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- PDB-5v5t: Crystal structure of leucine-rich protein regulator, ElrR, from E... -

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基本情報

登録情報
データベース: PDB / ID: 5v5t
タイトルCrystal structure of leucine-rich protein regulator, ElrR, from Enterococcus faecalis
要素Conserved domain protein
キーワードTRANSCRIPTION / TRANSCRIPTION REGULATOR
機能・相同性Transcriptional regulator
機能・相同性情報
生物種Enterococcus faecalis (乳酸球菌)
手法X線回折 / 単波長異常分散, 分子置換 / 分子置換 / 解像度: 2.15 Å
データ登録者De Groote, M.C.R. / Camargo, I.L. / Serror, P. / Horjales, E.
資金援助 ブラジル, フランス, 2件
組織認可番号国
Sao Paulo Research Foundation (FAPESP)2013/26313-5 ブラジル
USP/COFECUB International agreement2012-22 フランス
引用ジャーナル: To be published
タイトル: Crystal structure and functional characterization of ElrR, a member of the RRNPP family of transcriptional regulators.
著者: De Groote, M.C.R. / Camargo, I.L. / Repoila, F. / Horjales, E. / Serror, P.
履歴
登録2017年3月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02018年9月19日Provider: repository / タイプ: Initial release
改定 1.12019年4月17日Group: Author supporting evidence / Data collection / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.22020年1月1日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32024年10月23日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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集合体

登録構造単位
A: Conserved domain protein
B: Conserved domain protein
C: Conserved domain protein
D: Conserved domain protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)144,9805
ポリマ－144,8624
非ポリマー1181
水3,333185
1
A: Conserved domain protein
D: Conserved domain protein


