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- PDB-4dv2: Crystal structure of the Thermus thermophilus 30S ribosomal subun... -

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基本情報

登録情報
データベース: PDB / ID: 4dv2
タイトルCrystal structure of the Thermus thermophilus 30S ribosomal subunit with a 16S rRNA mutation, C912A
要素
  • (ribosomal protein ...) x 20
  • 16S rRNA
キーワードRIBOSOME / decoding / Streptomycin / RNA structure / antibiotic resistance
機能・相同性
機能・相同性情報


ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding ...ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / 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 / 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 S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, 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 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 / Few Secondary Structures / Irregular / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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
類似検索 - ドメイン・相同性
: / 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 ...: / 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: 3.646 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: To be Published
タイトル: A structural basis for streptomycin resistance
著者: Demirci, H. / Murphy IV, F. / Murphy, E. / Gregory, S.T. / Dahlberg, A.E. / Jogl, G.
履歴
登録2012年2月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年2月27日Provider: repository / タイプ: Initial release

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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: 16S rRNA
B: ribosomal protein S2
C: ribosomal protein S3
D: ribosomal protein S4
E: ribosomal protein S5
F: ribosomal protein S6
G: ribosomal protein S7
H: ribosomal protein S8
I: ribosomal protein S9
J: ribosomal protein S10
K: ribosomal protein S11
L: ribosomal protein S12
M: ribosomal protein S13
N: ribosomal protein S14
O: ribosomal protein S15
P: ribosomal protein S16
Q: ribosomal protein S17
R: ribosomal protein S18
S: ribosomal protein S19
T: ribosomal protein S20
U: ribosomal protein THX
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)791,115312
ポリマ－783,96021
非ポリマー7,155291
水7,494416
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)403.743, 403.743, 173.221
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 , 1種, 1分子 A

#1: RNA鎖 16S rRNA


分子量: 494194.812 Da / 分子数: 1 / 変異: C912A / 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

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Ribosomal protein ... , 20種, 20分子 BCDEFGHIJKLMNOPQRSTU

#2: タンパク質 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 , 3種, 707分子

#22: 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: 289 / 由来タイプ: 合成 / 式: Mg
#23: 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
#24: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 416 / 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: 72.68 %
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-E / 波長: 0.98 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2010年4月19日
放射モノクロメーター: single crystal Si(220) side-bounce
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
反射解像度: 3.646→30 Å / Num. all: 153457 / Num. obs: 153457 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / 冗長度: 3.1 % / Rmerge(I) obs: 0.12 / Χ2: 1.681 / Net I/σ(I): 12.2
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.646-3.783.10.759152551.369197.5
3.78-3.933.20.539153841.365198.6
3.93-4.113.20.399154421.39199
4.11-4.333.20.279155211.428199
4.33-4.63.20.201154771.54198.9
4.6-4.953.20.146154961.547198.5
4.95-5.443.10.112154261.605197.9
5.44-6.233.10.09152561.652196.4
6.23-7.823.10.092152972.425196
7.82-303.10.084149032.574190.8

