resseq 11:34)K11 - 34
61X-RAY DIFFRACTION61chain 'K' and (resseq 35:99)K35 - 99
62X-RAY DIFFRACTION62chain 'K' and (resseq 100:110)K100 - 110
63X-RAY DIFFRACTION63chain 'K' and (resseq 111:120)K111 - 120
64X-RAY DIFFRACTION64chain 'K' and (resseq 121:129)K121 - 129
65X-RAY DIFFRACTION65chain 'L' and (resseq 5:12)L5 - 12
66X-RAY DIFFRACTION66chain 'L' and (resseq 13:22)L13 - 22
67X-RAY DIFFRACTION67chain 'L' and (resseq 23:31)L23 - 31
68X-RAY DIFFRACTION68chain 'L' and (resseq 32:122)L32 - 122
69X-RAY DIFFRACTION69chain 'L' and (resseq 123:129)L123 - 129
70X-RAY DIFFRACTION70chain 'M' and (resseq 2:14)M2 - 14
71X-RAY DIFFRACTION71chain 'M' and (resseq 15:49)M15 - 49
72X-RAY DIFFRACTION72chain 'M' and (resseq 50:61)M50 - 61
73X-RAY DIFFRACTION73chain 'M' and (resseq 62:66)M62 - 66
74X-RAY DIFFRACTION74chain 'M' and (resseq 67:83)M67 - 83
75X-RAY DIFFRACTION75chain 'M' and (resseq 84:93)M84 - 93
76X-RAY DIFFRACTION76chain 'M' and (resseq 94:119)M94 - 119
77X-RAY DIFFRACTION77chain 'N' and (resseq 2:9)N2 - 9
78X-RAY DIFFRACTION78chain 'N' and (resseq 10:14)N10 - 14
79X-RAY DIFFRACTION79chain 'N' and (resseq 15:19)N15 - 19
80X-RAY DIFFRACTION80chain 'N' and (resseq 20:24)N20 - 24
81X-RAY DIFFRACTION81chain 'N' and (resseq 25:29)N25 - 29
82X-RAY DIFFRACTION82chain 'N' and (resseq 30:50)N30 - 50
83X-RAY DIFFRACTION83chain 'N' and (resseq 51:61)N51 - 61
84X-RAY DIFFRACTION84chain 'O' and (resseq 2:15)O2 - 15
85X-RAY DIFFRACTION85chain 'O' and (resseq 16:44)O16 - 44
86X-RAY DIFFRACTION86chain 'O' and (resseq 45:73)O45 - 73
87X-RAY DIFFRACTION87chain 'O' and (resseq 74:89)O74 - 89
88X-RAY DIFFRACTION88chain 'P' and (resseq 1:39)P1 - 39
89X-RAY DIFFRACTION89chain 'P' and (resseq 40:48)P40 - 48
90X-RAY DIFFRACTION90chain 'P' and (resseq 49:61)P49 - 61
91X-RAY DIFFRACTION91chain 'P' and (resseq 62:84)P62 - 84
92X-RAY DIFFRACTION92chain 'Q' and (resseq 2:12)Q2 - 12
93X-RAY DIFFRACTION93chain 'Q' and (resseq 13:28)Q13 - 28
94X-RAY DIFFRACTION94chain 'Q' and (resseq 29:45)Q29 - 45
95X-RAY DIFFRACTION95chain 'Q' and (resseq 46:81)Q46 - 81
96X-RAY DIFFRACTION96chain 'Q' and (resseq 82:97)Q82 - 97
97X-RAY DIFFRACTION97chain 'Q' and (resseq 98:101)Q98 - 101
98X-RAY DIFFRACTION98chain 'R' and (resseq 16:20)R16 - 20
99X-RAY DIFFRACTION99chain 'R' and (resseq 21:43)R21 - 43
100X-RAY DIFFRACTION100chain 'R' and (resseq 44:59)R44 - 59
101X-RAY DIFFRACTION101chain 'R' and (resseq 60:88)R60 - 88
102X-RAY DIFFRACTION102chain 'S' and (resseq 2:12)S2 - 12
103X-RAY DIFFRACTION103chain 'S' and (resseq 13:25)S13 - 25
104X-RAY DIFFRACTION104chain 'S' and (resseq 26:30)S26 - 30
105X-RAY DIFFRACTION105chain 'S' and (resseq 31:47)S31 - 47
106X-RAY DIFFRACTION106chain 'S' and (resseq 48:82)S48 - 82
107X-RAY DIFFRACTION107chain 'T' and (resseq 8:45)T8 - 45
108X-RAY DIFFRACTION108chain 'T' and (resseq 46:68)T46 - 68
109X-RAY DIFFRACTION109chain 'T' and (resseq 69:75)T69 - 75
110X-RAY DIFFRACTION110chain 'T' and (resseq 76:106)T76 - 106
111X-RAY DIFFRACTION111chain 'U' and (resseq 2:8)U2 - 8
112X-RAY DIFFRACTION112chain 'U' and (resseq 9:26)U9 - 26
113X-RAY DIFFRACTION113chain 'V' and (resseq 1:3)V1 - 3
114X-RAY DIFFRACTION114chain 'W' and (resseq 28:42)W28 - 42

+
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://pdbjlvh1.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