分子量 (理論値)分子数
合計 (水以外)72,4312
ポリマ－72,4312
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-55 kcal/mol
Surface area28110 Å2
手法PISA
2
B: Conserved domain protein
C: Conserved domain protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,5493
ポリマ－72,4312
非ポリマー1181
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-45 kcal/mol
Surface area27950 Å2
手法PISA
単位格子
Length a, b, c (Å)70.800, 75.330, 85.280
Angle α, β, γ (deg.)112.990, 89.930, 103.880
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 9:37 or resseq 39:44 or resid...
21(chain B and (resseq 9:37 or resseq 39:44 or resseq...
31(chain C and (resseq 9:37 or resseq 39:44 or resseq...
41(chain D and (resseq 9:37 or resseq 39:44 or resseq...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRSERSER(chain A and (resseq 9:37 or resseq 39:44 or resid...AA9 - 377 - 35
12SERSERVALVAL(chain A and (resseq 9:37 or resseq 39:44 or resid...AA39 - 4437 - 42
13GLYGLYGLYGLY(chain A and (resseq 9:37 or resseq 39:44 or resid...AA4644
14SERSERSERSER(chain A and (resseq 9:37 or resseq 39:44 or resid...AA4846
15LEULEUPROPRO(chain A and (resseq 9:37 or resseq 39:44 or resid...AA50 - 6648 - 64
16GLUGLUMSEMSE(chain A and (resseq 9:37 or resseq 39:44 or resid...AA68 - 6966 - 67
17LYSLYSPROPRO(chain A and (resseq 9:37 or resseq 39:44 or resid...AA72 - 7570 - 73
18SERSERALAALA(chain A and (resseq 9:37 or resseq 39:44 or resid...AA77 - 8275 - 80
19GLUGLUSERSER(chain A and (resseq 9:37 or resseq 39:44 or resid...AA84 - 9282 - 90
110ASNASNASNASN(chain A and (resseq 9:37 or resseq 39:44 or resid...AA9492
111GLUGLUGLUGLU(chain A and (resseq 9:37 or resseq 39:44 or resid...AA97 - 11095 - 108
112SERSERPROPRO(chain A and (resseq 9:37 or resseq 39:44 or resid...AA112 - 134110 - 132
113THRTHRALAALA(chain A and (resseq 9:37 or resseq 39:44 or resid...AA136 - 157134 - 155
114VALVALGLNGLN(chain A and (resseq 9:37 or resseq 39:44 or resid...AA159 - 171157 - 169
115ASNASNARGARG(chain A and (resseq 9:37 or resseq 39:44 or resid...AA173 - 194171 - 192
116ILEILEILEILE(chain A and (resseq 9:37 or resseq 39:44 or resid...AA196194
117ILEILELEULEU(chain A and (resseq 9:37 or resseq 39:44 or resid...AA199 - 226197 - 224
118VALVALPHEPHE(chain A and (resseq 9:37 or resseq 39:44 or resid...AA228 - 232226 - 230
119GLUGLUILEILE(chain A and (resseq 9:37 or resseq 39:44 or resid...AA234 - 263232 - 261
120ALAALAALAALA(chain A and (resseq 9:37 or resseq 39:44 or resid...AA265263
121TRPTRPLYSLYS(chain A and (resseq 9:37 or resseq 39:44 or resid...AA267 - 271265 - 269
122ILEILEPROPRO(chain A and (resseq 9:37 or resseq 39:44 or resid...AA274 - 283272 - 281
123ALAALALEULEU(chain A and (resseq 9:37 or resseq 39:44 or resid...AA285 - 301283 - 299
124GLUGLULYSLYS(chain A and (resseq 9:37 or resseq 39:44 or resid...AA303 - 305301 - 303
21TYRTYRSERSER(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB9 - 377 - 35
22SERSERVALVAL(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB39 - 4437 - 42
23GLYGLYGLYGLY(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB4644
24SERSERSERSER(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB4846
25LEULEUPROPRO(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB50 - 6648 - 64
26GLUGLUMSEMSE(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB68 - 6966 - 67
27LYSLYSPROPRO(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB72 - 7570 - 73
28SERSERALAALA(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB77 - 8275 - 80
29GLUGLUSERSER(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB84 - 9282 - 90
210ASNASNASNASN(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB9492
211GLUGLUGLUGLU(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB97 - 11095 - 108
212SERSERPROPRO(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB112 - 134110 - 132
213THRTHRALAALA(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB136 - 157134 - 155
214VALVALGLNGLN(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB159 - 171157 - 169
215ASNASNARGARG(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB173 - 194171 - 192
216ILEILEILEILE(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB196194
217ILEILELEULEU(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB199 - 226197 - 224
218VALVALPHEPHE(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB228 - 232226 - 230
219GLUGLUILEILE(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB234 - 263232 - 261
220ALAALAALAALA(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB265263