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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: 3.646→29.771 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8474 / SU ML: 0.35 / σ(F): 1.34 / 位相誤差: 22.22 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.223 7637 4.98 %FROM PDB ENTRY 2VQE
Rwork0.1645 ---
obs0.1675 153299 96.99 %-
all-153299 --
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: 110.176 Å2 / ksol: 0.244 e/Å3
原子変位パラメータBiso max: 530.31 Å2 / Biso mean: 173.9463 Å2 / Biso min: 31.94 Å2
Baniso -1Baniso -2Baniso -3
1--9.8508 Å2-0 Å20 Å2
2---9.8508 Å20 Å2
3---16.0687 Å2
精密化ステップサイクル: LAST / 解像度: 3.646→29.771 Å
タンパク質核酸リガンド溶媒全体
原子数19088 32509 291 416 52304
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01356357
X-RAY DIFFRACTIONf_angle_d1.5983571
X-RAY DIFFRACTIONf_chiral_restr0.08910413
X-RAY DIFFRACTIONf_plane_restr0.0094888
X-RAY DIFFRACTIONf_dihedral_angle_d20.33626123
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 (%)
3.646-3.68760.3362570.29944479473690
3.6876-3.73090.33562470.27254830507798
3.7309-3.77630.31282870.25214822510998
3.7763-3.8240.30822140.25044906512098
3.824-3.87430.27772700.22994883515399
3.8743-3.92720.2812470.22964900514799
3.9272-3.98320.28632490.21784862511199
3.9832-4.04250.2532770.21024895517299
4.0425-4.10550.26112950.24880517599
4.1055-4.17270.26262330.19254940517399
4.1727-4.24440.26152390.1814926516599
4.2444-4.32140.23462760.17194914519099
4.3214-4.40420.23372560.17154907516399
4.4042-4.49380.22542940.16784872516699
4.4938-4.59120.20912490.15834930517999
4.5912-4.69760.19482300.15354945517599
4.6976-4.81460.21082530.14644913516699
4.8146-4.94420.20252620.13694894515698
4.9442-5.0890.20582580.14164905516398
5.089-5.25240.20832260.13524938516498
5.2524-5.4390.18912530.12534887514098
5.439-5.65540.19592610.12684840510197
5.6554-5.91090.19112500.1314860511097
5.9109-6.21980.22672430.1424824506796
6.2198-6.60550.19912510.1394869512097
6.6055-7.10910.19252500.13134870512096
7.1091-7.81280.19192480.12364824507295
7.8128-8.91670.1882590.13454778503794
8.9167-11.13540.20062490.14594783503293
11.1354-29.77160.24622540.21234586484086
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)
10.75240.1096-0.22810.9434-0.10550.6883-0.0142-0.1233-0.26530.26530.04310.25160.29080.0547-0.0260.91570.13410.12970.76740.03241.1826143.548283.3661-12.8814
25.308-0.64041.28690.70140.11130.65370.1646-2.63110.77930.48610.1987-0.59890.0157-0.2725-0.31311.4162-0.35750.04262.8583-0.89171.9287222.9104128.91719.8539
35.07293.0824-1.13292.136-0.78220.58470.0308-0.7921-1.2238-0.0254-0.1622-0.91590.34480.26260.13281.21790.21230.02521.28130.02591.6187166.827271.7978-26.3993
40.86740.39370.48551.0304-1.10462.3758-1.3380.4985-0.3846-0.45250.931-0.0903-0.18840.41560.41591.8545-0.29270.30881.09180.31042.1009156.6417157.6805-34.5617
59.78351.4203-1.71422.4239-1.67812.0779-0.56810.41760.3851-1.7246-0.5011-0.58520.98130.12731.04392.2055-0.02240.60780.97280.10162.2064153.0954150.8427-37.2611
69.62942.37894.85769.72955.24274.27030.0436-1.5173-0.106-0.61410.14891.8198-0.3618-1.3577-0.12071.3977-0.34550.47941.007-0.12082.0796148.6319160.3254-20.078
