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- PDB-6ny6: Structure of dimeric Escherichia coli toxin YoeB bound to the The... -

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基本情報

登録情報
データベース: PDB / ID: 6ny6
タイトルStructure of dimeric Escherichia coli toxin YoeB bound to the Thermus thermophilus 30S ribosome
要素
  • (30S ribosomal protein ...) x 20
  • 16S rRNA
  • Toxin YoeB
キーワードRIBOSOME
機能・相同性
機能・相同性情報


global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / RNA catabolic process / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism ...global gene silencing by mRNA cleavage / toxin-antitoxin complex / single-species biofilm formation / regulation of growth / RNA catabolic process / mRNA catabolic process / ribosomal small subunit binding / negative regulation of translational initiation / RNA endonuclease activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / ribosomal small subunit biogenesis / ribosomal small subunit assembly / response to heat / small ribosomal subunit / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / endonuclease activity / 加水分解酵素; エステル加水分解酵素 / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / regulation of DNA-templated transcription / protein homodimerization activity / RNA binding / zinc ion binding / metal ion binding / cytosol / cytoplasm
類似検索 - 分子機能
Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 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 ...Toxin YoeB / YoeB-like toxin of bacterial type II toxin-antitoxin system / RelE-like / YaeB-like fold / Toxin-antitoxin system, RelE/ParE toxin domain superfamily / 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 S3 C-terminal domain / Ribosomal protein S6/Translation elongation factor EF1B / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Helix hairpin bin / Ribosomal Protein S7 / Ribosomal protein S7/S5 / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Double Stranded RNA Binding Domain - #20 / Glucose-6-phosphate isomerase like protein; 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 / Ribosomal protein S14, type Z / Double Stranded RNA Binding Domain / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribosomal protein S19, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S14/S29 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S12, bacterial-type / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / 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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily
類似検索 - ドメイン・相同性
IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Toxin YoeB / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 ...IRON/SULFUR CLUSTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Toxin YoeB / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Toxin YoeB / 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 / 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Escherichia coli (大腸菌)
Thermus thermophilus HB8 (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: 3.74 Å
データ登録者Pavelich, I.J. / Hoffer, E.D. / Maehigashi, T. / Dunham, C.M.
資金援助 米国, 2件
組織認可番号国
National Science Foundation (NSF, United States)MCB 0953714 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093278 米国
引用ジャーナル: Nucleic Acids Res. / 年: 2019
タイトル: Monomeric YoeB toxin retains RNase activity but adopts an obligate dimeric form for thermal stability.
著者: Pavelich, I.J. / Maehigashi, T. / Hoffer, E.D. / Ruangprasert, A. / Miles, S.J. / Dunham, C.M.
履歴
登録2019年2月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年8月21日Provider: repository / タイプ: Initial release
改定 1.12019年10月2日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22019年11月6日Group: Data collection / Database references / Structure summary
カテゴリ: audit_author / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32019年11月27日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42023年10月11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_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _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_conn_type.id
改定 1.52024年10月30日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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 type Z
O: 30S ribosomal protein S15
P: 30S ribosomal protein S16
Q: 30S ribosomal protein S17
R: 30S ribosomal protein S18
S: 30S ribosomal protein S19
T: 30S ribosomal protein S20
U: 30S ribosomal protein Thx
Y: Toxin YoeB
Z: Toxin YoeB
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)809,056209
ポリマ－804,16723
非ポリマー4,889186
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)401.710, 401.710, 175.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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要素

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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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SHQ5
#6: タンパク質 30S ribosomal protein S6 / TS9


分子量: 11988.753 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P0DOY9
#9: タンパク質 30S ribosomal protein S9


分子量: 14410.614 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80376
#12: タンパク質 30S ribosomal protein S12


分子量: 14637.384 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SHN3
#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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80377
#14: タンパク質 30S ribosomal protein S14 type Z


分子量: 7158.725 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P0DOY6
#15: タンパク質 30S ribosomal protein S15


分子量: 10578.407 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SJH3
#17: タンパク質 30S ribosomal protein S17


分子量: 12325.655 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P0DOY7
#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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 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 HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: P80380
#21: タンパク質・ペプチド 30S ribosomal protein Thx / S31