221TRPTRPLYSLYS(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB267 - 271265 - 269
222ILEILEPROPRO(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB274 - 283272 - 281
223ALAALALEULEU(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB285 - 301283 - 299
224GLUGLULYSLYS(chain B and (resseq 9:37 or resseq 39:44 or resseq...BB303 - 305301 - 303
31TYRTYRSERSER(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC9 - 377 - 35
32SERSERVALVAL(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC39 - 4437 - 42
33GLYGLYGLYGLY(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC4644
34SERSERSERSER(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC4846
35LEULEUPROPRO(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC50 - 6648 - 64
36GLUGLUMSEMSE(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC68 - 6966 - 67
37LYSLYSPROPRO(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC72 - 7570 - 73
38SERSERALAALA(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC77 - 8275 - 80
39GLUGLUSERSER(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC84 - 9282 - 90
310ASNASNASNASN(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC9492
311GLUGLUGLUGLU(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC97 - 11095 - 108
312SERSERPROPRO(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC112 - 134110 - 132
313THRTHRALAALA(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC136 - 157134 - 155
314VALVALGLNGLN(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC159 - 171157 - 169
315ASNASNARGARG(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC173 - 194171 - 192
316ILEILEILEILE(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC196194
317ILEILELEULEU(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC199 - 226197 - 224
318VALVALPHEPHE(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC228 - 232226 - 230
319GLUGLUILEILE(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC234 - 263232 - 261
320ALAALAALAALA(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC265263
321TRPTRPLYSLYS(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC267 - 271265 - 269
322ILEILEPROPRO(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC274 - 283272 - 281
323ALAALALEULEU(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC285 - 301283 - 299
324GLUGLULYSLYS(chain C and (resseq 9:37 or resseq 39:44 or resseq...CC303 - 305301 - 303
41TYRTYRSERSER(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD9 - 377 - 35
42SERSERVALVAL(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD39 - 4437 - 42
43GLYGLYGLYGLY(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD4644
44SERSERSERSER(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD4846
45LEULEUPROPRO(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD50 - 6648 - 64
46GLUGLUMSEMSE(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD68 - 6966 - 67
47LYSLYSPROPRO(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD72 - 7570 - 73
48SERSERALAALA(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD77 - 8275 - 80
49GLUGLUSERSER(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD84 - 9282 - 90
410ASNASNASNASN(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD9492
411GLUGLUGLUGLU(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD97 - 11095 - 108
412SERSERPROPRO(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD112 - 134110 - 132
413THRTHRALAALA(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD136 - 157134 - 155
414VALVALGLNGLN(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD159 - 171157 - 169
415ASNASNARGARG(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD173 - 194171 - 192
416ILEILEILEILE(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD196194
417ILEILELEULEU(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD199 - 226197 - 224
418VALVALPHEPHE(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD228 - 232226 - 230
419GLUGLUILEILE(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD234 - 263232 - 261
420ALAALAALAALA(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD265263
421TRPTRPLYSLYS(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD267 - 271265 - 269
422ILEILEPROPRO(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD274 - 283272 - 281
423ALAALALEULEU(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD285 - 301283 - 299
424GLUGLULYSLYS(chain D and (resseq 9:37 or resseq 39:44 or resseq...DD303 - 305301 - 303

