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- PDB-7mpl: Bartonella henselae NrnC bound to pGG -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 7mpl
タイトルBartonella henselae NrnC bound to pGG
要素
  • 5'-phosphorylated GG
  • NanoRNase C
キーワードRNA BINDING PROTEIN/RNA / RNase / bacteria / enzyme / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
機能・相同性
機能・相同性情報


nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / nucleic acid binding / metal ion binding
類似検索 - 分子機能
: / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
類似検索 - ドメイン・相同性
RNA / 3'-5' exonuclease
類似検索 - 構成要素
生物種Bartonella henselae (バクテリア)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.8 Å
データ登録者Lormand, J.D. / Sondermann, H.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI142400 米国
引用ジャーナル: Elife / 年: 2021
タイトル: Structural characterization of NrnC identifies unifying features of dinucleotidases.
著者: Justin D Lormand / Soo-Kyoung Kim / George A Walters-Marrah / Bryce A Brownfield / J Christopher Fromme / Wade C Winkler / Jonathan R Goodson / Vincent T Lee / Holger Sondermann /
要旨: RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. ...RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses, we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC and Orn employ similar structural features that distinguish these two classes of dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures, together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases, indicate convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.
履歴
登録2021年5月4日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年9月15日Provider: repository / タイプ: Initial release
改定 1.12021年9月29日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: NanoRNase C
B: 5'-phosphorylated GG
C: NanoRNase C
D: 5'-phosphorylated GG
E: NanoRNase C
F: 5'-phosphorylated GG
G: NanoRNase C
H: 5'-phosphorylated GG
I: NanoRNase C
J: 5'-phosphorylated GG
K: NanoRNase C
L: 5'-phosphorylated GG
M: NanoRNase C
N: 5'-phosphorylated GG
O: NanoRNase C
P: 5'-phosphorylated GG


分子量 (理論値)分子数
合計 (水以外)192,73716
ポリマ－192,73716
非ポリマー00
水33,6161866
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: light scattering
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area28670 Å2
ΔGint-164 kcal/mol
Surface area63960 Å2
手法PISA
単位格子
Length a, b, c (Å)71.160, 128.263, 129.281
Angle α, β, γ (deg.)90.000, 94.680, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
32
42
52
62
72
82