分子量: 3350.030 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus HB8 (バクテリア) / Variant: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SIH3

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RNA鎖 / タンパク質 , 2種, 3分子 AYZ

#1: RNA鎖 16S rRNA


分子量: 494263.469 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Thermus thermophilus HB8 (バクテリア)
#22: タンパク質 Toxin YoeB


分子量: 10233.658 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: yoeB / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A127GIW6, UniProt: P69348*PLUS

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非ポリマー , 3種, 186分子

#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: 184 / 由来タイプ: 合成 / 式: Mg
#24: 化合物 ChemComp-SF4 / IRON/SULFUR CLUSTER


分子量: 351.640 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Fe4S4
#25: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 1 / 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: 4.44 Å3/Da / 溶媒含有率: 72.28 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: MPD, AMMONIUM CHLORIDE, POTASSIUM CHLORIDE, MAGNESIUM ACETATE, SODIUM CACODYLATE, pH 6.5

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.9792 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2012年12月12日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9792 Å / 相対比: 1
反射解像度: 3.74→49.826 Å / Num. obs: 145546 / % possible obs: 96.9 % / 冗長度: 3.29 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06808 / Net I/σ(I): 10.95
反射 シェル解像度: 3.74→3.874 Å / 冗長度: 2.17 % / Rmerge(I) obs: 0.4847 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 9392 / CC1/2: 0.673 / % possible all: 85.1

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類NB
PHENIXdev_3406精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
PDB_EXTRACT3.24データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 1J5E