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要素

#1: タンパク質
Conserved domain protein


分子量: 36215.434 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Enterococcus faecalis (strain ATCC 700802 / V583) (乳酸球菌)
株: ATCC 700802 / V583 / 遺伝子: EF_2687 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q830T5
#2: 化合物 ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / (S)-2-メチル-2,4-ペンタンジオ-ル


分子量: 118.174 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 185 / 由来タイプ: 天然 / 式: H2O
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: 2.79 Å3/Da / 溶媒含有率: 55.93 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: PEG 1000, PEG 3350, MPD, MOPS/HEPES-Na, L-glutamate, DL-alanine, glycine, DL-lysine, DL-serine

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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: 回転陽極 / タイプ: RIGAKU MICROMAX-007 HF / 波長: 1.5418 Å
検出器タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2014年9月18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: 1.5418 Å / 相対比: 1
反射解像度: 2.15→36.55 Å / Num. all: 76473 / Num. obs: 76473 / % possible obs: 89.8 % / 冗長度: 2.4 % / Biso Wilson estimate: 54.7 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.062 / Rsym value: 0.047 / Net I/av σ(I): 8.6 / Net I/σ(I): 9.3 / Num. measured all: 185116
反射 シェル

Diffraction-ID: 1 / 冗長度: 2.4 %

解像度 (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.15-2.270.5421.21791775520.4470.7050.5421.660.7
2.27-2.40.4961.425893107770.4090.6450.4961.791.7
2.4-2.570.2672.825178103530.220.3470.267393.5
2.57-2.780.1644.52362997120.1350.2130.1644.794.3
2.78-3.040.10172179889780.0830.1310.1017.594.8
3.04-3.40.05711.91997282160.0470.0750.05712.295.6
3.4-3.930.0416.21773272960.0330.0520.0417.496.3
3.93-4.810.03317.21495561490.0270.0430.03321.596.9
4.81-6.80.03515.91169748130.0280.0450.03522.397.5
6.8-36.550.02418.9634526270.0190.0310.02425.297.4

