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- PDB-4kvb: Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal... -

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基本情報

登録情報
データベース: PDB / ID: 4kvb
タイトルThermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17
要素
  • (30S ribosomal protein ...) x 19
  • 16S rRNA
キーワードRIBOSOME / 30S ribosomal subunit / translation / 50S ribosomal subunit
機能・相同性
機能・相同性情報


ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / zinc ion binding / cytoplasm / cytosol
類似検索 - 分子機能
30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S14/S29 / Ribosomal protein S6 signature. ...30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein S14, type Z / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S14/S29 / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / 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 S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / : / K homology domain superfamily, prokaryotic type / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S15 signature. / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / K homology domain-like, alpha/beta / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S10p/S20e / Ribosomal protein S13-like, H2TH / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / S4 RNA-binding domain
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 bS16 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS10 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9
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 / 分子置換 / 解像度: 4.198 Å
データ登録者Murphy, E.L. / Jogl, G.
引用ジャーナル: To be Published
タイトル: Structural robustness of the ribosome inferred from the X-ray crystal structure of a 30S ribosomal subunit lacking ribosomal protein S17
著者: Connetti, J.L. / Murphy, E.L. / Dahlberg, A.E. / Gregory, S.T. / Jogl, G.
履歴
登録2013年5月22日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年6月4日Provider: repository / タイプ: Initial release
改定 1.12017年11月15日Group: Refinement description / カテゴリ: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
改定 1.22023年9月20日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 1.32023年12月6日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
改定 1.42025年2月19日Group: Data collection / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order

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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: 30S ribosomal protein S2
C: 30S ribosomal protein S3
D: 30S ribosomal protein S4
E: 30S ribosomal protein S5
F: 30S ribosomal protein S6
G: 30S ribosomal protein S7
H: 30S ribosomal protein S8
I: 30S ribosomal protein S9
J: 30S ribosomal protein S10
K: 30S ribosomal protein S11
L: 30S ribosomal protein S12
M: 30S ribosomal protein S13
N: 30S ribosomal protein S14 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein Thx
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)776,896215
ポリマ－771,55720
非ポリマー5,339195
水00
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)397.316, 397.316, 215.505
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: 494210.781 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB27 / 参照: GenBank: AE017221.1

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30S ribosomal protein ... , 19種, 19分子 BCDEFGHIJKLMNOPRSTU

#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: HB27 / 参照: UniProt: P62662
#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: HB27 / 参照: UniProt: P62663
#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: HB27 / 参照: UniProt: P62664
#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: HB27 / 参照: UniProt: P62665
#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: HB27 / 参照: UniProt: P62666
#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: HB27 / 参照: UniProt: P62667
#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: HB27 / 参照: UniProt: P62668
#9: タンパク質 30S ribosomal protein S9


分子量: 14429.661 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB27 / 参照: UniProt: P62669
#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: HB27 / 参照: UniProt: P62653
#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: HB27 / 参照: UniProt: P62654
#12: タンパク質 30S ribosomal protein S12


分子量: 14867.713 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB27 / 参照: UniProt: P61941
#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: HB27 / 参照: UniProt: P62655
#14: タンパク質 30S ribosomal protein S14 type Z


分子量: 7158.725 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB27 / 参照: UniProt: P62656
#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: HB27 / 参照: UniProt: P62657
#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: HB27 / 参照: UniProt: P62238
#17: 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: HB27 / 参照: UniProt: P62659
#18: 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: HB27 / 参照: UniProt: P62660
#19: タンパク質 30S ribosomal protein S20


分子量: 11722.116 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus (バクテリア) / 株: HB27 / 参照: UniProt: P62661
#20: 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: HB27 / 参照: UniProt: P62613

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非ポリマー , 3種, 195分子

#21: 化合物...
ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 158 / 由来タイプ: 合成 / 式: Mg
#22: 化合物...
ChemComp-K / POTASSIUM ION


