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- PDB-6goa: Structural basis for OXA-48 dimerization - R189A mutant -

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基本情報

登録情報
データベース: PDB / ID: 6goa
タイトルStructural basis for OXA-48 dimerization - R189A mutant
要素Beta-lactamase
キーワードHYDROLASE / dimerization / OXA-48 / Oxacillinase / carbapenemase / beta-lactamase / ANTIBIOTIC
機能・相同性
機能・相同性情報


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
類似検索 - 分子機能
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
生物種Klebsiella pneumoniae (肺炎桿菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.55 Å
データ登録者Lund, B.A. / Thomassen, A.M. / Leiros, H.K.S.
引用ジャーナル: FEBS J / 年: 2018
タイトル: The biological assembly of OXA-48 reveals a dimer interface with high charge complementarity and very high affinity.
著者: Bjarte Aarmo Lund / Ane Molden Thomassen / Birgit Helene Berg Nesheim / Trine Josefine Olsen Carlsen / Johan Isaksson / Tony Christopeit / Hanna-Kirsti S Leiros /
要旨: Many class D β-lactamases form dimers in solution. The functional basis of the dimerization of OXA-48-like class D β-lactamases is not known, but in order to understand the structural requirements ...Many class D β-lactamases form dimers in solution. The functional basis of the dimerization of OXA-48-like class D β-lactamases is not known, but in order to understand the structural requirements for dimerization of OXA-48, we have characterized the dimer interface. Size exclusion chromatography, small angle X-ray scattering (SAXS), and nuclear magnetic resonance (NMR) were used to confirm the oligomeric state of OXA-48 in solution. X-ray crystallographic structures were used to elucidate the key interactions of dimerization. In silico residue scanning combined with site-directed mutagenesis was used to probe hot spots of dimerization. The affinity of dimerization was quantified using microscale thermophoresis, and the overall thermostability was investigated using differential scanning calorimetry. OXA-48 was consistently found to be a dimer in solution regardless of the method used, and the biological assembly found from the SAXS envelope is consistent with the dimer identified from the crystal structures. The buried chloride that interacts with Arg206 and Arg206' at the dimer interface was found to enhance the thermal stability by > 4 °C and crystal structures and mutations (R189A, R189A/R206A) identified several additional important ionic interactions. The affinity for OXA-48 R206A dimerization was in the picomolar range, thus revealing very high dimer affinity. In summary, OXA-48 has a very stable dimer interface, facilitated by noncovalent and predominantly charged interactions, which is stronger than the dimer interfaces previously described for other class D β-lactamases. PDB CODES: The oxacillinase-48 (OXA-48) R206A structure has PDB ID: 5OFT and OXA-48 R189A has PDB ID: 6GOA.
履歴
登録2018年6月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02018年7月18日Provider: repository / タイプ: Initial release
改定 1.12018年8月29日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
改定 1.22018年9月5日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.32018年11月28日Group: Data collection / Database references / カテゴリ: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.42024年1月17日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

ダウンロードとリンク

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集合体

登録構造単位
A: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
E: Beta-lactamase
F: Beta-lactamase
G: Beta-lactamase
H: Beta-lactamase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)225,86716
ポリマ－225,5838
非ポリマー2848
水7,638424
1
A: Beta-lactamase
D: Beta-lactamase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,4313
ポリマ－56,3962
非ポリマー351
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-11 kcal/mol
Surface area20740 Å2
手法PISA
2
B: Beta-lactamase
C: Beta-lactamase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,5025
ポリマ－56,3962
非ポリマー1063
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-29 kcal/mol
Surface area20730 Å2
手法PISA
3
E: Beta-lactamase
H: Beta-lactamase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,4674
ポリマ－56,3962
非ポリマー712
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-23 kcal/mol
Surface area20630 Å2
手法PISA
4
F: Beta-lactamase
G: Beta-lactamase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)56,4674
ポリマ－56,3962
非ポリマー712
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-22 kcal/mol
Surface area20760 Å2
手法PISA
単位格子
Length a, b, c (Å)107.726, 85.545, 125.805
Angle α, β, γ (deg.)90.000, 90.076, 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

NCSドメイン領域:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 24 - 265 / Label seq-ID: 3 - 244