74.514-1.85864.26769.75712.78516.965-0.6172-0.7619-0.1064-0.2827-0.6345-0.5891-0.01991.13311.10561.3882-0.09460.3641.29270.08951.4539166.2379162.7862-17.6458
89.60412.89952.33014.5938-0.96734.1678-0.035-0.87720.7624-0.19231.0775-0.4311-1.22351.2911-0.95160.9964-0.24190.5281.2643-0.62391.6217174.3846156.1031-6.4129
90.34790.18120.22750.15410.11460.1495-0.11820.74781.1006-0.02690.3934-1.8471-0.84581.4219-0.21352.1733-0.97140.63672.5701-0.68892.4188193.3282166.85962.4129
103.84.62961.9086.07721.18763.95790.12980.16480.30130.07960.7012-1.1765-0.49821.0222-0.85411.234-0.18540.53131.0509-0.4992.1215174.1648155.5079-10.7261
111.801-2.71580.74027.22460.0494.9609-0.1757-0.2326-0.2271-1.4810.55840.0881-0.09150.4046-0.18241.951-0.32890.69420.546-0.27382.0811157.3234151.8205-23.1106
123.9385-0.480.09855.09423.21383.3758-0.4650.38820.61950.0790.2918-0.398-1.30120.32810.04322.0418-0.32070.86330.59820.00172.4462158.0663167.8693-20.9053
131.03480.6995-1.3610.4709-0.91551.76720.08640.03360.50490.0610.5306-0.1472-0.75220.0187-0.47614.3398-0.57580.28081.0356-0.14823.4947163.3382174.6092-22.8155
140.35260.00110.80130.71080.53992.1464-0.0493-0.25390.3216-0.1576-0.00180.1972-0.084-0.74540.30951.6578-0.1330.11074.5291-2.04111.6074209.5626138.236527.8702
156.08660.315-0.47111.835-0.48650.15240.2333-2.35510.83760.4466-1.1348-0.65910.0290.53330.74931.3353-0.48870.30085.0573-0.29682.2079206.217144.002635.3483
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1024.0701-0.58193.29380.1556-0.4242.73380.1060.5093-0.05610.28750.2135-0.5775-0.10480.6749-0.20981.2167-0.12470.57531.3163-0.00621.7698118.303178.454814.904
1039.6397-3.0090.14447.5293-6.52666.709-0.74560.8682-0.77210.4716-0.3442-0.07560.9177-0.18741.04041.7954-0.18820.38420.8205-0.17511.1047117.547873.22084.1958
1044.33472.17533.26174.42984.97195.76670.1219-0.61461.42020.46630.53491.4397-1.07590.3597-0.52671.425-0.38680.75671.2862-0.12842.1016110.811684.178318.3649
1058.79046.56192.27165.07741.48522.2083-0.26860.13191.2553-0.7292-0.27740.3159-1.1125-0.31470.43971.16870.31190.38471.48460.9022.9755100.472979.68694.7591
1063.3829-3.23555.1818.2063-6.1918.23090.6644-0.3047-0.65030.17580.1960.16921.2116-0.4451-0.82061.93770.00440.82370.66550.39452.1169103.894570.46167.2963
1075.64664.28860.31937.74840.26474.91990.1338-0.4757-0.5370.5226-0.24950.48540.4884-0.4544-0.06722.5003-0.87740.85421.43930.3442.4273103.914674.231117.8833
1087.20662.17388.14436.93861.79069.8321-0.7466-1.18-1.97020.8129-1.03011.35431.7994-1.46971.53292.2134-0.34830.95411.2024-0.04692.383793.394779.196315.4765
1095.9711-1.79020.4887.93674.37429.7206-0.2762-0.09630.58730.23690.0735-0.0055-0.0325-0.2620.22920.7037-0.05190.13830.89340.57231.9608119.378985.1274-34.8698
1105.62566.8788-6.4519.5799-6.82818.38031.2734-0.96690.72730.3754-0.3495-1.1156-1.23830.6709-0.83591.6703-0.0973-0.05551.6392-0.30641.79122.398672.9716-46.3178
1114.94134.78714.72044.66014.54474.5022-0.05390.23220.2893-0.16320.3856-0.0455-0.52710.7587-0.30150.893-0.21680.20840.91620.13931.7961126.654188.0485-34.0835