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUILEILE(chain 'A' and (resid 3 through 19 or resid 21...AA3 - 194 - 20
121ALAALAVALVAL(chain 'A' and (resid 3 through 19 or resid 21...AA21 - 6622 - 67
131LEULEULEULEU(chain 'A' and (resid 3 through 19 or resid 21...AA68 - 6969 - 70
141ASPASPASPASP(chain 'A' and (resid 3 through 19 or resid 21...AA7172
151ASPASPASPASP(chain 'A' and (resid 3 through 19 or resid 21...AA73 - 11474 - 115
161HISHISLYSLYS(chain 'A' and (resid 3 through 19 or resid 21...AA116 - 119117 - 120
171ILEILELEULEU(chain 'A' and (resid 3 through 19 or resid 21...AA121 - 126122 - 127
181VALVALILEILE(chain 'A' and (resid 3 through 19 or resid 21...AA128 - 149129 - 150
191TYRTYRLYSLYS(chain 'A' and (resid 3 through 19 or resid 21...AA151 - 163152 - 164
1101ILEILEPHEPHE(chain 'A' and (resid 3 through 19 or resid 21...AA165 - 183166 - 184
1111PHEPHEPROPRO(chain 'A' and (resid 3 through 19 or resid 21...AA185 - 187186 - 188
1121ARGARGARGARG(chain 'A' and (resid 3 through 19 or resid 21...AA189190
1131LEULEUSERSER(chain 'A' and (resid 3 through 19 or resid 21...AA192 - 206193 - 207
211GLUGLUILEILE(chain 'C' and (resid 3 through 19 or resid 21...CC3 - 194 - 20
221ALAALAVALVAL(chain 'C' and (resid 3 through 19 or resid 21...CC21 - 6622 - 67
231LEULEULEULEU(chain 'C' and (resid 3 through 19 or resid 21...CC68 - 6969 - 70
241ASPASPASPASP(chain 'C' and (resid 3 through 19 or resid 21...CC7172
251ASPASPASPASP(chain 'C' and (resid 3 through 19 or resid 21...CC73 - 11474 - 115
261HISHISLYSLYS(chain 'C' and (resid 3 through 19 or resid 21...CC116 - 119117 - 120
271ILEILELEULEU(chain 'C' and (resid 3 through 19 or resid 21...CC121 - 126122 - 127
281VALVALILEILE(chain 'C' and (resid 3 through 19 or resid 21...CC128 - 149129 - 150
291TYRTYRLYSLYS(chain 'C' and (resid 3 through 19 or resid 21...CC151 - 163152 - 164
2101ILEILEPHEPHE(chain 'C' and (resid 3 through 19 or resid 21...CC165 - 183166 - 184
2111PHEPHEPROPRO(chain 'C' and (resid 3 through 19 or resid 21...CC185 - 187186 - 188
2121ARGARGARGARG(chain 'C' and (resid 3 through 19 or resid 21...CC189190
2131LEULEUSERSER(chain 'C' and (resid 3 through 19 or resid 21...CC192 - 206193 - 207
311GLUGLUILEILE(chain 'E' and (resid 3 through 19 or resid 21...EE3 - 194 - 20
321ALAALAVALVAL(chain 'E' and (resid 3 through 19 or resid 21...EE21 - 6622 - 67
331LEULEULEULEU(chain 'E' and (resid 3 through 19 or resid 21...EE68 - 6969 - 70
341ASPASPASPASP(chain 'E' and (resid 3 through 19 or resid 21...EE7172
351ASPASPASPASP(chain 'E' and (resid 3 through 19 or resid 21...EE73 - 11474 - 115
361HISHISLYSLYS(chain 'E' and (resid 3 through 19 or resid 21...EE116 - 119117 - 120
371ILEILELEULEU(chain 'E' and (resid 3 through 19 or resid 21...EE121 - 126122 - 127
381VALVALILEILE(chain 'E' and (resid 3 through 19 or resid 21...EE128 - 149129 - 150
391TYRTYRLYSLYS(chain 'E' and (resid 3 through 19 or resid 21...EE151 - 163152 - 164