1j5e


解像度: 3.74→49.826 Å / SU ML: 0.42 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 23.25 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2242 7165 5 %
Rwork0.2057 --
obs0.2067 143162 97.27 %
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
精密化ステップサイクル: LAST / 解像度: 3.74→49.826 Å
タンパク質核酸リガンド溶媒全体
原子数20542 32514 193 0 53249
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00857292
X-RAY DIFFRACTIONf_angle_d1.16384853
X-RAY DIFFRACTIONf_dihedral_angle_d22.85331455
X-RAY DIFFRACTIONf_chiral_restr0.05810612
X-RAY DIFFRACTIONf_plane_restr0.0075128
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7401-3.78250.35572270.3433915X-RAY DIFFRACTION86
3.7825-3.8270.30621880.31614312X-RAY DIFFRACTION93
3.827-3.87370.28462210.29734427X-RAY DIFFRACTION96
3.8737-3.92270.29742480.29364523X-RAY DIFFRACTION98
3.9227-3.97430.27142300.2664614X-RAY DIFFRACTION100
3.9743-4.02870.26492520.27164543X-RAY DIFFRACTION100
4.0287-4.08620.25842690.26164591X-RAY DIFFRACTION100
4.0862-4.14720.27852340.25174593X-RAY DIFFRACTION99
4.1472-4.2120.28282520.24654592X-RAY DIFFRACTION100
4.212-4.2810.26122210.24564629X-RAY DIFFRACTION99
4.281-4.35480.27172700.24114520X-RAY DIFFRACTION99
4.3548-4.43390.24122320.23864549X-RAY DIFFRACTION98
4.4339-4.51910.24732640.22874516X-RAY DIFFRACTION98
4.5191-4.61130.22442330.22224590X-RAY DIFFRACTION99
4.6113-4.71150.25742270.21064615X-RAY DIFFRACTION99
4.7115-4.8210.23912130.2084607X-RAY DIFFRACTION99
4.821-4.94150.24292540.20714596X-RAY DIFFRACTION99
4.9415-5.0750.23732520.20254584X-RAY DIFFRACTION99
5.075-5.22410.22312120.19754630X-RAY DIFFRACTION99
5.2241-5.39260.22552290.19534583X-RAY DIFFRACTION99
5.3926-5.58510.21662310.19324516X-RAY DIFFRACTION97
5.5851-5.80840.20282390.1894618X-RAY DIFFRACTION99
5.8084-6.07230.24042130.19624608X-RAY DIFFRACTION98
6.0723-6.39180.20912420.19444574X-RAY DIFFRACTION98
6.3918-6.79130.23162570.19044547X-RAY DIFFRACTION97
6.7913-7.31420.19852470.18584547X-RAY DIFFRACTION96
7.3142-8.04750.22052380.17974532X-RAY DIFFRACTION96
8.0475-9.20560.20782620.1894520X-RAY DIFFRACTION96
9.2056-11.57410.16772460.17984471X-RAY DIFFRACTION93
11.5741-49.83040.19972620.18244535X-RAY DIFFRACTION91
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)
10.5269181012510.386520018846-0.2257031520630.7911361426990.006433937686710.587238991528-0.106994136885-0.113348736264-0.06947376324850.1385805519840.1193245710770.2772871759990.324212094733-0.0985870867984-0.01372559130961.25552055590.1145694492920.1992445450041.109743252320.1013132138191.49979797329121.6274617261.6511034915-5.71502745402
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1407.69849488158-4.205289189772.150399343557.987691816676.929853354442.00195777763-0.148687843447-0.0001208981653210.1174918560280.25001941396-0.0339021371556-0.03298560387530.0260604524140.149250639750.09255331391882.047636151010.350957520584-0.5610777089013.20673577959-0.8960914732792.70470278286257.30235002796.608753081534.0409480632
1410.8696989228270.804898681887-0.8599624542750.969121713078-0.513238178781.211430346790.08103754766260.2036681943440.05477678817180.220138736472-0.295372016454-0.1619499621140.2068432517050.2229057705640.1574748791942.070831488150.9028370740440.4309117193982.88616323708-0.3035599957112.66224492898244.01895928394.056205635430.6367984834
1423.59778691731-0.2068290142040.6857106722482.33952907271-1.021785572492.26090599633-1.317457839320.1051764510070.4455976023640.1053461599160.6769803315820.260175244291-0.464633889295-0.487236189130.5561448670462.084687705140.0036987278191-0.09974021459762.394862548350.07269962393881.60141554694245.10745148795.035678741721.0953320233
