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- PDB-4dv3: 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: 4dv3
タイトルCrystal structure of the Thermus thermophilus 30S ribosomal subunit with a 16S rRNA mutation, C912A, bound with streptomycin
要素
  • (ribosomal protein ...) x 20
  • 16S rRNA
キーワードRIBOSOME/ANTIBIOTIC / decoding / Streptomycin (ストレプトマイシン) / RNA structure (核酸構造) / antibiotic resistance (抗微生物薬耐性) / RIBOSOME-ANTIBIOTIC complex
機能・相同性
機能・相同性情報


small ribosomal subunit / tRNA binding / rRNA binding / リボソーム / structural constituent of ribosome / ribonucleoprotein complex / 翻訳 (生物学) / mRNA binding / zinc ion binding / metal ion binding / 細胞質
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 / KHドメイン / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / KHドメイン / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Few Secondary Structures / イレギュラー / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S17, conserved site / K homology domain superfamily, prokaryotic type / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S13, conserved site
類似検索 - ドメイン・相同性
ストレプトマイシン / : / リボ核酸 / 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 ...ストレプトマイシン / : / リボ核酸 / 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 (サーマス・サーモフィルス)
手法X線回折 / シンクロトロン / フーリエ合成 / 解像度: 3.547 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

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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)791,502305
ポリマ－783,96021
非ポリマー7,542284
水6,882382
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)402.977, 402.977, 172.607
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
株: HB8 / 参照: UniProt: Q5SLQ0
#19: タンパク質 ribosomal protein S19 / 40S 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 (サーマス・サーモフィルス)
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 (サーマス・サーモフィルス)
株: HB8 / 参照: UniProt: P80380
#21: タンパク質・ペプチド ribosomal protein THX / リボソーム


分子量: 3350.030 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (サーマス・サーモフィルス)
株: HB8 / 参照: UniProt: Q5SIH3

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非ポリマー , 4種, 666分子

#22: 化合物 ChemComp-SRY / STREPTOMYCIN / STREPTOMYCIN A / ストレプトマイシン / ストレプトマイシン


分子量: 581.574 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C21H39N7O12 / コメント: 薬剤, 抗生剤*YM
#23: 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: 281 / 由来タイプ: 合成 / 式: Mg
#24: 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
#25: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 382 / 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: 4.47 Å3/Da / 溶媒含有率: 72.48 %
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: 3.546→30 Å / Num. all: 164584 / Num. obs: 164584 / % possible obs: 96.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / 冗長度: 2.8 % / Rmerge(I) obs: 0.156 / Χ2: 2.183 / Net I/σ(I): 10.4
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.546-3.682.60.77152781.244190.9
3.68-3.822.70.581159251.439194.3
3.82-42.80.45163381.606196.8
4-4.212.90.364166691.747198.6
4.21-4.4730.27167261.923199
4.47-4.8130.207168162.141199.1