1125.81580.44335.60969.2182-0.41085.7302-0.437-0.6079-0.8640.546-0.89170.08181.1280.37361.08760.68510.06880.11970.97840.40111.4041137.876298.5288-21.8106
1132.56792.18922.00834.64315.91627.9238-1.1403-0.61080.1945-0.42760.98910.71750.4640.08750.24380.82980.15920.0060.91730.30921.5726127.754485.7798-33.6503
1148.18318.5445-1.52998.942-1.78352.27450.71241.1111-0.4633-0.72110.37051.42070.8167-1.0774-0.88861.22-0.0707-0.87771.79040.57712.3832116.14380.2332-46.7673
1154.83774.4092-1.11967.3531-5.17295.42830.3236-0.12171.06440.6154-0.3484-0.1254-2.745-1.07880.10830.91650.08090.13180.73970.24011.7995116.329384.8188-35.4181
1166.1664-4.79965.20873.7879-4.27466.2214-0.14330.33130.05011.1469-0.44860.2182-0.57310.55860.45971.0506-0.27440.20830.91080.07391.279117.757480.0599-36.9001
1176.265-4.5041-0.21395.0723-1.17624.97530.22130.5224-0.4269-0.12480.2994-0.4490.06730.6868-0.49331.4423-0.01290.16581.2161-0.2911.271138.002985.9101-45.222
1181.7918-3.56111.27969.4332-4.44432.7258-1.19-1.27242.85040.122-0.24030.0854-3.0030.43991.42291.773-0.22120.47641.465-0.63862.6898179.9836140.7853-64.2835
1193.36833.52751.61493.87852.83018.1377-0.28670.57031.4438-1.3384-0.5012-0.037-1.5998-0.30690.8271.65340.1972-0.09371.6510.44021.543173.0894132.729-76.0771
1204.33855.16074.03217.30114.39676.77030.57581.38541.7383-1.5409-0.1621-1.373-1.2540.8361-0.54791.12310.46260.72331.25660.75692.0853181.4305133.6157-74.9757
1214.4386-4.9571-3.76615.53524.20713.1997-0.2898-0.6097-0.2368-0.06720.4667-3.0975-0.20982.8354-0.28420.81030.0722-0.12681.6111-0.17811.4013186.8375128.9706-66.528
1227.6313-1.6239-0.77793.57333.24233.01210.1092-1.26570.35180.29580.1307-0.2214-0.00550.7361-0.15791.6028-0.06340.80951.649-0.20730.6626178.1643134.1995-61.0591
1237.8599-2.966-6.51931.76783.91348.66381.0176-0.07310.19160.137-0.03250.4068-0.4879-0.996-0.68851.2363-0.17510.38471.37710.62980.8062174.8062124.8529-69.432
1245.63940.23793.98080.43880.33476.092-0.52040.271-0.14710.0299-0.2448-0.6113-0.44851.32130.70421.7170.20780.30841.47140.54761.2551192.4045126.0094-72.0013
1253.15982.23973.44631.68331.77439.03430.33270.2824-0.4204-0.71430.77010.67611.2842-1.6431-1.21572.52091.3327-1.30783.6762-0.94442.2658252.627111.746628.2807
1261.2039-0.1007-0.78770.14580.07030.5118-0.9074-1.22751.02531.8352-0.6594-1.1522-0.22770.39641.3863.40891.3874-1.34774.8546-0.88652.7162251.898998.72242.1192
1270.0316-0.05590.06070.2098-0.35610.6784-0.41690.20672.3263-0.36880.1634-0.2208-1.63150.8560.25591.9459-0.4786-0.55832.85170.56024.2847252.505188.241438.759
1280.4237-1.35371.54884.8158-5.52776.3426-0.2905-1.5517-0.99210.5215-0.31360.78550.0005-0.52930.52381.6589-0.1888-0.02723.5920.35492.6886244.8084100.321731.9092
1295.44054.5931-0.24684.20561.1826.2080.347-1.1337-0.16490.0061-1.04380.45110.10010.67710.64231.83250.0046-0.59323.88780.71133.2922251.737995.814832.4613
1300.4351-0.60071.2442.2624-1.07784.0979-0.23570.17920.684-0.00970.0643-0.6729-0.35160.2420.21771.3567-0.0769-0.60293.46850.76613.1528248.572692.868426.3479