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位相決定

位相決定手法: 分子置換
Phasing MRModel details: Phaser MODE: MR_AUTO
最高解像度最低解像度
Rotation4.65 Å36.55 Å
Translation4.65 Å36.55 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
SCALA3.3.21データスケーリング
PHASER2.5.6モデル構築
PDB_EXTRACT3.22データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 単波長異常分散, 分子置換 / 解像度: 2.15→36.55 Å / SU ML: 0.34 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 30.6 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2416 5800 7.59 %
Rwork0.1957 70598 -
obs0.1992 76398 89.71 %
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: 225.95 Å2 / Biso mean: 80.2784 Å2 / Biso min: 30.02 Å2
精密化ステップサイクル: final / 解像度: 2.15→36.55 Å
タンパク質核酸リガンド溶媒全体
原子数9981 0 8 185 10174
Biso mean--86.25 62.54 -
残基数----1213
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00910224
X-RAY DIFFRACTIONf_angle_d1.1413790
X-RAY DIFFRACTIONf_chiral_restr0.0641562
X-RAY DIFFRACTIONf_plane_restr0.0071754
X-RAY DIFFRACTIONf_dihedral_angle_d20.0816296
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A4879X-RAY DIFFRACTION14.807TORSIONAL
12B4879X-RAY DIFFRACTION14.807TORSIONAL
13C4879X-RAY DIFFRACTION14.807TORSIONAL
14D4879X-RAY DIFFRACTION14.807TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.17450.42261020.35341312141450
2.1745-2.20.3851120.34681440155255
2.2-2.22690.36571320.33441606173862
2.2269-2.25510.44911590.36951807196669
2.2551-2.28470.33491730.32632146231981
2.2847-2.3160.35131760.31742461263793
2.316-2.34910.34812030.29972466266993
2.3491-2.38420.34472040.28732395259993
2.3842-2.42140.30922190.26672414263393
2.4214-2.46110.31222110.27232463267493
2.4611-2.50350.2862210.2532426264793
2.5035-2.5490.32672080.25982443265194
2.549-2.59810.29871930.25312483267694
2.5981-2.65110.31131820.25522477265994
2.6511-2.70870.30452100.24522505271595
2.7087-2.77170.30272310.23172408263994
2.7717-2.8410.28481890.24122527271694
2.841-2.91780.28751820.24652490267295
2.9178-3.00360.29532050.25122508271395
3.0036-3.10050.30011950.2432510270595
3.1005-3.21120.27851990.2352502270196
3.2112-3.33970.25752230.21922490271396
3.3397-3.49160.27092160.21332513272996
3.4916-3.67550.24672120.20392511272396
3.6755-3.90560.24232400.18982507274796
3.9056-4.20670.22262070.17172516272397
4.2067-4.62930.18662080.14872566277497
4.6293-5.29740.1922020.13842558276097
5.2974-6.66760.21851900.16692564275498
6.6676-36.55490.16711960.14712584278097
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)
11.11150.0191-0.26770.1309-0.61013.14240.06190.2736-0.3714-0.29380.13280.42650.8615-2.01180.00490.4912-0.12-0.03161.40570.26840.7768-95.33884.8061-70.8394
20.9436-1.4009-1.1041.97361.52171.1261-0.4079-0.43310.23080.15640.7604-0.1730.2604-0.20450.02640.7074-0.07560.03480.80130.16930.6122-78.170276.5403-72.9624
31.36470.84560.15161.71320.73234.42530.0197-0.1508-0.0225-0.01850.0266-0.1576-0.09010.7014-0.02160.34-0.01260.03720.54280.1090.4386-51.286187.9067-81.4474
42.33290.33071.47132.6673-1.42031.9059-0.1208-0.37040.30720.3849-0.199-0.8412-0.63780.5130.11580.5124-0.0637-0.00070.7660.09990.6839-9.390568.3216-31.4779
51.0236-1.43420.03841.6848-0.0229-0.0415-0.4495-0.6719-0.31510.4170.32070.2748-0.5282-0.26580.16910.91790.2233-0.03681.02860.00790.6029-26.468676.2774-26.6361
62.16450.69-0.11523.6441-1.24731.2545-0.0486-0.1083-0.1066-0.08690.25420.32530.0255-0.2576-0.08010.3714-0.018-0.01210.5061-0.00170.3303-53.3174.1449-40.847
73.52220.15920.56941.2149-1.19122.4020.470.98470.9794-0.1526-0.7843-1.0190.49740.8157-0.05950.53410.0490.00090.85310.25850.8541-16.764883.3-45.1862
80.2078-0.58710.09251.5483-0.0723-0.0174-0.030.79020.36490.21530.1086-0.19871.0342-0.45460.20941.2439-0.0913-0.02310.9257-0.0660.6871-22.656863.889-49.2064
93.58280.8187-1.6241.6454-0.58591.5896-0.44450.0995-0.5238-0.27670.0749-0.21790.40480.09130.12320.5446-0.02740.09370.412-0.01590.5259-42.124347.7442-31.6863
102.68580.5219-0.09050.8809-0.75132.64760.58810.87870.4910.0521-0.09860.3918-0.3386-1.3367-0.1460.5354-0.01540.01621.09970.21010.6968-87.948784.9014-91.116
110.0605-0.4082-0.392.21231.91061.61070.12250.6181-0.00950.39790.0402-0.0175-0.4924-0.322-0.10920.98740.10790.07170.97270.15520.8082-81.5182100.5444-79.7352
122.7005-0.65510.76791.6479-0.40372.638-0.1035-0.00920.14690.16820.249-0.0295-0.5235-0.1655-0.06410.5050.02270.0510.42420.00430.4496-62.274799.0232-55.793
133.1691-0.5695-1.50651.84270.90292.5923-0.29560.0821-0.7579-0.0670.1520.18551.0183-0.50260.0060.747-0.1967-0.00730.53070.08080.5882-70.689568.0577-87.2212
144.0576-1.35320.66852.9409-0.64431.2272-0.3896-0.99361.10490.93670.1894-0.4715-0.70670.06560.05190.7609-0.0113-0.19080.7137-0.22240.6425-33.979892.3745-30.3838
153.22960.274-1.58392.7856-1.0261.1728-0.61850.4865-1.1574-1.11060.1633-0.63810.86470.27610.17890.973-0.06250.32370.6663-0.17520.8315-15.989247.4141-45.1235
162.36420.1521.0021.96420.77751.8946-0.1590.13760.6292-0.14130.22260.4631-0.9904-0.8883-0.07740.81140.3710.10570.81560.24020.6408-88.053109.1233-65.0927
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 61 )A3 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 94 )A62 - 94
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 308 )A170 - 308
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 61 )B4 - 61
5X-RAY DIFFRACTION5chain 'B' and (resid 62 through 94 )B62 - 94
6X-RAY DIFFRACTION6chain 'B' and (resid 170 through 308 )B170 - 308
7X-RAY DIFFRACTION7chain 'C' and (resid 8 through 61 )C8 - 61
8X-RAY DIFFRACTION8chain 'C' and (resid 62 through 94 )C62 - 94
9X-RAY DIFFRACTION9chain 'C' and (resid 170 through 307 )C170 - 307
10X-RAY DIFFRACTION10chain 'D' and (resid 8 through 61 )D8 - 61
11X-RAY DIFFRACTION11chain 'D' and (resid 62 through 94 )D62 - 94
12X-RAY DIFFRACTION12chain 'D' and (resid 170 through 308 )D170 - 308
13X-RAY DIFFRACTION13chain 'A' and (resid 95 through 169 )A95 - 169
14X-RAY DIFFRACTION14chain 'B' and (resid 95 through 169 )B95 - 169
15X-RAY DIFFRACTION15chain 'C' and (resid 95 through 169 )C95 - 169
16X-RAY DIFFRACTION16chain 'D' and (resid 95 through 169 )D95 - 169

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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