4.81-5.32.90.165167932.404198.8
5.3-6.062.90.14167742.765198.4
6.06-7.612.90.117167053.086197
7.61-302.80.094165603.207193.5

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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: 3.547→29.752 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8461 / SU ML: 0.3 / σ(F): 1.33 / 位相誤差: 22.29 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2202 8254 5.02 %FROM PDB ENTRY 2VQE
Rwork0.1661 ---
obs0.1689 164335 96.52 %-
all-164335 --
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: 89.15 Å2 / ksol: 0.249 e/Å3
原子変位パラメータBiso max: 490.41 Å2 / Biso mean: 152.5027 Å2 / Biso min: 39.61 Å2
Baniso -1Baniso -2Baniso -3
1--17.4238 Å2-0 Å20 Å2
2---17.4238 Å20 Å2
3---21.6558 Å2
精密化ステップサイクル: LAST / 解像度: 3.547→29.752 Å
タンパク質核酸リガンド溶媒全体
原子数19088 32509 323 382 52302
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01356210
X-RAY DIFFRACTIONf_angle_d1.59883428
X-RAY DIFFRACTIONf_chiral_restr0.0910400
X-RAY DIFFRACTIONf_plane_restr0.0094882
X-RAY DIFFRACTIONf_dihedral_angle_d19.82226010
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 (%)
3.547-3.58750.32852690.27994746501589
3.5875-3.62960.28322660.26114839510591
3.6296-3.67380.32242590.25394871513092
3.6738-3.72020.30952740.23594961523593
3.7202-3.7690.26193040.2235015531994
3.769-3.82060.28382280.22835094532295
3.8206-3.8750.2622590.21355151541096
3.875-3.93280.25762570.20725162541997
3.9328-3.99410.25032810.19645196547797
3.9941-4.05940.25762890.18935239552898
4.0594-4.12920.22963120.18735226553899
4.1292-4.20410.26072590.17255318557799
4.2041-4.28470.22422610.16745309557099
4.2847-4.37190.2312990.1685247554699
4.3719-4.46670.20283070.15915272557999
4.4667-4.57020.19812820.14895327560999
4.5702-4.68410.20232460.14475356560299
4.6841-4.81020.212720.14345325559799
4.8102-4.95120.18182900.13265309559999
4.9512-5.11020.20522690.13825326559599
5.1102-5.29190.19832740.1345318559298
5.2919-5.50250.18062800.12575314559499
5.5025-5.75120.21032850.13715312559798
5.7512-6.0520.20882580.14245310556898
6.052-6.42760.19432710.14045315558698
6.4276-6.91810.21732720.14235303557597
6.9181-7.60380.20272890.13565245553496
7.6038-8.68010.19792710.14195262553396
8.6801-10.84720.19192800.15295262554295
10.8472-29.75330.23012910.20735151544290
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)
10.70850.0522-0.18350.7083-0.02640.61270.0013-0.0539-0.2070.21320.0340.15510.25160.0269-0.03440.76980.0780.10090.6384-0.02781.0685143.138983.1906-12.844
23.1723-0.56810.20.59350.18460.5702-0.0111-1.64150.8520.36430.2358-0.4882-0.04020.3013-0.20681.1284-0.2020.04872.2547-0.83611.9631222.5416127.773210.1549
31.61540.5034-0.74850.201-0.45970.4301-0.2528-0.2037-0.6081-0.13730.2007-0.48640.25980.14570.03161.19120.16780.08041.1045-0.0061.5994165.300570.5906-25.8264
41.2906-0.080.2992.8247-0.72110.2486-0.99020.6191-0.2799-1.15750.6034-1.76940.53430.0840.38272.234-0.0620.69681.03440.52061.7626156.8546157.5038-34.43
59.6452-1.4291.52992.31093.78517.9148-0.64640.70460.8036-1.5712-1.0655-0.8122-0.20940.55921.54292.0311-0.01490.61360.9950.37862.1146153.1479150.7382-37.22