1317.5153-4.56115.13714.203-3.74163.78220.79393.80451.0167-2.2257-0.89530.3618-0.7416-0.51950.16622.42520.3301-0.81562.85681.31212.7606253.3203102.249225.2716
1329.1979-4.8460.87048.3748-5.25934.0495-0.9673-1.76280.45630.43460.1415-1.1596-0.94722.22580.71892.1501-0.0961-0.10653.08440.37351.7904241.927295.739116.3117
1334.57930.13874.23542.33550.78254.0528-0.3297-0.06850.45040.37170.51750.62530.30490.5768-0.26581.3952-0.20350.44540.80360.12641.7217113.337141.2647-15.4817
1346.06773.02020.31054.2759-0.17861.08760.4083-1.32190.22970.2352-0.36520.85830.9336-0.4652-0.00821.4889-0.00560.31560.70010.88051.7694100.296844.8115-26.5587
1355.0195-0.72193.06225.59922.78293.74780.29770.25730.4633-0.2019-0.84650.0937-0.15080.28190.47721.209-0.44630.08311.43850.58972.060499.336850.1838-35.7648
1364.7174-4.44083.96075.8616-2.08714.92780.1106-0.3709-1.19410.1326-0.23210.6740.5613-0.29510.05551.5942-0.61330.11832.4087-0.75363.9135252.0875124.86393.1901
1372.68761.2719-0.41525.6537-0.14680.18670.2616-1.51031.51080.6808-0.3054-0.0137-1.3530.66240.04152.297-0.3489-0.47871.8728-0.99722.5311251.8095131.41178.8063
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 7:25)B7 - 25
5X-RAY DIFFRACTION5chain 'B' and (resseq 26:43)B26 - 43
6X-RAY DIFFRACTION6chain 'B' and (resseq 44:63)B44 - 63
7X-RAY DIFFRACTION7chain 'B' and (resseq 64:87)B64 - 87
8X-RAY DIFFRACTION8chain 'B' and (resseq 88:121)B88 - 121
9X-RAY DIFFRACTION9chain 'B' and (resseq 122:131)B122 - 131
10X-RAY DIFFRACTION10chain 'B' and (resseq 132:180)B132 - 180
11X-RAY DIFFRACTION11chain 'B' and (resseq 181:207)B181 - 207
12X-RAY DIFFRACTION12chain 'B' and (resseq 208:226)B208 - 226
13X-RAY DIFFRACTION13chain 'B' and (resseq 227:240)B227 - 240
14X-RAY DIFFRACTION14chain 'C' and (resseq 2:50)C2 - 50
15X-RAY DIFFRACTION15chain 'C' and (resseq 51:70)C51 - 70
16X-RAY DIFFRACTION16chain 'C' and (resseq 71:82)C71 - 82
17X-RAY DIFFRACTION17chain 'C' and (resseq 83:101)C83 - 101
18X-RAY DIFFRACTION18chain 'C' and (resseq 102:112)C102 - 112
19X-RAY DIFFRACTION19chain 'C' and (resseq 113:169)C113 - 169
20X-RAY DIFFRACTION20chain 'C' and (resseq 170:182)C170 - 182
21X-RAY DIFFRACTION21chain 'C' and (resseq 183:193)C183 - 193
22X-RAY DIFFRACTION22chain 'C' and (resseq 194:207)C194 - 207
23X-RAY DIFFRACTION23chain 'D' and (resseq 2:34)D2 - 34
24X-RAY DIFFRACTION24chain 'D' and (resseq 35:68)D35 - 68
25X-RAY DIFFRACTION25chain 'D' and (resseq 69:99)D69 - 99
26X-RAY DIFFRACTION26chain 'D' and (resseq 100:194)D100 - 194
27X-RAY DIFFRACTION27chain 'D' and (resseq 195:209)D195 - 209
28X-RAY DIFFRACTION28chain 'E' and (resseq 5:16)E5 - 16
29X-RAY DIFFRACTION29chain 'E' and (resseq 17:27)E17 - 27
30X-RAY DIFFRACTION30chain 'E' and (resseq 28:50)E28 - 50
31X-RAY DIFFRACTION31chain 'E' and (resseq 51:63)E51 - 63
32X-RAY DIFFRACTION32chain 'E' and (resseq 64:79)E64 - 79
33X-RAY DIFFRACTION33chain 'E' and (resseq 80:103)E80 - 103
34X-RAY DIFFRACTION34chain 'E' and (resseq 104:127)E104 - 127
35X-RAY DIFFRACTION35chain 'E' and (resseq 128:141)E128 - 141
36X-RAY DIFFRACTION36chain 'E' and (resseq 142:154)E142 - 154
37X-RAY DIFFRACTION37chain 'F' and (resseq 1:10)F1 - 10