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and (resid 24 through 59 or (resid 60...AA
2(chain 'B' and (resid 24 through 59 or (resid 60...BB
3(chain 'C' and (resid 24 through 59 or (resid 60...CC
4(chain 'D' and (resid 24 through 59 or (resid 60...DD
5(chain 'E' and (resid 24 through 59 or (resid 60...EE
6(chain 'F' and (resid 24 through 59 or (resid 60...FF
7(chain 'G' and (resid 24 through 86 or (resid 87...GG
8(chain 'H' and (resid 24 through 86 or (resid 87...HH

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要素

#1: タンパク質
Beta-lactamase


分子量: 28197.887 Da / 分子数: 8 / 変異: R189A / 由来タイプ: 組換発現 / 由来: (組換発現) Klebsiella pneumoniae (肺炎桿菌) / 遺伝子: bla OXA-48, blaOXA-48, KPE71T_00045 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q6XEC0, beta-lactamase
#2: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Cl
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 424 / 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: 2.57 Å3/Da / 溶媒含有率: 52.13 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 0.1 M BIS-Tris-propane pH 9.5, 16% PEG MME 5000

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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: BESSY / ビームライン: 14.1 / 波長: 0.9184109 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2018年2月27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: 0.9184109 Å / 相対比: 1
反射解像度: 2.55→24.67 Å / Num. obs: 72154 / % possible obs: 96.19 % / 冗長度: 1.9 % / Biso Wilson estimate: 30.57 Å2 / CC1/2: 0.982 / Rrim(I) all: 0.2062 / Net I/σ(I): 5
反射 シェル解像度: 2.55→2.641 Å / 冗長度: 1.9 % / Mean I/σ(I) obs: 1.09 / CC1/2: 0.568 / % possible all: 96.56

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_3150精密化
XDS20180126データ削減
Aimless0.5.31データスケーリング
PHASER2.8位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5QB0