69.32132.95124.98577.89263.30323.0899-0.3767-0.9999-0.4116-0.1556-0.16711.78680.7578-2.30460.5051.2016-0.20370.49490.9189-0.13982.1301148.7023159.6884-20.7183
77.1929-4.1187-2.84749.04934.827.69420.76390.51121.7731-0.8571-0.4666-1.6283-1.85190.7698-0.3291.0851-0.09650.10440.85910.28911.5456165.4546162.6209-17.0406
87.2481.54510.73436.09-2.86264.5342-0.0606-0.55631.04530.10591.1078-0.5597-1.09890.9385-0.9110.9665-0.20450.50310.9848-0.53091.5876174.7912155.9854-6.0571
92.2713-3.05364.56048.1152-5.08579.5311-0.36910.38310.21310.28980.402-1.9153-0.68692.0472-0.10641.2136-0.35370.39681.6448-0.70541.8729190.0705161.2801-3.8169
104.89342.46672.91333.4989-0.01792.72450.2288-0.31350.6588-0.45930.1013-0.1892-0.94610.3037-0.34230.98130.13670.50060.8443-0.24192.0995165.2989155.6902-12.2638
111.3246-2.26471.2726.7245-2.16336.22120.03460.03370.0941-1.30710.5994-0.3042-0.35480.5497-0.59411.251-0.17970.47580.6087-0.34432.0392158.8151149.7252-20.3308
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984.12280.88441.79163.3772.68132.4323-0.0758-0.8390.7725-0.13290.68620.3827-0.6259-0.0622-0.50811.467-0.12460.87621.03060.06051.7753110.470684.794321.5604
996.18741.5826-5.72972.3528-0.7245.6409-0.10260.61251.3698-0.91180.05930.3538-0.5001-0.3962-0.10761.1384-0.18160.42931.50370.58341.9907100.145579.44344.8148
1002.69883.77341.72655.89024.13765.94990.4372-0.3737-0.62350.6886-0.6346-0.40950.8915-0.22610.16451.726-0.31250.7430.67760.16891.8813103.455972.810514.1647
1012.75451.60382.20974.058-2.39856.1219-0.7207-0.4849-1.62680.7679-0.79951.83271.5632-1.25231.38441.9279-0.07290.61781.1157-0.24531.913793.166778.864815.318
1025.51752.33871.98298.35885.12413.26260.26430.4460.0247-0.320.5279-0.1796-0.42910.0879-0.89160.7481-0.14390.05330.91590.28251.0271122.697683.7721-36.9557
1032.04752.98380.3616.7461.98191.653-0.3845-0.11390.2749-0.68910.0683-0.0371-0.05990.2690.25140.6593-0.02430.05830.80620.15721.1167130.880790.0789-29.5811
1044.7663-2.13670.17087.1427-6.72197.36530.45160.0948-0.6352-0.19130.34391.3050.2341-0.154-0.77520.8312-0.178-0.14360.88970.11611.1943116.677480.7352-39.4262
1059.2469-6.37080.89444.9349-2.68097.93050.2359-0.5562-0.6631-0.85250.92060.0011-0.33410.8032-1.03440.9202-0.23680.13440.8896-0.19191.1486137.539585.6924-45.0483
1064.5534-4.4023.02437.6463-3.75477.88480.0418-0.61240.5291-0.5111-0.161-0.0857-1.1963-0.66820.0791.3984-0.04680.44681.40990.30982.8122177.7572140.6109-67.5235
1075.6101-7.018-5.32962.00117.47345.5856-0.17530.90310.0066-1.2054-0.3529-0.7682-0.35570.65910.42041.39850.19870.29852.04030.50561.4685172.5876128.9983-77.2517
1087.44786.03946.43115.77144.33436.43840.18991.31821.1608-0.92610.3559-0.3289-1.48050.677-0.63741.45460.2860.80831.08670.42411.6512181.302133.3186-74.8621
1094.7264-4.49910.75364.67970.19792.30670.0464-1.00450.32650.17510.434-3.519-0.70343.2103-0.48610.8371-0.1078-0.00371.6221-0.1231.49186.5859128.4418-66.3992
1107.3845-0.1526-2.0918.10933.6822.90790.0527-1.1885-0.09950.0807-0.179-0.65270.68461.79160.1171.6620.64170.68981.61680.35440.9922177.8758133.7971-60.9416