3101ILEILEPHEPHE(chain 'E' and (resid 3 through 19 or resid 21...EE165 - 183166 - 184
3111PHEPHEPROPRO(chain 'E' and (resid 3 through 19 or resid 21...EE185 - 187186 - 188
3121ARGARGARGARG(chain 'E' and (resid 3 through 19 or resid 21...EE189190
3131LEULEUSERSER(chain 'E' and (resid 3 through 19 or resid 21...EE192 - 206193 - 207
411GLUGLUILEILE(chain 'G' and (resid 3 through 19 or resid 21...GG3 - 194 - 20
421ALAALAVALVAL(chain 'G' and (resid 3 through 19 or resid 21...GG21 - 6622 - 67
431LEULEULEULEU(chain 'G' and (resid 3 through 19 or resid 21...GG68 - 6969 - 70
441ASPASPASPASP(chain 'G' and (resid 3 through 19 or resid 21...GG7172
451ASPASPASPASP(chain 'G' and (resid 3 through 19 or resid 21...GG73 - 11474 - 115
461HISHISLYSLYS(chain 'G' and (resid 3 through 19 or resid 21...GG116 - 119117 - 120
471ILEILELEULEU(chain 'G' and (resid 3 through 19 or resid 21...GG121 - 126122 - 127
481VALVALILEILE(chain 'G' and (resid 3 through 19 or resid 21...GG128 - 149129 - 150
491TYRTYRLYSLYS(chain 'G' and (resid 3 through 19 or resid 21...GG151 - 163152 - 164
4101ILEILEPHEPHE(chain 'G' and (resid 3 through 19 or resid 21...GG165 - 183166 - 184
4111PHEPHEPROPRO(chain 'G' and (resid 3 through 19 or resid 21...GG185 - 187186 - 188
4121ARGARGARGARG(chain 'G' and (resid 3 through 19 or resid 21...GG189190
4131LEULEUSERSER(chain 'G' and (resid 3 through 19 or resid 21...GG192 - 206193 - 207
511GLUGLUILEILE(chain 'I' and (resid 3 through 19 or resid 21...II3 - 194 - 20
521ALAALAVALVAL(chain 'I' and (resid 3 through 19 or resid 21...II21 - 6622 - 67
531LEULEULEULEU(chain 'I' and (resid 3 through 19 or resid 21...II68 - 6969 - 70
541ASPASPASPASP(chain 'I' and (resid 3 through 19 or resid 21...II7172
551ASPASPASPASP(chain 'I' and (resid 3 through 19 or resid 21...II73 - 11474 - 115
561HISHISLYSLYS(chain 'I' and (resid 3 through 19 or resid 21...II116 - 119117 - 120
571ILEILELEULEU(chain 'I' and (resid 3 through 19 or resid 21...II121 - 126122 - 127
581VALVALILEILE(chain 'I' and (resid 3 through 19 or resid 21...II128 - 149129 - 150
591TYRTYRLYSLYS(chain 'I' and (resid 3 through 19 or resid 21...II151 - 163152 - 164
5101ILEILEPHEPHE(chain 'I' and (resid 3 through 19 or resid 21...II165 - 183166 - 184
5111PHEPHEPROPRO(chain 'I' and (resid 3 through 19 or resid 21...II185 - 187186 - 188
5121ARGARGARGARG(chain 'I' and (resid 3 through 19 or resid 21...II189190
5131LEULEUSERSER(chain 'I' and (resid 3 through 19 or resid 21...II192 - 206193 - 207
611GLUGLUILEILE(chain 'K' and (resid 3 through 19 or resid 21...KK3 - 194 - 20
621ALAALAVALVAL(chain 'K' and (resid 3 through 19 or resid 21...KK21 - 6622 - 67
631LEULEULEULEU(chain 'K' and (resid 3 through 19 or resid 21...KK68 - 6969 - 70
641ASPASPASPASP(chain 'K' and (resid 3 through 19 or resid 21...KK7172
651ASPASPASPASP(chain 'K' and (resid 3 through 19 or resid 21...KK73 - 11474 - 115
661HISHISLYSLYS(chain 'K' and (resid 3 through 19 or resid 21...KK116 - 119117 - 120