分子量: 39.098 Da / 分子数: 35 / 由来タイプ: 合成 / 式: K
#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

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詳細

Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 5.51 Å3/Da / 溶媒含有率: 77.68 %
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: NSLS / ビームライン: X25 / 波長: 1.1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2013年3月1日
放射モノクロメーター: double crystal Si(111) / 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: 1.1 Å / 相対比: 1
反射解像度: 3.993→30 Å / Num. all: 134627 / Num. obs: 145334 / % possible obs: 92.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
反射 シェル解像度: 3.993→4.23 Å / % possible all: 93.1

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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_1370精密化
PDB_EXTRACT3.11データ抽出
CBASSデータ収集
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 4JI5

4ji5


解像度: 4.198→29.915 Å / SU ML: 0.7 / σ(F): 1.33 / 位相誤差: 28.51 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2576 5804 5 %
Rwork0.2171 110383 -
obs0.2192 116187 92.99 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 682.45 Å2 / Biso mean: 200.5256 Å2 / Biso min: 48.47 Å2
精密化ステップサイクル: LAST / 解像度: 4.198→29.915 Å
タンパク質核酸リガンド溶媒全体
原子数18381 32552 195 0 51128
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00255116
X-RAY DIFFRACTIONf_angle_d0.581925
X-RAY DIFFRACTIONf_chiral_restr0.02210285
X-RAY DIFFRACTIONf_plane_restr0.0034765
X-RAY DIFFRACTIONf_dihedral_angle_d15.26325749
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 (%)
4.1982-4.24570.3921750.36693473364889
4.2457-4.29550.40961990.3553661386094
4.2955-4.34780.40181730.3413730390395
4.3478-4.40260.38232260.33593631385794
4.4026-4.46040.38571700.33273731390195
4.4604-4.52130.35541720.32463714388694
4.5213-4.58560.36341820.31653663384593
4.5856-4.65380.34482060.31253718392495
4.6538-4.72630.3611940.29943682387694
4.7263-4.80350.32051900.28813697388794
4.8035-4.8860.29751890.27663699388894
4.886-4.97440.30461880.27193683387194
4.9744-5.06960.32581750.27453707388294
5.0696-5.17260.31551960.25743674387094
5.1726-5.28450.28822070.24973671387893
5.2845-5.40670.26991990.22973649384893
5.4067-5.54110.27011950.2153675387093
5.5411-5.68990.27911750.21483684385993
5.6899-5.85610.25681660.21383707387393
5.8561-6.04370.26182020.21363672387493
6.0437-6.25780.27272090.20793667387693
6.2578-6.50590.27871960.20223686388293
6.5059-6.79870.22422100.19213668387893
6.7987-7.15250.23891950.17833688388392
7.1525-7.59370.19941830.16533678386192
7.5937-8.1690.20472070.16123638384592
8.169-8.97090.21722120.16733671388392
8.9709-10.22330.19281870.17083722390992