1112.4574-0.61191.46091.20860.98462.58390.74390.33410.4408-0.3880.10190.332-0.5002-0.4792-0.75561.11160.07440.16331.10730.30790.7835174.7307124.3533-69.3511
1124.7038-0.52581.92090.1287-0.12513.73720.06550.41810.3251-0.9135-0.1228-0.6134-0.24770.31110.06611.57260.36070.24061.18120.30561.1285192.1219125.5575-71.9671
1130.9032.467-1.53826.7989-4.73267.7654-0.22520.5638-0.5209-0.8033-0.38230.95120.5001-1.32050.47422.39951.388-1.13383.1536-1.58832.6471251.8032110.99227.9896
1149.217-2.6374.50656.3462-3.2968.4785-1.9137-0.98280.69411.83870.1422-0.6565-0.38520.03641.54121.81090.5091-0.21043.4790.28961.4364249.058495.076237.4527
1152.52063.47422.53096.51953.77132.5876-0.6507-1.5955-0.8406-0.1473-0.11244.00850.1638-4.9450.7861.2522-0.3028-0.24954.15880.2172.9634256.686198.866932.8143
1162.3261.9483-3.1972.5289-3.25335.136-0.709-1.02660.45381.2376-0.1672-0.33660.0342-0.23640.8912.39750.4487-0.19132.3174-0.28371.6986248.682191.76830.8641
1173.45272.5999-2.27371.9703-1.6881.5459-0.0280.7105-0.8821-0.4118-0.02220.2065-0.3155-0.5795-0.00641.6950.0569-0.3112.78560.26421.8731242.65489.866126.0647
1187.8571-1.81164.6024.0119-2.10742.99630.1096-1.4097-0.51860.4367-0.2873-1.7050.28571.78810.16621.53090.2319-0.17392.75090.07772.1972248.681495.917920.3835
1193.35110.25734.56272.06680.42387.82580.0865-0.12110.08710.53340.05660.25840.37410.3791-0.14691.2349-0.1020.32710.58510.21631.3774112.915941.0652-16.2964
1203.88420.768-0.11274.4612-2.85547.86510.4529-0.44280.11850.6829-0.15011.11250.6521-0.3591-0.24481.235-0.1097-0.05530.79830.68771.7898100.130544.8428-25.8823
1214.33991.58593.41116.75564.68914.6013-0.1420.41290.61620.0584-0.69210.29080.5289-0.21210.73521.3189-0.3880.12261.00340.42411.665399.292249.9419-35.7807
1224.0462-3.7144-0.33086.61572.72352.5230.6959-1.0267-2.0554-0.0881-0.3292.24311.281-1.1291-0.39251.5574-0.50080.26941.7438-0.31932.9761251.6245124.23513.4488
1231.9388-2.7959-1.13685.3184-0.4314.0011-0.284-0.47480.7960.25020.2347-0.1408-1.02010.42110.02141.89170.0332-0.17521.3981-1.03761.9096248.6952130.10544.695
1240.92190.0873-0.35050.1795-0.18750.27390.0605-0.46290.36080.7766-0.51480.0383-0.76310.30190.44361.6762-0.5888-0.04852.755-1.45072.9324252.9079131.306611.7401
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 44:62)B44 - 62
7X-RAY DIFFRACTION7chain 'B' and (resseq 63:87)B63 - 87
8X-RAY DIFFRACTION8chain 'B' and (resseq 88:122)B88 - 122
9X-RAY DIFFRACTION9chain 'B' and (resseq 123:149)B123 - 149
10X-RAY DIFFRACTION10chain 'B' and (resseq 150:170)B150 - 170
11X-RAY DIFFRACTION11chain 'B' and (resseq 171:207)B171 - 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 51:66)C51 - 66
16X-RAY DIFFRACTION16chain 'C' and (resseq 67:93)C67 - 93
17X-RAY DIFFRACTION17chain 'C' and (resseq 94:112)C94 - 112
18X-RAY DIFFRACTION18chain 'C' and (resseq 113:181)C113 - 181
19X-RAY DIFFRACTION19chain 'C' and (resseq 182:207)C182 - 207
20X-RAY DIFFRACTION20chain 'D' and (resseq 2:14)D2 - 14
21X-RAY DIFFRACTION21chain 'D' and (resseq 15:34)D15 - 34
22X-RAY DIFFRACTION22chain 'D' and (resseq 35:68)D35 - 68