38X-RAY DIFFRACTION38chain 'F' and (resseq 11:15)F11 - 15
39X-RAY DIFFRACTION39chain 'F' and (resseq 16:32)F16 - 32
40X-RAY DIFFRACTION40chain 'F' and (resseq 33:42)F33 - 42
41X-RAY DIFFRACTION41chain 'F' and (resseq 43:47)F43 - 47
42X-RAY DIFFRACTION42chain 'F' and (resseq 48:56)F48 - 56
43X-RAY DIFFRACTION43chain 'F' and (resseq 57:68)F57 - 68
44X-RAY DIFFRACTION44chain 'F' and (resseq 69:81)F69 - 81
45X-RAY DIFFRACTION45chain 'F' and (resseq 82:92)F82 - 92
46X-RAY DIFFRACTION46chain 'F' and (resseq 93:101)F93 - 101
47X-RAY DIFFRACTION47chain 'G' and (resseq 2:11)G2 - 11
48X-RAY DIFFRACTION48chain 'G' and (resseq 12:35)G12 - 35
49X-RAY DIFFRACTION49chain 'G' and (resseq 36:69)G36 - 69
50X-RAY DIFFRACTION50chain 'G' and (resseq 70:78)G70 - 78
51X-RAY DIFFRACTION51chain 'G' and (resseq 79:92)G79 - 92
52X-RAY DIFFRACTION52chain 'G' and (resseq 93:110)G93 - 110
53X-RAY DIFFRACTION53chain 'G' and (resseq 111:129)G111 - 129
54X-RAY DIFFRACTION54chain 'G' and (resseq 130:144)G130 - 144
55X-RAY DIFFRACTION55chain 'G' and (resseq 145:156)G145 - 156
56X-RAY DIFFRACTION56chain 'H' and (resseq 1:19)H1 - 19
57X-RAY DIFFRACTION57chain 'H' and (resseq 20:42)H20 - 42
58X-RAY DIFFRACTION58chain 'H' and (resseq 43:62)H43 - 62
59X-RAY DIFFRACTION59chain 'H' and (resseq 63:95)H63 - 95
60X-RAY DIFFRACTION60chain 'H' and (resseq 96:116)H96 - 116
61X-RAY DIFFRACTION61chain 'H' and (resseq 117:138)H117 - 138
62X-RAY DIFFRACTION62chain 'I' and (resseq 2:32)I2 - 32
63X-RAY DIFFRACTION63chain 'I' and (resseq 33:40)I33 - 40
64X-RAY DIFFRACTION64chain 'I' and (resseq 41:69)I41 - 69
65X-RAY DIFFRACTION65chain 'I' and (resseq 70:88)I70 - 88
66X-RAY DIFFRACTION66chain 'I' and (resseq 89:106)I89 - 106
67X-RAY DIFFRACTION67chain 'I' and (resseq 107:128)I107 - 128
68X-RAY DIFFRACTION68chain 'J' and (resseq 3:12)J3 - 12
69X-RAY DIFFRACTION69chain 'J' and (resseq 13:29)J13 - 29
70X-RAY DIFFRACTION70chain 'J' and (resseq 30:42)J30 - 42
71X-RAY DIFFRACTION71chain 'J' and (resseq 43:49)J43 - 49
72X-RAY DIFFRACTION72chain 'J' and (resseq 50:71)J50 - 71
73X-RAY DIFFRACTION73chain 'J' and (resseq 72:84)J72 - 84
74X-RAY DIFFRACTION74chain 'J' and (resseq 85:94)J85 - 94
75X-RAY DIFFRACTION75chain 'J' and (resseq 95:100)J95 - 100
76X-RAY DIFFRACTION76chain 'K' and (resseq 11:34)K11 - 34
77X-RAY DIFFRACTION77chain 'K' and (resseq 35:52)K35 - 52
78X-RAY DIFFRACTION78chain 'K' and (resseq 53:75)K53 - 75
79X-RAY DIFFRACTION79chain 'K' and (resseq 76:86)K76 - 86
80X-RAY DIFFRACTION80chain 'K' and (resseq 87:99)K87 - 99
81X-RAY DIFFRACTION81chain 'K' and (resseq 100:110)K100 - 110
82X-RAY DIFFRACTION82chain 'K' and (resseq 111:126)K111 - 126
83X-RAY DIFFRACTION83chain 'L' and (resseq 5:12)L5 - 12
84X-RAY DIFFRACTION84chain 'L' and (resseq 13:22)L13 - 22
85X-RAY DIFFRACTION85chain 'L' and (resseq 23:32)L23 - 32
86X-RAY DIFFRACTION86chain 'L' and (resseq 33:69)L33 - 69
87X-RAY DIFFRACTION87chain 'L' and (resseq 70:101)L70 - 101
88X-RAY DIFFRACTION88chain 'L' and (resseq 102:128)L102 - 128
89X-RAY DIFFRACTION89chain 'M' and (resseq 2:14)M2 - 14