10.2233-12.71370.21062180.17093685390391
12.7137-29.91570.22692080.19933759396789
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)
10.5017-0.8069-0.29741.53470.03690.1707-0.1421-0.13580.06570.24380.1489-0.33710.15240.1887-0.00472.1592-0.0979-0.03662.0988-0.15452.339993.071-171.181-18.43
20.48640.092-0.18830.60640.1780.57280.056-0.06580.0056-0.0630.0661-0.1285-0.00090.1222-0.12931.9215-0.202-0.03641.967-0.04612.079275.867-128.485-7.121
31.1247-0.39950.22431.2185-0.58430.71320.21930.2822-0.0535-0.14010.02660.1815-0.06380.1518-0.21492.0024-0.20890.2281.9697-0.11741.899946.278-98.377-9.896
42.5423-0.4424-0.07281.1755-0.37110.23350.49560.79090.5177-0.4034-0.00190.1867-0.1847-0.2247-0.35462.22860.03540.41682.11820.23362.075539.334-71.868-35.381
51.543-0.0391-0.281.22710.00250.52140.12050.17750.4212-0.14290.16250.4088-0.3662-0.2112-0.26562.34580.07320.34532.19220.30312.261216.145-60.807-19.813
60.8394-0.756-0.01350.2028-0.1942-0.05720.13960.1283-0.4791-0.10280.03310.76460.09660.0447-0.1542.449-0.1087-0.0292.3711-0.06932.110949.009-125.5670.819
72.71830.264-0.19723.8679-2.63088.0035-0.3012-0.322-0.21320.2552-0.3167-0.55980.3197-0.06810.5242.0105-0.4507-0.02211.7475-0.48832.130999.733-71.7499.395
83.11073.5517-0.64964.3046-0.44297.3709-0.37611.12171.06352.0891.3593-1.4666-0.5757-1.7185-1.02191.56670.21360.06751.7132-0.39172.30687.165-63.279-3.957
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968.5305-2.73947.55389.5155-2.57948.84121.1781.06351.0202-0.4103-1.30291.93721.6140.04370.22292.4676-0.02250.7761.2555-0.29682.4765117.757-164.815-39.543
970.00740.0282-0.01180.0928-0.03570.01290.30071.019-2.9512-0.746-0.1216-1.45833.71861.6458-0.23164.08310.62940.87814.7901-0.36712.245368.008-77.60941.39
982.2427-2.0797-0.51779.1796-4.55053.62821.5669-1.68770.8340.5559-1.7246-2.9995-3.12382.42580.10332.3328-0.91480.05872.3386-0.55652.804573.95-89.39256.267
996.2366-0.6587-5.7122.7629-0.38725.59122.75270.04522.5788-2.56990.4242-1.5231-3.10261.1367-3.05951.6706-0.19140.54321.8187-0.07481.334966.734-88.05646.452
1004.5817-6.59460.1599.60570.47023.09710.9934-3.07431.4149-2.20620.7517-1.2739-0.01090.2034-1.67092.04-0.59510.31382.3976-0.29412.001664.623-94.54752.501
1010.74412.26752.70586.97278.28449.86271.35211.4303-0.75550.82731.1593-1.45481.9171-0.788-2.0891.53930.0102-0.4693.01170.40943.077-9.892-72.346-41.574
1023.6089-3.19190.56773.33880.72922.9494-2.0080.91390.6079-0.2473-0.87480.2246-0.6641-0.27892.84783.4202-0.8108-0.41522.7079-0.05632.0974-15.13-83.808-56.38
1030.3492-1.42780.30887.6881-2.25576.0019-0.5775-0.9949-0.21770.7435-0.01270.8888-0.359600.53112.79750.3280.15433.33410.21833.9549-19.594-94.243-54.788