1439.556193034411.017883226471.661920445020.1067186316410.1871278058090.2875195594020.139152955408-0.32054613029-0.08033437125271.333675261140.214877950287-0.3563027719280.1027336752820.144784938813-0.246835907331.71227551101-0.1036665072770.19182511861.247343465860.1343042895641.33611411923126.59920736942.95818316687.93913376501
1443.33069271146-0.9395572544553.904075994662.46099804409-0.5800079403094.608423423950.204418356558-0.487754105755-0.417647438462-0.1671486936150.3822602659770.7089280964060.991001069471-0.802087483734-0.4776473267041.52093368798-0.1410456731650.3988631272771.255933930150.2928336944721.75160056748106.29345896543.0233516531-21.591279054
1455.21235513613-0.06407375591471.908009707322.196723305982.163713145636.128425707420.1313508944790.1723692597540.989450486682-0.520798483943-1.42906227634-0.73463024102-0.9821230834281.144579815590.9583186433271.61588320167-0.167999336230.05573009183681.312746404530.6278955295942.0733397538699.390573387850.5959808048-35.2095053209
1460.00714117133964-0.0841071994309-0.05912580806933.19926588035-0.3215234940546.013137164760.05125403101880.109398520452-0.5966083239830.220175210654-0.2452820520711.218392788490.287717887711-1.208679230240.1685768370471.0813249672-0.2586696379450.3577357115923.30750307215-1.070780224072.88408287149251.335231446124.4610612982.54472471943
1471.10648171091-0.869802846761.197534526051.11025120288-0.08792178809383.00602987543-0.2771058290540.52758151131-0.0816810477021-0.6799647142950.04450221716390.0845707148094-0.06801536224890.3081118776670.2618610379912.564296114080.2030450107680.3070125745832.64431525815-1.480850111123.03079624096248.149733966129.4371703274.49345166833
1487.5559536069-0.346525317211-2.491793067130.01696086486420.1185049641190.818353254157-0.110610028341.46197711945-1.4353091754-0.221268943817-0.05354139291790.101445154131-0.302452483833-0.5262682077870.1239501849621.80225379304-0.270736379684-0.09595989826512.17771421536-0.562972452141.62694719674254.876223868133.83028765310.6445612088
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 329 )
2X-RAY DIFFRACTION2chain 'A' and (resid 330 through 661 )
3X-RAY DIFFRACTION3chain 'A' and (resid 662 through 907 )
4X-RAY DIFFRACTION4chain 'A' and (resid 908 through 1142 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1143 through 1382 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1383 through 1540 )
7X-RAY DIFFRACTION7chain 'Y' and (resid 1 through 6 )
8X-RAY DIFFRACTION8chain 'Y' and (resid 7 through 20 )
9X-RAY DIFFRACTION9chain 'Y' and (resid 21 through 36 )
10X-RAY DIFFRACTION10chain 'Y' and (resid 37 through 55 )
11X-RAY DIFFRACTION11chain 'Y' and (resid 56 through 64 )
12X-RAY DIFFRACTION12chain 'Y' and (resid 65 through 71 )
13X-RAY DIFFRACTION13chain 'Y' and (resid 72 through 78 )
14X-RAY DIFFRACTION14chain 'Y' and (resid 79 through 84 )
15X-RAY DIFFRACTION15chain 'Z' and (resid 1 through 20 )
16X-RAY DIFFRACTION16chain 'Z' and (resid 21 through 55 )
17X-RAY DIFFRACTION17chain 'Z' and (resid 56 through 84 )
18X-RAY DIFFRACTION18chain 'B' and (resid 5 through 28 )
19X-RAY DIFFRACTION19chain 'B' and (resid 29 through 120 )
20X-RAY DIFFRACTION20chain 'B' and (resid 121 through 136 )
21X-RAY DIFFRACTION21chain 'B' and (resid 137 through 219 )
22X-RAY DIFFRACTION22chain 'B' and (resid 220 through 240 )
23X-RAY DIFFRACTION23chain 'C' and (resid 2 through 28 )
24X-RAY DIFFRACTION24chain 'C' and (resid 29 through 49 )
25X-RAY DIFFRACTION25chain 'C' and (resid 50 through 62 )
26X-RAY DIFFRACTION26chain 'C' and (resid 63 through 93 )
27X-RAY DIFFRACTION27chain 'C' and (resid 94 through 112 )