671ILEILELEULEU(chain 'K' and (resid 3 through 19 or resid 21...KK121 - 126122 - 127
681VALVALILEILE(chain 'K' and (resid 3 through 19 or resid 21...KK128 - 149129 - 150
691TYRTYRLYSLYS(chain 'K' and (resid 3 through 19 or resid 21...KK151 - 163152 - 164
6101ILEILEPHEPHE(chain 'K' and (resid 3 through 19 or resid 21...KK165 - 183166 - 184
6111PHEPHEPROPRO(chain 'K' and (resid 3 through 19 or resid 21...KK185 - 187186 - 188
6121ARGARGARGARG(chain 'K' and (resid 3 through 19 or resid 21...KK189190
6131LEULEUSERSER(chain 'K' and (resid 3 through 19 or resid 21...KK192 - 206193 - 207
711GLUGLUILEILE(chain 'M' and (resid 3 through 19 or resid 21...MM3 - 194 - 20
721ALAALAVALVAL(chain 'M' and (resid 3 through 19 or resid 21...MM21 - 6622 - 67
731LEULEULEULEU(chain 'M' and (resid 3 through 19 or resid 21...MM68 - 6969 - 70
741ASPASPASPASP(chain 'M' and (resid 3 through 19 or resid 21...MM7172
751ASPASPASPASP(chain 'M' and (resid 3 through 19 or resid 21...MM73 - 11474 - 115
761HISHISLYSLYS(chain 'M' and (resid 3 through 19 or resid 21...MM116 - 119117 - 120
771ILEILELEULEU(chain 'M' and (resid 3 through 19 or resid 21...MM121 - 126122 - 127
781VALVALILEILE(chain 'M' and (resid 3 through 19 or resid 21...MM128 - 149129 - 150
791TYRTYRLYSLYS(chain 'M' and (resid 3 through 19 or resid 21...MM151 - 163152 - 164
7101ILEILEPHEPHE(chain 'M' and (resid 3 through 19 or resid 21...MM165 - 183166 - 184
7111PHEPHEPROPRO(chain 'M' and (resid 3 through 19 or resid 21...MM185 - 187186 - 188
7121ARGARGARGARG(chain 'M' and (resid 3 through 19 or resid 21...MM189190
7131LEULEUSERSER(chain 'M' and (resid 3 through 19 or resid 21...MM192 - 206193 - 207
811GLUGLUILEILE(chain 'O' and (resid 3 through 19 or resid 21...OO3 - 194 - 20
821ALAALAVALVAL(chain 'O' and (resid 3 through 19 or resid 21...OO21 - 6622 - 67
831LEULEULEULEU(chain 'O' and (resid 3 through 19 or resid 21...OO68 - 6969 - 70
841ASPASPASPASP(chain 'O' and (resid 3 through 19 or resid 21...OO7172
851ASPASPASPASP(chain 'O' and (resid 3 through 19 or resid 21...OO73 - 11474 - 115
861HISHISLYSLYS(chain 'O' and (resid 3 through 19 or resid 21...OO116 - 119117 - 120
871ILEILELEULEU(chain 'O' and (resid 3 through 19 or resid 21...OO121 - 126122 - 127
881VALVALILEILE(chain 'O' and (resid 3 through 19 or resid 21...OO128 - 149129 - 150
891TYRTYRLYSLYS(chain 'O' and (resid 3 through 19 or resid 21...OO151 - 163152 - 164
8101ILEILEPHEPHE(chain 'O' and (resid 3 through 19 or resid 21...OO165 - 183166 - 184
8111PHEPHEPROPRO(chain 'O' and (resid 3 through 19 or resid 21...OO185 - 187186 - 188
8121ARGARGARGARG(chain 'O' and (resid 3 through 19 or resid 21...OO189190
8131LEULEUSERSER(chain 'O' and (resid 3 through 19 or resid 21...OO192 - 206193 - 207
112GGGGchain 'B'BB603 - 6041 - 2
212GGGGchain 'D'DD603 - 6041 - 2
312GGGGchain 'F'FF603 - 6041 - 2
412GGGGchain 'H'HH603 - 6041 - 2
512GGGGchain 'J'JJ603 - 6041 - 2
612GGGGchain 'L'LL603 - 6041 - 2
712GGGGchain 'N'NN603 - 6041 - 2
812GGGGchain 'P'PP603 - 6041 - 2