1040.5218-0.82810.83533.0028-2.76784.04630.15310.08480.0914-0.2911-0.29491.25130.48950.69280.28581.9397-0.0394-0.30392.6130.17432.6651-10.88-88.619-41.797
1052.32711.16464.11082.67340.27886.970.1802-0.0135-0.34010.56460.1280.1403-0.12580.6527-0.45682.10420.04820.31861.5684-0.08532.003194.263-193.394-9.672
1068.1114-2.9283-3.46814.4879-3.29557.48960.84840.0566-0.6609-1.93610.1166-2.66270.9090.0623-1.08592.1241-0.5781-0.41151.2599-0.36471.7041107.777-195.302-0.542
1073.82992.2221.32012.7882-3.02559.7433-0.3545-0.98311.20530.2542-0.4593-1.2004-0.69340.1990.66242.10650.2158-0.19651.8533-0.55722.3472110.345-191.4449.816
1086.5976-1.465-2.86121.654-1.25284.0586-0.55160.4361-0.86871.1361-1.0282-1.88941.6433-0.23751.53852.454-0.00420.34791.58350.6214.0887-3.127-64.145-15.412
1098.9299-2.98281.16423.058-0.85477.87951.00360.3716-0.76781.3645-0.1097-0.4105-1.1833-1.3562-0.79662.1499-0.04040.51872.4040.56162.7946-0.873-57.041-20.134
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:342 )A4 - 342
2X-RAY DIFFRACTION2( CHAIN A AND RESID 343:834 )A343 - 834
3X-RAY DIFFRACTION3( CHAIN A AND RESID 835:1009 )A835 - 1009
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1010:1132 )A1010 - 1132
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1133:1346 )A1133 - 1346
6X-RAY DIFFRACTION6( CHAIN A AND RESID 1347:1544 )A1347 - 1544
7X-RAY DIFFRACTION7( CHAIN B AND RESID 6:80 )B6 - 80
8X-RAY DIFFRACTION8( CHAIN B AND RESID 81:104 )B81 - 104
9X-RAY DIFFRACTION9( CHAIN B AND RESID 105:148 )B105 - 148
10X-RAY DIFFRACTION10( CHAIN B AND ( RESID 149:240 OR RESID 301:301 ) )B149 - 240
11X-RAY DIFFRACTION10( CHAIN B AND ( RESID 149:240 OR RESID 301:301 ) )B301
12X-RAY DIFFRACTION11( CHAIN C AND RESID 2:28 )C2 - 28
13X-RAY DIFFRACTION12( CHAIN C AND RESID 29:66 )C29 - 66
14X-RAY DIFFRACTION13( CHAIN C AND RESID 67:112 )C67 - 112
15X-RAY DIFFRACTION14( CHAIN C AND RESID 113:169 )C113 - 169
16X-RAY DIFFRACTION15( CHAIN A AND RESID 1786:1786 ) OR ( CHAIN C AND RESID 170:207 )A1786
17X-RAY DIFFRACTION15( CHAIN A AND RESID 1786:1786 ) OR ( CHAIN C AND RESID 170:207 )C170 - 207
18X-RAY DIFFRACTION16( CHAIN D AND RESID 2:15 )D2 - 15
19X-RAY DIFFRACTION17( CHAIN D AND RESID 16:36 )D16 - 36
20X-RAY DIFFRACTION18( CHAIN D AND RESID 37:52 )D37 - 52
21X-RAY DIFFRACTION19( CHAIN D AND RESID 53:98 )D53 - 98
22X-RAY DIFFRACTION20( CHAIN D AND RESID 99:138 )D99 - 138
23X-RAY DIFFRACTION21( CHAIN D AND RESID 139:148 )D139 - 148
24X-RAY DIFFRACTION22( CHAIN D AND RESID 149:164 )D149 - 164
25X-RAY DIFFRACTION23( CHAIN D AND RESID 165:185 )D165 - 185