28X-RAY DIFFRACTION28chain 'C' and (resid 113 through 125 )
29X-RAY DIFFRACTION29chain 'C' and (resid 126 through 171 )
30X-RAY DIFFRACTION30chain 'C' and (resid 172 through 206 )
31X-RAY DIFFRACTION31chain 'D' and (resid 2 through 15 )
32X-RAY DIFFRACTION32chain 'D' and (resid 16 through 35 )
33X-RAY DIFFRACTION33chain 'D' and (resid 36 through 68 )
34X-RAY DIFFRACTION34chain 'D' and (resid 69 through 83 )
35X-RAY DIFFRACTION35chain 'D' and (resid 84 through 148 )
36X-RAY DIFFRACTION36chain 'D' and (resid 149 through 163 )
37X-RAY DIFFRACTION37chain 'D' and (resid 164 through 185 )
38X-RAY DIFFRACTION38chain 'D' and (resid 186 through 199 )
39X-RAY DIFFRACTION39chain 'D' and (resid 200 through 209 )
40X-RAY DIFFRACTION40chain 'E' and (resid 5 through 35 )
41X-RAY DIFFRACTION41chain 'E' and (resid 36 through 50 )
42X-RAY DIFFRACTION42chain 'E' and (resid 51 through 64 )
43X-RAY DIFFRACTION43chain 'E' and (resid 65 through 79 )
44X-RAY DIFFRACTION44chain 'E' and (resid 80 through 103 )
45X-RAY DIFFRACTION45chain 'E' and (resid 104 through 112 )
46X-RAY DIFFRACTION46chain 'E' and (resid 113 through 141 )
47X-RAY DIFFRACTION47chain 'E' and (resid 142 through 155 )
48X-RAY DIFFRACTION48chain 'F' and (resid 1 through 15 )
49X-RAY DIFFRACTION49chain 'F' and (resid 16 through 32 )
50X-RAY DIFFRACTION50chain 'F' and (resid 33 through 47 )
51X-RAY DIFFRACTION51chain 'F' and (resid 48 through 67 )
52X-RAY DIFFRACTION52chain 'F' and (resid 68 through 80 )
53X-RAY DIFFRACTION53chain 'F' and (resid 81 through 100 )
54X-RAY DIFFRACTION54chain 'G' and (resid 2 through 11 )
55X-RAY DIFFRACTION55chain 'G' and (resid 12 through 35 )
56X-RAY DIFFRACTION56chain 'G' and (resid 36 through 52 )
57X-RAY DIFFRACTION57chain 'G' and (resid 53 through 69 )
58X-RAY DIFFRACTION58chain 'G' and (resid 70 through 92 )
59X-RAY DIFFRACTION59chain 'G' and (resid 93 through 109 )
60X-RAY DIFFRACTION60chain 'G' and (resid 110 through 115 )
61X-RAY DIFFRACTION61chain 'G' and (resid 116 through 129 )
62X-RAY DIFFRACTION62chain 'G' and (resid 130 through 156 )
63X-RAY DIFFRACTION63chain 'H' and (resid 2 through 19 )
64X-RAY DIFFRACTION64chain 'H' and (resid 20 through 29 )
65X-RAY DIFFRACTION65chain 'H' and (resid 30 through 63 )
66X-RAY DIFFRACTION66chain 'H' and (resid 64 through 85 )
67X-RAY DIFFRACTION67chain 'H' and (resid 86 through 102 )
68X-RAY DIFFRACTION68chain 'H' and (resid 103 through 119 )
69X-RAY DIFFRACTION69chain 'H' and (resid 120 through 130 )
70X-RAY DIFFRACTION70chain 'H' and (resid 131 through 138 )
71X-RAY DIFFRACTION71chain 'I' and (resid 2 through 12 )
72X-RAY DIFFRACTION72chain 'I' and (resid 13 through 32 )
73X-RAY DIFFRACTION73chain 'I' and (resid 33 through 42 )
74X-RAY DIFFRACTION74chain 'I' and (resid 43 through 58 )
75X-RAY DIFFRACTION75chain 'I' and (resid 59 through 84 )
76X-RAY DIFFRACTION76chain 'I' and (resid 85 through 96 )
77X-RAY DIFFRACTION77chain 'I' and (resid 97 through 106 )
78X-RAY DIFFRACTION78chain 'I' and (resid 107 through 121 )
79X-RAY DIFFRACTION79chain 'I' and (resid 122 through 127 )
80X-RAY DIFFRACTION80chain 'J' and (resid 5 through 12 )
81X-RAY DIFFRACTION81chain 'J' and (resid 13 through 28 )
82X-RAY DIFFRACTION82chain 'J' and (resid 29 through 37 )
83X-RAY DIFFRACTION83chain 'J' and (resid 38 through 42 )
84X-RAY DIFFRACTION84chain 'J' and (resid 43 through 60 )
85X-RAY DIFFRACTION85chain 'J' and (resid 61 through 72 )
86X-RAY DIFFRACTION86chain 'J' and (resid 73 through 84 )
87X-RAY DIFFRACTION87chain 'J' and (resid 85 through 94 )
88X-RAY DIFFRACTION88chain 'J' and (resid 95 through 100 )
89X-RAY DIFFRACTION89chain 'K' and (resid 11 through 23 )