5qb0


解像度: 2.55→24.67 Å / SU ML: 0.3265 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 31.974 / 立体化学のターゲット値: CDL v1.2
Rfactor反射数%反射
Rfree0.2748 2200 3.06 %
Rwork0.2395 69789 -
obs0.2406 71989 96.32 %
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: 42.34 Å2
精密化ステップサイクル: LAST / 解像度: 2.55→24.67 Å
タンパク質核酸リガンド溶媒全体
原子数15792 0 8 424 16224
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003116184
X-RAY DIFFRACTIONf_angle_d0.570921920
X-RAY DIFFRACTIONf_chiral_restr0.04482312
X-RAY DIFFRACTIONf_plane_restr0.00352824
X-RAY DIFFRACTIONf_dihedral_angle_d18.34119496
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.34671370.33664306X-RAY DIFFRACTION96.31
2.61-2.670.37441370.3294386X-RAY DIFFRACTION97.02
2.67-2.730.33911490.32024318X-RAY DIFFRACTION96.54
2.73-2.810.38331370.32524346X-RAY DIFFRACTION96.04
2.81-2.890.33881190.29644152X-RAY DIFFRACTION92.99
2.89-2.980.35181310.30374378X-RAY DIFFRACTION96.28
2.98-3.090.32611230.28144429X-RAY DIFFRACTION98.12
3.09-3.210.36941330.28794463X-RAY DIFFRACTION98.37
3.21-3.360.30011480.24664420X-RAY DIFFRACTION97.96
3.36-3.530.25891740.23624378X-RAY DIFFRACTION97.96
3.53-3.750.28421360.22064438X-RAY DIFFRACTION97.86
3.75-4.040.21911440.20534426X-RAY DIFFRACTION97.28
4.04-4.450.25861450.18654342X-RAY DIFFRACTION96.23
4.45-5.090.16551150.17714361X-RAY DIFFRACTION95.11
5.09-6.390.23071240.20684282X-RAY DIFFRACTION93.53
6.39-24.670.22931480.19644364X-RAY DIFFRACTION93.65
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)
15.247731977161.27160051947-2.530460408433.59068746072-1.40202994612.89053913597-0.5822744045940.7540770493540.694766183246-0.09487554900710.4865390096210.0813764221481-0.459492365797-0.3315069046470.08313734385690.7747790165870.1333400163-0.004449595141490.3433957518610.1733329317650.374389819699-198.82034527997.315947978747.2286081137
21.964887725960.486627166862-0.4908031109840.9243978186060.4491065111282.44762708662-0.0900256999268-0.000963945720147-0.07540985660470.05705484531940.0163020945262-0.07275559194950.1487041408120.1506079202870.07166537238010.2954477362690.0861870014802-0.001031970352540.427929363770.09806832041210.252697149416-188.75278440279.143014260560.6008415698
31.872733078230.544908502499-1.054191498970.804179435187-0.9501294079312.91492080891-0.1138056627510.3182667961540.233338932722-0.1839848483570.06756061079630.009219384282180.1261274338820.006715045549650.1417434166080.3543891545670.070045687366-0.009489978574920.3555174746230.02843489732830.214203674719-191.33224209490.741015494660.5485404402
43.632933451140.6822835409780.6095981413951.36432797956-0.406810254362.015871953220.1258049767830.1520865586840.3434451424130.019924681212-0.07530347463440.166674327585-0.692524454655-0.0400179403951-0.004935852067110.3812090308410.209518804510.04271858418190.4160031876890.06462805204770.269930125625-196.93153520294.96662389356.8830177051
52.130581822592.096482046350.3868724192843.94502640582-0.4744315057974.06770600596-0.332630630094-1.168923873260.03071179251060.738818347280.0339311137384-0.0353497033809-0.486074257647-0.03844233370040.1880953336730.390026130014-0.02819560381410.1100571113920.999522415372-0.09401212273920.373328972292-144.78072404699.132957145365.4322310196
61.975286517161.090740911790.8316765986031.147495507510.7352758902182.17074210236-0.095757507707-0.0763658487494-0.1639609235930.02403776511170.0601300860253-0.0522064796983-0.137627922277-0.05593991434220.02523123472970.2378224291980.1091442678050.02988924907960.5368331072430.0857686262930.28599327659-149.93791226884.179308210855.1141229473
71.699359846860.357405298113-0.1852261985211.04888461242-0.6470126911510.81362303257-0.02681122954160.1995349680020.219835447919-0.1484481918420.0566390588308-0.07259961784960.3418227887440.049465586151-0.07669847581250.3351706482070.02470173114310.03495149255610.6787663402210.0164599906190.260143251734-164.99673261782.672771856241.9658613469
88.427529746430.6057342880212.08227553124.25098213398-0.809746032197.57645991298-0.736804266985-0.0660908222814-0.3030273545110.4013675189310.05393216102360.03429747693240.858354786023-0.1507809821980.7806851323780.5056482031890.1309680207680.05660505676890.4594988107490.06709179414590.301564324758-156.45109154967.604659408855.1237856701
91.444007725270.06963274449860.0189509926996-0.00122786821403-0.00672320847450.00325807102533-0.203097505279-0.2406689653-0.389733743630.191636811244-0.2645102600810.06911346165840.2842713927930.3877989710080.1520226138790.3730422145090.254639426622-0.07032771720480.5826739020410.1918708656210.467459932201-158.84132470274.066842016458.9051194808
103.410513098510.761421256828-0.09154136360321.881236337531.127375340620.7972454053210.227281900838-0.647041841913-0.1839746323780.462445501874-0.204306321638-0.1416787456580.4865913831810.140306497709-0.04920605998610.257791037290.117314845335-0.01929825160390.5241017696010.1796880666030.280046518079-151.87460894380.525323574857.9095197822