NCSアンサンブル:
ID
1
2

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要素

#1: タンパク質
NanoRNase C


分子量: 23446.725 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Bartonella henselae (バクテリア)
遺伝子: BM1374165_00260 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: X5MEI1
#2: RNA鎖
5'-phosphorylated GG


分子量: 645.454 Da / 分子数: 8 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1866 / 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: 3.07 Å3/Da / 溶媒含有率: 59.93 %
結晶化温度: 294 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 / 詳細: 0.1 M Succinic acid; 10% PEG 3,350; 20% xylitol

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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-E / 波長: 0.97918 Å
検出器タイプ: DECTRIS EIGER2 X 16M / 検出器: PIXEL / 日付: 2019年6月20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: 0.97918 Å / 相対比: 1
反射解像度: 1.799→64.39 Å / Num. obs: 212143 / % possible obs: 99.21 % / 冗長度: 4.2 % / Biso Wilson estimate: 30.72 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.5
反射 シェル解像度: 1.799→1.864 Å / Num. unique obs: 20933 / CC1/2: 0.602 / % possible all: 98.12

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
XDSデータ削減
Aimlessデータスケーリング
pointlessデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1yt3

1yt3


解像度: 1.8→64.39 Å / SU ML: 0.1836 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 18.7349
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.1711 10608 5 %
Rwork0.1509 201387 -
obs0.1519 211995 99.21 %
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 mean: 37.17 Å2
精密化ステップサイクル: LAST / 解像度: 1.8→64.39 Å
タンパク質核酸リガンド溶媒全体
原子数13055 376 0 1866 15297
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006213882
X-RAY DIFFRACTIONf_angle_d0.765318899
X-RAY DIFFRACTIONf_chiral_restr0.05822161
X-RAY DIFFRACTIONf_plane_restr0.00532404
X-RAY DIFFRACTIONf_dihedral_angle_d15.2878417
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.30863730.29456447X-RAY DIFFRACTION95.61
1.82-1.840.2623330.25366736X-RAY DIFFRACTION99.48
1.84-1.860.27513670.24166673X-RAY DIFFRACTION99.29
1.86-1.890.26333340.23736681X-RAY DIFFRACTION99.05
1.89-1.910.26193360.24216662X-RAY DIFFRACTION98.74
1.91-1.940.29423430.2546514X-RAY DIFFRACTION95.98
1.94-1.970.25383220.21046688X-RAY DIFFRACTION99.38
1.97-20.20953150.18936780X-RAY DIFFRACTION99.85
2-2.030.21283220.18246784X-RAY DIFFRACTION99.8
2.03-2.060.22143650.18336713X-RAY DIFFRACTION99.62
2.06-2.10.21383390.18586728X-RAY DIFFRACTION98.74
2.1-2.130.18533850.15586646X-RAY DIFFRACTION99.79
2.13-2.170.19614070.15476697X-RAY DIFFRACTION99.79
2.17-2.220.18493680.15226766X-RAY DIFFRACTION99.87
2.22-2.270.20973700.17876576X-RAY DIFFRACTION98.52
2.27-2.320.20133600.15676723X-RAY DIFFRACTION99.86
2.32-2.380.19343690.15596768X-RAY DIFFRACTION99.85
2.38-2.440.22023500.15836755X-RAY DIFFRACTION99.83
2.44-2.510.19083620.1516701X-RAY DIFFRACTION99.7
2.51-2.60.18563790.14876721X-RAY DIFFRACTION99.59
2.6-2.690.19743230.15296733X-RAY DIFFRACTION98.93
2.69-2.80.1853690.14916667X-RAY DIFFRACTION98.72
2.8-2.920.16913390.14476757X-RAY DIFFRACTION99.83
2.92-3.080.18463220.15216820X-RAY DIFFRACTION99.75
3.08-3.270.18233250.14636749X-RAY DIFFRACTION99.75
3.27-3.520.14573340.14116794X-RAY DIFFRACTION99.71
3.52-3.880.14873360.136786X-RAY DIFFRACTION99.41
3.88-4.440.12274140.11296754X-RAY DIFFRACTION99.56
4.44-5.590.12563820.12616690X-RAY DIFFRACTION98.98
5.59-64.390.14913650.14916878X-RAY DIFFRACTION99.41
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)
10.63654991599-0.0197970507485-0.1155354669340.5986869082470.5687375334011.87615329628-0.002115943817780.09251317002270.061798757005-0.132944552451-0.00555722548240.0693760924787-0.280906202083-0.1687123866330.002779106343010.2861018220710.00894491882976-0.01302361264750.2287160903680.02173615574590.23149835359928.614474673229.660674353513.9194624781
20.903540682628-0.316941456715-0.4489005294970.743744213840.8263319365761.83844662484-0.03408876252470.0968278275394-0.126385932516-0.00348042975881-0.1039636012520.1646685546520.178504515939-0.4235140625420.1046277292110.24077517731-0.0337290343748-0.003424824675270.288735663501-0.01232627802050.28944137079620.394758905618.393329369619.2862620771
31.16645761405-0.034213154252-0.07556494086910.4277631975840.1844010809251.10300376738-0.00920382596049-0.01635809842070.0134277732606-0.004938066730880.03060326364620.0396335485413-0.182139830259-0.00313766250571-0.01720628777180.272179944897-0.0119279885525-0.004083766793820.2120451972090.01642802795040.2309203889735.459215979829.695222582526.7412124925