90X-RAY DIFFRACTION90chain 'K' and (resid 24 through 34 )
91X-RAY DIFFRACTION91chain 'K' and (resid 35 through 43 )
92X-RAY DIFFRACTION92chain 'K' and (resid 44 through 57 )
93X-RAY DIFFRACTION93chain 'K' and (resid 58 through 72 )
94X-RAY DIFFRACTION94chain 'K' and (resid 73 through 78 )
95X-RAY DIFFRACTION95chain 'K' and (resid 79 through 90 )
96X-RAY DIFFRACTION96chain 'K' and (resid 91 through 99 )
97X-RAY DIFFRACTION97chain 'K' and (resid 100 through 110 )
98X-RAY DIFFRACTION98chain 'K' and (resid 111 through 120 )
99X-RAY DIFFRACTION99chain 'K' and (resid 121 through 126 )
100X-RAY DIFFRACTION100chain 'L' and (resid 5 through 12 )
101X-RAY DIFFRACTION101chain 'L' and (resid 13 through 22 )
102X-RAY DIFFRACTION102chain 'L' and (resid 23 through 32 )
103X-RAY DIFFRACTION103chain 'L' and (resid 33 through 69 )
104X-RAY DIFFRACTION104chain 'L' and (resid 70 through 81 )
105X-RAY DIFFRACTION105chain 'L' and (resid 82 through 110 )
106X-RAY DIFFRACTION106chain 'L' and (resid 111 through 126 )
107X-RAY DIFFRACTION107chain 'M' and (resid 2 through 14 )
108X-RAY DIFFRACTION108chain 'M' and (resid 15 through 49 )
109X-RAY DIFFRACTION109chain 'M' and (resid 50 through 66 )
110X-RAY DIFFRACTION110chain 'M' and (resid 67 through 81 )
111X-RAY DIFFRACTION111chain 'M' and (resid 82 through 107 )
112X-RAY DIFFRACTION112chain 'M' and (resid 108 through 117 )
113X-RAY DIFFRACTION113chain 'N' and (resid 2 through 11 )
114X-RAY DIFFRACTION114chain 'N' and (resid 12 through 29 )
115X-RAY DIFFRACTION115chain 'N' and (resid 30 through 39 )
116X-RAY DIFFRACTION116chain 'N' and (resid 40 through 44 )
117X-RAY DIFFRACTION117chain 'N' and (resid 45 through 61 )
118X-RAY DIFFRACTION118chain 'O' and (resid 2 through 24 )
119X-RAY DIFFRACTION119chain 'O' and (resid 25 through 49 )
120X-RAY DIFFRACTION120chain 'O' and (resid 50 through 73 )
121X-RAY DIFFRACTION121chain 'O' and (resid 74 through 88 )
122X-RAY DIFFRACTION122chain 'P' and (resid 1 through 36 )
123X-RAY DIFFRACTION123chain 'P' and (resid 37 through 48 )
124X-RAY DIFFRACTION124chain 'P' and (resid 49 through 62 )
125X-RAY DIFFRACTION125chain 'P' and (resid 63 through 84 )
126X-RAY DIFFRACTION126chain 'Q' and (resid 2 through 12 )
127X-RAY DIFFRACTION127chain 'Q' and (resid 13 through 34 )
128X-RAY DIFFRACTION128chain 'Q' and (resid 35 through 70 )
129X-RAY DIFFRACTION129chain 'Q' and (resid 71 through 101 )
130X-RAY DIFFRACTION130chain 'R' and (resid 19 through 24 )
131X-RAY DIFFRACTION131chain 'R' and (resid 25 through 36 )
132X-RAY DIFFRACTION132chain 'R' and (resid 37 through 43 )
133X-RAY DIFFRACTION133chain 'R' and (resid 44 through 52 )
134X-RAY DIFFRACTION134chain 'R' and (resid 53 through 59 )
135X-RAY DIFFRACTION135chain 'R' and (resid 60 through 76 )
136X-RAY DIFFRACTION136chain 'R' and (resid 77 through 88 )
137X-RAY DIFFRACTION137chain 'S' and (resid 2 through 15 )
138X-RAY DIFFRACTION138chain 'S' and (resid 16 through 30 )
139X-RAY DIFFRACTION139chain 'S' and (resid 31 through 41 )
140X-RAY DIFFRACTION140chain 'S' and (resid 42 through 47 )
141X-RAY DIFFRACTION141chain 'S' and (resid 48 through 52 )
142X-RAY DIFFRACTION142chain 'S' and (resid 53 through 85 )
143X-RAY DIFFRACTION143chain 'T' and (resid 8 through 12 )
144X-RAY DIFFRACTION144chain 'T' and (resid 13 through 75 )
145X-RAY DIFFRACTION145chain 'T' and (resid 76 through 106 )
146X-RAY DIFFRACTION146chain 'U' and (resid 2 through 8 )
147X-RAY DIFFRACTION147chain 'U' and (resid 9 through 15 )
148X-RAY DIFFRACTION148chain 'U' and (resid 16 through 26 )

+
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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る