23X-RAY DIFFRACTION23chain 'D' and (resseq 69:175)D69 - 175
24X-RAY DIFFRACTION24chain 'D' and (resseq 176:209)D176 - 209
25X-RAY DIFFRACTION25chain 'E' and (resseq 5:16)E5 - 16
26X-RAY DIFFRACTION26chain 'E' and (resseq 17:27)E17 - 27
27X-RAY DIFFRACTION27chain 'E' and (resseq 28:50)E28 - 50
28X-RAY DIFFRACTION28chain 'E' and (resseq 51:63)E51 - 63
29X-RAY DIFFRACTION29chain 'E' and (resseq 64:79)E64 - 79
30X-RAY DIFFRACTION30chain 'E' and (resseq 80:86)E80 - 86
31X-RAY DIFFRACTION31chain 'E' and (resseq 87:103)E87 - 103
32X-RAY DIFFRACTION32chain 'E' and (resseq 104:141)E104 - 141
33X-RAY DIFFRACTION33chain 'E' and (resseq 142:154)E142 - 154
34X-RAY DIFFRACTION34chain 'F' and (resseq 1:10)F1 - 10
35X-RAY DIFFRACTION35chain 'F' and (resseq 11:33)F11 - 33
36X-RAY DIFFRACTION36chain 'F' and (resseq 34:47)F34 - 47
37X-RAY DIFFRACTION37chain 'F' and (resseq 48:56)F48 - 56
38X-RAY DIFFRACTION38chain 'F' and (resseq 57:68)F57 - 68
39X-RAY DIFFRACTION39chain 'F' and (resseq 69:81)F69 - 81
40X-RAY DIFFRACTION40chain 'F' and (resseq 82:92)F82 - 92
41X-RAY DIFFRACTION41chain 'F' and (resseq 93:101)F93 - 101
42X-RAY DIFFRACTION42chain 'G' and (resseq 2:11)G2 - 11
43X-RAY DIFFRACTION43chain 'G' and (resseq 12:53)G12 - 53
44X-RAY DIFFRACTION44chain 'G' and (resseq 54:68)G54 - 68
45X-RAY DIFFRACTION45chain 'G' and (resseq 69:78)G69 - 78
46X-RAY DIFFRACTION46chain 'G' and (resseq 79:92)G79 - 92
47X-RAY DIFFRACTION47chain 'G' and (resseq 93:110)G93 - 110
48X-RAY DIFFRACTION48chain 'G' and (resseq 111:144)G111 - 144
49X-RAY DIFFRACTION49chain 'G' and (resseq 145:156)G145 - 156
50X-RAY DIFFRACTION50chain 'H' and (resseq 1:29)H1 - 29
51X-RAY DIFFRACTION51chain 'H' and (resseq 30:63)H30 - 63
52X-RAY DIFFRACTION52chain 'H' and (resseq 64:73)H64 - 73
53X-RAY DIFFRACTION53chain 'H' and (resseq 74:96)H74 - 96
54X-RAY DIFFRACTION54chain 'H' and (resseq 97:102)H97 - 102
55X-RAY DIFFRACTION55chain 'H' and (resseq 103:116)H103 - 116
56X-RAY DIFFRACTION56chain 'H' and (resseq 117:138)H117 - 138
57X-RAY DIFFRACTION57chain 'I' and (resseq 2:13)I2 - 13
58X-RAY DIFFRACTION58chain 'I' and (resseq 14:32)I14 - 32
59X-RAY DIFFRACTION59chain 'I' and (resseq 33:40)I33 - 40
60X-RAY DIFFRACTION60chain 'I' and (resseq 41:52)I41 - 52
61X-RAY DIFFRACTION61chain 'I' and (resseq 53:69)I53 - 69
62X-RAY DIFFRACTION62chain 'I' and (resseq 70:88)I70 - 88
63X-RAY DIFFRACTION63chain 'I' and (resseq 89:119)I89 - 119
64X-RAY DIFFRACTION64chain 'I' and (resseq 120:128)I120 - 128
65X-RAY DIFFRACTION65chain 'J' and (resseq 3:12)J3 - 12
66X-RAY DIFFRACTION66chain 'J' and (resseq 13:27)J13 - 27
67X-RAY DIFFRACTION67chain 'J' and (resseq 28:42)J28 - 42
68X-RAY DIFFRACTION68chain 'J' and (resseq 43:47)J43 - 47
69X-RAY DIFFRACTION69chain 'J' and (resseq 48:62)J48 - 62
70X-RAY DIFFRACTION70chain 'J' and (resseq 63:78)J63 - 78
71X-RAY DIFFRACTION71chain 'J' and (resseq 79:94)J79 - 94
72X-RAY DIFFRACTION72chain 'J' and (resseq 95:100)J95 - 100
73X-RAY DIFFRACTION73chain 'K' and (resseq 11:15)K11 - 15
74X-RAY DIFFRACTION74chain 'K' and (resseq 16:57)K16 - 57
75X-RAY DIFFRACTION75chain 'K' and (resseq 58:75)K58 - 75