40.5179027027030.009087241757630.1013599214471.66309890547-0.3480122521460.796680743195-0.0155678464176-0.08242744914760.02831764761430.2654978807540.01286615900550.120946197168-0.0819437815722-0.1087881380780.007206770645570.2973517619230.01704405671330.03505405007680.273804728353-0.0191965338480.21114665723625.024518972621.32771900159.8628454976
50.908654310774-0.06116739384190.04568117281681.72541379802-0.6414362161321.0555722970.06223579412470.0471912864341-0.0551524756594-0.283988392245-0.04273048544310.2261634911530.125407374844-0.136640613276-0.001014444722470.265107881104-0.001622594113010.003404556230940.281489454341-0.009408035181330.2555215767919.427158620311.885275737947.981302214
60.935054010543-0.0873759376742-0.03764428921540.6079250848040.1873171347320.219342753342-0.0205223645671-0.082083917428-0.0713269846460.164275835354-0.006580141345230.0363453513040.063954123664-0.01902896524020.02369808645980.3067996177010.005011292665140.005963663743950.2873937427020.01795751960810.22114045986932.83472866588.027544277459.9356733653
70.5362699288910.13254852670.002047656991852.42166974843-0.2745974419330.5858221842450.003932170487990.0340502905245-0.062103051744-0.1806002660160.02172409027410.2294880987170.114442687599-0.0798676740842-0.02182098185130.278935790618-0.030795471039-0.006159478512140.264212674182-0.06136756049520.27293557909828.8864522677-13.70744766825.46719955368
82.244669226930.2632233421860.343776705513.49537890061-0.2205006718171.919558201290.0664479930302-0.05851480012440.04121863372850.216857360595-0.08884389625840.6487014805350.0624984405935-0.3739667215880.04372353186350.310940688534-0.06810410847170.03270770752460.361315048301-0.03748187306420.40782710934320.1271974104-18.852027470116.791265867
90.700755909762-0.1424886746980.05575747297171.139097303-0.1890347983140.3665993310320.009519727420610.0380578381753-0.0492813224474-0.1648413282490.008078848348640.01808719241260.0617307770613-0.00366274783419-0.01703061676880.282624752989-0.01756024623540.0243162969640.285009749794-0.07020764892640.26838482512737.1886273068-3.585062913614.90808389307
100.9379821188090.01829180947970.288281095340.690625036250.4582792272791.91773663768-0.0921143159077-0.09673410872420.0965114770493-0.01236935977080.0982904678114-0.0870983188162-0.3587669469490.224925389346-0.005401445899890.306942550036-0.0608781415361-0.02491937922480.324448144272-0.02866847225060.26835836438260.601353319135.157289625839.6752947991
110.8913392380.153745008232-0.3160709176740.651763164662-0.1626756218551.49793288898-0.0363119066488-0.116063668433-0.1317195437990.03098255470620.105455893469-0.175392105720.1840647202860.634161061194-0.04180151237970.2389760924490.00711417826136-0.03022483868170.429830369494-0.01627907245190.32290685202268.455919661822.257291187839.3622574764
121.06905234325-0.140935052860.2686336912750.3064139239820.2818193026110.916211889107-0.0545816352739-0.02937675922620.0265608034493-0.03332729171820.0758070698921-0.116433537143-0.1345146927190.162728010538-0.02868551454310.266658094351-0.04768356478570.002205575510140.266755650213-0.005809281380770.24118773296853.957089459829.7107517727.7972363144
130.3738865836260.0181771096017-0.2366395990750.4269199484460.1182180956631.5898609828-0.00242187979521-0.0334659121107-0.1041475132440.07122704952690.0343801363160.09285021541730.215200488367-0.159589968294-0.03834067903950.356247686413-0.02652044995440.01105450348820.2430048426130.06504591393540.32547917625526.2486037887-25.495089682749.6585120607
140.720218459899-0.0801540474698-0.005431776556350.7109766677740.7599379577372.013017959710.07698308176380.05128935240450.103205706023-0.09493340579380.02104486585990.194988573159-0.27160657376-0.434306602771-0.1573852851040.3311693431650.006576013678960.01339866856770.3154318886820.09572388856230.39342040510818.7377225975-14.449886879442.9606933624
150.771132852962-0.09438478414090.1389297128560.427617812066-0.08124720775641.343293626790.01686478360420.0434548636315-0.119103253570.02870837087040.0491057437973-0.02695891475110.290906576743-0.0139699957954-0.05072883501220.3410671073680.0009232634617220.001283735807690.2228497709760.04015426006570.3237042968834.857640244-25.545390693837.8689759536
160.378319874031-0.2701314305950.01155519999881.67203690302-0.4706571864990.7256308360070.00349474547772-0.198950769662-0.1394988735080.459536493436-0.0256865069247-0.174184388920.04104966066840.1311365933250.009589689963320.3868280041820.029247358265-0.1031680114890.3933714867620.07295396710550.3518241323558.73115702-3.0494965869167.1074135517