90X-RAY DIFFRACTION90chain 'M' and (resseq 15:66)M15 - 66
91X-RAY DIFFRACTION91chain 'M' and (resseq 67:94)M67 - 94
92X-RAY DIFFRACTION92chain 'M' and (resseq 95:119)M95 - 119
93X-RAY DIFFRACTION93chain 'N' and (resseq 2:11)N2 - 11
94X-RAY DIFFRACTION94chain 'N' and (resseq 12:21)N12 - 21
95X-RAY DIFFRACTION95chain 'N' and (resseq 22:31)N22 - 31
96X-RAY DIFFRACTION96chain 'N' and (resseq 32:40)N32 - 40
97X-RAY DIFFRACTION97chain 'N' and (resseq 41:61)N41 - 61
98X-RAY DIFFRACTION98chain 'O' and (resseq 2:49)O2 - 49
99X-RAY DIFFRACTION99chain 'O' and (resseq 50:73)O50 - 73
100X-RAY DIFFRACTION100chain 'O' and (resseq 74:88)O74 - 88
101X-RAY DIFFRACTION101chain 'P' and (resseq 1:8)P1 - 8
102X-RAY DIFFRACTION102chain 'P' and (resseq 9:23)P9 - 23
103X-RAY DIFFRACTION103chain 'P' and (resseq 24:33)P24 - 33
104X-RAY DIFFRACTION104chain 'P' and (resseq 34:52)P34 - 52
105X-RAY DIFFRACTION105chain 'P' and (resseq 53:61)P53 - 61
106X-RAY DIFFRACTION106chain 'P' and (resseq 62:67)P62 - 67
107X-RAY DIFFRACTION107chain 'P' and (resseq 68:76)P68 - 76
108X-RAY DIFFRACTION108chain 'P' and (resseq 77:83)P77 - 83
109X-RAY DIFFRACTION109chain 'Q' and (resseq 2:12)Q2 - 12
110X-RAY DIFFRACTION110chain 'Q' and (resseq 13:17)Q13 - 17
111X-RAY DIFFRACTION111chain 'Q' and (resseq 18:28)Q18 - 28
112X-RAY DIFFRACTION112chain 'Q' and (resseq 29:34)Q29 - 34
113X-RAY DIFFRACTION113chain 'Q' and (resseq 35:45)Q35 - 45
114X-RAY DIFFRACTION114chain 'Q' and (resseq 46:55)Q46 - 55
115X-RAY DIFFRACTION115chain 'Q' and (resseq 56:61)Q56 - 61
116X-RAY DIFFRACTION116chain 'Q' and (resseq 62:81)Q62 - 81
117X-RAY DIFFRACTION117chain 'Q' and (resseq 82:100)Q82 - 100
118X-RAY DIFFRACTION118chain 'R' and (resseq 19:24)R19 - 24
119X-RAY DIFFRACTION119chain 'R' and (resseq 25:36)R25 - 36
120X-RAY DIFFRACTION120chain 'R' and (resseq 37:43)R37 - 43
121X-RAY DIFFRACTION121chain 'R' and (resseq 44:52)R44 - 52
122X-RAY DIFFRACTION122chain 'R' and (resseq 53:59)R53 - 59
123X-RAY DIFFRACTION123chain 'R' and (resseq 60:75)R60 - 75
124X-RAY DIFFRACTION124chain 'R' and (resseq 76:88)R76 - 88
125X-RAY DIFFRACTION125chain 'S' and (resseq 2:12)S2 - 12
126X-RAY DIFFRACTION126chain 'S' and (resseq 13:25)S13 - 25
127X-RAY DIFFRACTION127chain 'S' and (resseq 26:30)S26 - 30
128X-RAY DIFFRACTION128chain 'S' and (resseq 31:40)S31 - 40
129X-RAY DIFFRACTION129chain 'S' and (resseq 41:52)S41 - 52
130X-RAY DIFFRACTION130chain 'S' and (resseq 53:66)S53 - 66
131X-RAY DIFFRACTION131chain 'S' and (resseq 67:71)S67 - 71
132X-RAY DIFFRACTION132chain 'S' and (resseq 72:81)S72 - 81
133X-RAY DIFFRACTION133chain 'T' and (resseq 8:45)T8 - 45
134X-RAY DIFFRACTION134chain 'T' and (resseq 46:75)T46 - 75
135X-RAY DIFFRACTION135chain 'T' and (resseq 76:106)T76 - 106
136X-RAY DIFFRACTION136chain 'U' and (resseq 2:8)U2 - 8
137X-RAY DIFFRACTION137chain 'U' and (resseq 9:25)U9 - 25

+
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。

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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

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