26X-RAY DIFFRACTION24( CHAIN D AND RESID 186:209 )D186 - 209
27X-RAY DIFFRACTION25( CHAIN E AND RESID 5:12 )E5 - 12
28X-RAY DIFFRACTION26( CHAIN E AND RESID 13:22 )E13 - 22
29X-RAY DIFFRACTION27( CHAIN E AND RESID 23:35 )E23 - 35
30X-RAY DIFFRACTION28( CHAIN E AND RESID 36:50 )E36 - 50
31X-RAY DIFFRACTION29( CHAIN E AND RESID 51:64 )E51 - 64
32X-RAY DIFFRACTION30( CHAIN E AND RESID 65:79 )E65 - 79
33X-RAY DIFFRACTION31( CHAIN E AND RESID 80:86 )E80 - 86
34X-RAY DIFFRACTION32( CHAIN E AND RESID 87:103 )E87 - 103
35X-RAY DIFFRACTION33( CHAIN E AND RESID 104:140 )E104 - 140
36X-RAY DIFFRACTION34( CHAIN E AND ( RESID 141:154 OR RESID 201:201 ) )E141 - 154
37X-RAY DIFFRACTION34( CHAIN E AND ( RESID 141:154 OR RESID 201:201 ) )E201
38X-RAY DIFFRACTION35( CHAIN F AND RESID 1:15 )F1 - 15
39X-RAY DIFFRACTION36( CHAIN F AND RESID 16:32 )F16 - 32
40X-RAY DIFFRACTION37( CHAIN F AND RESID 33:42 )F33 - 42
41X-RAY DIFFRACTION38( CHAIN F AND RESID 43:47 )F43 - 47
42X-RAY DIFFRACTION39( CHAIN F AND RESID 48:68 )F48 - 68
43X-RAY DIFFRACTION40( CHAIN F AND RESID 69:81 )F69 - 81
44X-RAY DIFFRACTION41( CHAIN F AND RESID 82:92 )F82 - 92
45X-RAY DIFFRACTION42( CHAIN F AND RESID 93:101 )F93 - 101
46X-RAY DIFFRACTION43( CHAIN G AND RESID 2:11 )G2 - 11
47X-RAY DIFFRACTION44( CHAIN G AND RESID 12:128 )G12 - 128
48X-RAY DIFFRACTION45( CHAIN G AND RESID 129:156 )G129 - 156
49X-RAY DIFFRACTION46( CHAIN H AND RESID 1:18 )H1 - 18
50X-RAY DIFFRACTION47( CHAIN H AND RESID 19:29 )H19 - 29
51X-RAY DIFFRACTION48( CHAIN H AND RESID 30:41 )H30 - 41
52X-RAY DIFFRACTION49( CHAIN H AND RESID 42:85 )H42 - 85
53X-RAY DIFFRACTION50( CHAIN H AND RESID 86:95 )H86 - 95
54X-RAY DIFFRACTION51( CHAIN H AND RESID 96:108 )H96 - 108
55X-RAY DIFFRACTION52( CHAIN H AND RESID 109:138 )H109 - 138
56X-RAY DIFFRACTION53( CHAIN I AND RESID 2:12 )I2 - 12
57X-RAY DIFFRACTION54( CHAIN I AND RESID 13:21 )I13 - 21
58X-RAY DIFFRACTION55( CHAIN I AND RESID 22:32 )I22 - 32
59X-RAY DIFFRACTION56( CHAIN I AND RESID 33:40 )I33 - 40
60X-RAY DIFFRACTION57( CHAIN I AND RESID 41:52 )I41 - 52
61X-RAY DIFFRACTION58( CHAIN I AND RESID 53:58 )I53 - 58
62X-RAY DIFFRACTION59( CHAIN I AND RESID 59:69 )I59 - 69
63X-RAY DIFFRACTION60( CHAIN I AND RESID 70:88 )I70 - 88
64X-RAY DIFFRACTION61( CHAIN I AND RESID 89:119 )I89 - 119
65X-RAY DIFFRACTION62( CHAIN I AND RESID 120:128 )I120 - 128
66X-RAY DIFFRACTION63( CHAIN J AND RESID 3:28 )J3 - 28
67X-RAY DIFFRACTION64( CHAIN J AND RESID 29:80 )J29 - 80
68X-RAY DIFFRACTION65( CHAIN J AND RESID 81:94 )J81 - 94
69X-RAY DIFFRACTION66( CHAIN J AND RESID 95:100 )J95 - 100