76X-RAY DIFFRACTION76chain 'K' and (resseq 76:90)K76 - 90
77X-RAY DIFFRACTION77chain 'K' and (resseq 91:107)K91 - 107
78X-RAY DIFFRACTION78chain 'K' and (resseq 108:126)K108 - 126
79X-RAY DIFFRACTION79chain 'L' and (resseq 5:12)L5 - 12
80X-RAY DIFFRACTION80chain 'L' and (resseq 13:32)L13 - 32
81X-RAY DIFFRACTION81chain 'L' and (resseq 33:101)L33 - 101
82X-RAY DIFFRACTION82chain 'L' and (resseq 102:128)L102 - 128
83X-RAY DIFFRACTION83chain 'M' and (resseq 2:14)M2 - 14
84X-RAY DIFFRACTION84chain 'M' and (resseq 15:119)M15 - 119
85X-RAY DIFFRACTION85chain 'N' and (resseq 2:11)N2 - 11
86X-RAY DIFFRACTION86chain 'N' and (resseq 12:21)N12 - 21
87X-RAY DIFFRACTION87chain 'N' and (resseq 22:26)N22 - 26
88X-RAY DIFFRACTION88chain 'N' and (resseq 27:31)N27 - 31
89X-RAY DIFFRACTION89chain 'N' and (resseq 32:40)N32 - 40
90X-RAY DIFFRACTION90chain 'N' and (resseq 41:50)N41 - 50
91X-RAY DIFFRACTION91chain 'N' and (resseq 51:61)N51 - 61
92X-RAY DIFFRACTION92chain 'O' and (resseq 2:15)O2 - 15
93X-RAY DIFFRACTION93chain 'O' and (resseq 16:44)O16 - 44
94X-RAY DIFFRACTION94chain 'O' and (resseq 45:73)O45 - 73
95X-RAY DIFFRACTION95chain 'O' and (resseq 74:88)O74 - 88
96X-RAY DIFFRACTION96chain 'P' and (resseq 1:16)P1 - 16
97X-RAY DIFFRACTION97chain 'P' and (resseq 17:39)P17 - 39
98X-RAY DIFFRACTION98chain 'P' and (resseq 40:52)P40 - 52
99X-RAY DIFFRACTION99chain 'P' and (resseq 53:61)P53 - 61
100X-RAY DIFFRACTION100chain 'P' and (resseq 62:76)P62 - 76
101X-RAY DIFFRACTION101chain 'P' and (resseq 77:83)P77 - 83
102X-RAY DIFFRACTION102chain 'Q' and (resseq 2:28)Q2 - 28
103X-RAY DIFFRACTION103chain 'Q' and (resseq 29:45)Q29 - 45
104X-RAY DIFFRACTION104chain 'Q' and (resseq 46:81)Q46 - 81
105X-RAY DIFFRACTION105chain 'Q' and (resseq 82:100)Q82 - 100
106X-RAY DIFFRACTION106chain 'R' and (resseq 19:28)R19 - 28
107X-RAY DIFFRACTION107chain 'R' and (resseq 29:36)R29 - 36
108X-RAY DIFFRACTION108chain 'R' and (resseq 37:43)R37 - 43
109X-RAY DIFFRACTION109chain 'R' and (resseq 44:52)R44 - 52
110X-RAY DIFFRACTION110chain 'R' and (resseq 53:59)R53 - 59
111X-RAY DIFFRACTION111chain 'R' and (resseq 60:75)R60 - 75
112X-RAY DIFFRACTION112chain 'R' and (resseq 76:88)R76 - 88
113X-RAY DIFFRACTION113chain 'S' and (resseq 2:12)S2 - 12
114X-RAY DIFFRACTION114chain 'S' and (resseq 13:39)S13 - 39
115X-RAY DIFFRACTION115chain 'S' and (resseq 40:44)S40 - 44
116X-RAY DIFFRACTION116chain 'S' and (resseq 45:52)S45 - 52
117X-RAY DIFFRACTION117chain 'S' and (resseq 53:61)S53 - 61
118X-RAY DIFFRACTION118chain 'S' and (resseq 62:81)S62 - 81
119X-RAY DIFFRACTION119chain 'T' and (resseq 8:46)T8 - 46
120X-RAY DIFFRACTION120chain 'T' and (resseq 47:75)T47 - 75
121X-RAY DIFFRACTION121chain 'T' and (resseq 76:106)T76 - 106
122X-RAY DIFFRACTION122chain 'U' and (resseq 2:8)U2 - 8
123X-RAY DIFFRACTION123chain 'U' and (resseq 9:14)U9 - 14
124X-RAY DIFFRACTION124chain 'U' and (resseq 15:25)U15 - 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

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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