170.436014483379-0.07488508687-0.141951395191.757192118190.2117115147910.5451801182430.0606929461074-0.0611520197316-0.143710035306-0.157709878864-0.0865286521413-0.4711698773680.1047571067810.337357263630.02187294069820.2958841822030.0463653285025-0.05818624512620.4405238913440.06055137045050.47343822934766.9127421052-1.3372184949454.3748279817
180.822598930195-0.0921404018183-0.0864372718180.976661297911-0.2191429772020.4110381792980.0347152785041-0.118466340552-0.1228651585120.225084465059-0.0430243698615-0.184623931757-0.02125013001840.1849799586410.004518324726270.3203668143480.00589609053562-0.04939634348730.3402452491490.03092804508970.27533700799152.65156953227.4894749487961.2121434703
190.5700697679190.2383419118370.1892627082991.927509807520.1533486993780.456138504809-0.146633061180.20007765247-0.0812170419951-0.5394652757570.234800900663-0.417643826869-0.05724939594110.255681904133-0.08202249782720.335007336614-0.0807746971020.1282876928060.424500218544-0.09623673106280.36230497894563.69667261547.547900040411.94611136262
200.6915242262820.178746348275-0.1322385350691.544335294730.3535876679810.7990333974970.0239149742266-0.0377549401455-0.1138575640420.1784096810210.0775433689349-0.578863986668-0.02075739981450.366389310842-0.08173076407430.244303741989-0.0100712817122-0.00631813638780.502992877177-0.1072866847120.53410812469370.0660403736.2121717859715.9322048722
210.9818613027270.4073471785260.05071090125121.41579879860.03458431396490.73540990189-0.147271148422-0.043360068468-0.0280606195722-0.1578098616030.161750771598-0.3313327397930.1177717533560.24880452706-0.01735114870310.275854115968-0.0009759852892950.06247405406430.346117328417-0.09198255604720.34944038589457.0110323573-3.338713379516.90749060733
220.6089108256920.269798402897-0.448145291040.380290994751-0.0512755875821.60380285055-0.1438494165210.0193894712646-0.390203789104-0.0184994441882-0.0415918160523-0.3227962697330.5654704611750.2730202845170.1949690696970.4433024187850.1464454071670.04790769183490.3707424281290.01741603776930.57899951981261.8643911097-30.118768963529.5330078163
230.6296358448820.292714880618-0.0925986046990.773599593614-0.3840602997192.07712151634-0.0955092209084-0.0590159026722-0.204375150374-0.0476267856042-0.0848929070238-0.391872973065-0.1265470148670.5717706866960.08729789356330.3070033103360.08801624283670.001021676861160.5285749679890.03503322316590.61301505361669.3526468481-17.050535081731.0164227439
240.7126270280110.181419316146-0.3292775774120.394443207290.2323131433991.10716636895-0.0513888348767-0.0156131122677-0.07520552500820.127361056506-0.0182509109602-0.3066525582430.2834776899140.2440622625010.06952859010910.3504881709370.0914640414928-0.0202164725530.2910170265010.05541342185750.42396192061654.9988625831-24.875831276739.4571047181
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:114)
2X-RAY DIFFRACTION2(chain A and resid 115:152)
3X-RAY DIFFRACTION3(chain A and resid 153:206)
4X-RAY DIFFRACTION4(chain C and resid 2:109)
5X-RAY DIFFRACTION5(chain C and resid 110:151)
6X-RAY DIFFRACTION6(chain C and resid 152:206)
7X-RAY DIFFRACTION7(chain E and resid 2:131)
8X-RAY DIFFRACTION8(chain E and resid 132:151)
9X-RAY DIFFRACTION9(chain E and resid 152:206)
10X-RAY DIFFRACTION10(chain G and resid 2:113)
11X-RAY DIFFRACTION11(chain G and resid 114:152)
12X-RAY DIFFRACTION12(chain G and resid 153:206)
13X-RAY DIFFRACTION13(chain I and resid 2:114)
14X-RAY DIFFRACTION14(chain I and resid 115:152)
15X-RAY DIFFRACTION15(chain I and resid 153:206)
16X-RAY DIFFRACTION16(chain K and resid 2:113)
17X-RAY DIFFRACTION17(chain K and resid 114:148)
18X-RAY DIFFRACTION18(chain K and resid 149:206)
19X-RAY DIFFRACTION19(chain M and resid 3:113)
20X-RAY DIFFRACTION20(chain M and resid 114:149)
21X-RAY DIFFRACTION21(chain M and resid 150:206)
22X-RAY DIFFRACTION22(chain O and resid 3:114)
23X-RAY DIFFRACTION23(chain O and resid 115:148)
24X-RAY DIFFRACTION24(chain O and resid 149:206)

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万見について

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お知らせ

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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

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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