70X-RAY DIFFRACTION67( CHAIN K AND RESID 11:23 )K11 - 23
71X-RAY DIFFRACTION68( CHAIN K AND RESID 24:73 )K24 - 73
72X-RAY DIFFRACTION69( CHAIN K AND RESID 74:78 )K74 - 78
73X-RAY DIFFRACTION70( CHAIN K AND RESID 79:110 )K79 - 110
74X-RAY DIFFRACTION71( CHAIN K AND RESID 111:122 )K111 - 122
75X-RAY DIFFRACTION72( CHAIN K AND RESID 123:129 )K123 - 129
76X-RAY DIFFRACTION73( CHAIN L AND RESID 5:12 )L5 - 12
77X-RAY DIFFRACTION74( CHAIN L AND RESID 13:22 )L13 - 22
78X-RAY DIFFRACTION75( CHAIN L AND RESID 23:31 )L23 - 31
79X-RAY DIFFRACTION76( CHAIN L AND RESID 32:120 )L32 - 120
80X-RAY DIFFRACTION77( CHAIN L AND RESID 121:128 )L121 - 128
81X-RAY DIFFRACTION78( CHAIN M AND RESID 2:14 )M2 - 14
82X-RAY DIFFRACTION79( CHAIN M AND RESID 15:26 )M15 - 26
83X-RAY DIFFRACTION80( CHAIN M AND RESID 27:66 )M27 - 66
84X-RAY DIFFRACTION81( CHAIN M AND RESID 67:83 )M67 - 83
85X-RAY DIFFRACTION82( CHAIN M AND RESID 84:93 )M84 - 93
86X-RAY DIFFRACTION83( CHAIN M AND RESID 94:111 )M94 - 111
87X-RAY DIFFRACTION84( CHAIN M AND RESID 112:126 )M112 - 126
88X-RAY DIFFRACTION85( CHAIN N AND RESID 2:14 )N2 - 14
89X-RAY DIFFRACTION86( CHAIN N AND RESID 15:24 )N15 - 24
90X-RAY DIFFRACTION87( CHAIN N AND RESID 25:29 )N25 - 29
91X-RAY DIFFRACTION88( CHAIN N AND RESID 30:61 )N30 - 61
92X-RAY DIFFRACTION89( CHAIN O AND RESID 2:44 )O2 - 44
93X-RAY DIFFRACTION90( CHAIN O AND RESID 45:73 )O45 - 73
94X-RAY DIFFRACTION91( CHAIN O AND RESID 74:89 )O74 - 89
95X-RAY DIFFRACTION92( CHAIN P AND RESID 1:16 )P1 - 16
96X-RAY DIFFRACTION93( CHAIN P AND RESID 17:36 )P17 - 36
97X-RAY DIFFRACTION94( CHAIN P AND RESID 37:48 )P37 - 48
98X-RAY DIFFRACTION95( CHAIN P AND RESID 49:61 )P49 - 61
99X-RAY DIFFRACTION96( CHAIN P AND RESID 62:83 )P62 - 83
100X-RAY DIFFRACTION97( CHAIN R AND RESID 16:20 )R16 - 20
101X-RAY DIFFRACTION98( CHAIN R AND RESID 21:43 )R21 - 43
102X-RAY DIFFRACTION99( CHAIN R AND RESID 44:59 )R44 - 59
103X-RAY DIFFRACTION100( CHAIN R AND RESID 60:88 )R60 - 88
104X-RAY DIFFRACTION101( CHAIN S AND RESID 2:12 )S2 - 12
105X-RAY DIFFRACTION102( CHAIN S AND RESID 13:25 )S13 - 25
106X-RAY DIFFRACTION103( CHAIN S AND RESID 26:30 )S26 - 30
107X-RAY DIFFRACTION104( CHAIN S AND RESID 31:81 )S31 - 81
108X-RAY DIFFRACTION105( CHAIN T AND RESID 8:46 )T8 - 46
109X-RAY DIFFRACTION106( CHAIN T AND RESID 47:75 )T47 - 75
110X-RAY DIFFRACTION107( CHAIN T AND RESID 76:106 )T76 - 106
111X-RAY DIFFRACTION108( CHAIN U AND RESID 2:8 )U2 - 8
112X-RAY DIFFRACTION109( CHAIN U AND ( RESID 9:25 OR RESID 101:101 ) )U9 - 25
113X-RAY DIFFRACTION109( CHAIN U AND ( RESID 9:25 OR RESID 101:101 ) )U101

+
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