111.354971422850.131732546864-1.366244422391.224078718780.7717801983221.81867135353-0.0200187774094-0.2627644115390.0752717167998-0.01514318982960.256300625030.057196384713-0.0834887530462-0.122044652942-0.1923550622360.2256400933680.104834100181-0.02197404012460.4926379877030.08127971473380.262937101453-148.62568856387.206250799751.0285722723
122.778920234780.363486010359-0.2005557947071.81670630380.3627010416121.5672009969-0.22343352590.05165370984520.635329106895-0.4341490040840.146260833138-0.176726366715-0.536227469265-0.3788126745280.1146695298130.6118031050640.1783307972250.05677692559230.2584967764560.09534782448520.316275287853-147.541961596100.0704326554.2534061182
132.55526793337-0.3855888011830.211685294071.3696791007-0.3219067996632.32315734583-0.04766467755590.103507336720.237704496062-0.185323299720.1068842542080.168015714546-0.228226743077-0.440146728602-0.02803051119920.2887910081870.13934446090.0263034331260.5198281398320.118451099560.301791011296-142.31004133693.79678806917.2579844768
141.481708897460.234425490232-1.428694324252.4786602887-0.2700936295441.997538131190.100517469548-0.493075594343-0.04456848769760.207732347163-0.0778047474585-0.01812295055850.6655253296570.784789163655-0.07554222438390.4522977110510.122917135512-0.0593135825360.3673303812240.07451666898130.318365262059-122.90718347184.379483958537.9436241001
151.090781395670.201487475811-0.8999604489220.945365638308-0.4034319568121.81355841347-0.106557012436-0.2713636638720.0376484169549-0.1100309257990.120632779048-0.06223809576110.2012818389950.15830446616-0.009063204553770.1602662827030.0887497982555-0.004030904187340.3533326154110.05969800769390.302914798725-129.02642235483.618570479424.7797443491
162.09884406344-0.33107573727-0.7301070616071.219904483810.04750125600272.74240591798-0.08402909363590.04494891132610.07399036894630.01938329437470.1171379997330.0189041112682-0.233756945449-0.63320406985-0.06128810587220.2656245897790.08341319983530.0038147443320.3445505557520.07723291477950.253010486929-141.20448068492.892174378926.343024637
178.088579250930.241251138077-2.299785101380.964652360294-0.1432300172494.52315984255-0.226500031294-0.9366351743550.922342078064-0.09553809468520.252853238343-0.362827002969-0.3157656007210.5817114930370.07029497803860.935209904772-0.02452007608620.01763926233310.484804129797-0.1664565417560.394972359919-197.474026284102.10353964896.8530369281
181.75545588263-0.06867896604060.3224018166431.06339054028-0.1053977662091.52836338819-0.04242614131960.05427485627480.1380222315040.314577175198-0.004563900809230.251401908214-0.242563016983-0.4944354597030.0144736014120.4045982958570.1666823894060.133589429070.5835792822640.07162364802690.298611506371-210.14921717188.137585350985.8718482025
193.41441397693-0.2890454485670.7986364071781.906703840490.6536367284434.5411911179-0.168110187272-0.51684826227-0.462620073004-0.03718219564580.2798047895110.1760534597280.162119493821-1.21758031836-0.05740600248820.3521573192980.06829103558930.07341239559540.6159138058990.07652091649230.364285245152-217.67143725981.316643162584.5932301211
201.92275774545-0.722035682044-0.4104099346881.641407745880.3044007157361.07943359159-0.0359595337938-0.154461587217-0.4046862785380.333522383644-0.02849076916720.1336093965370.0404796309552-0.5020299242970.1271858226890.3711002030450.1104238252940.09054580535420.5729976864090.1551362081190.380033241472-206.2182453581.065656812487.4086820473
213.82395444244-0.115669656188-1.454116625841.18717331161-0.5010247154752.691018855290.103101724776-0.2252147039470.673131317170.1413336194450.268572799290.111149665741-0.407359674366-0.385105051576-0.2326148229370.4047731286450.104504944360.07865775244330.3708004180760.08768642153540.292490262183-204.32942042592.901386713584.0286321069
221.003335488780.803151733236-0.1697306101320.865860433786-0.9960716481714.944786736390.1763910381880.008934979791830.533928196813-0.1788322442020.240123272966-0.136976022021-1.0298919231-0.582904243582-0.2870177333040.7062724018990.02548124051270.1180040743770.3497726063130.07161539841490.365419375471-201.89490627299.93302634287.5202925363
232.032529203681.00383888891-1.789656706440.7781099851480.0294005174644.51030727419-0.49645897754-0.861156250067-0.8099163484110.203342556830.004680379925670.03286066911880.682727268940.03574255599930.2402068304650.530266831182-0.190328865862-0.1700079818790.7939457319150.3794816082470.496709273966-145.56545792772.12753198222.55161781036
242.50995489166-0.4333422431540.8370777473192.04967769369-1.074106468112.364728186950.374049229117-0.670759793441-0.19722660578-0.03915996950370.1383029637210.1842131725870.261971196061-0.719509156657-0.5179967868070.443919176055-0.05917974715640.01722565993820.7833363092680.1298623263720.315638661845-146.705657779.73274159340.767474517952
252.02906062012-0.526244047534-0.009630641459931.978593527021.103738897841.351624359930.2314513454380.2796246769760.279668639973-0.350744883496-0.0963625506477-0.05258360462520.0257140594001-0.036383388529-0.09102057411280.3324357726270.131497732220.01606831329550.474949801470.1083046498350.257570528014-128.74351406390.63518904-18.5182879085
267.40606374935-0.796742318899-2.035518145219.815390346190.4986517636292.007939401050.223540882541-0.172770768342-0.0906550047805-0.0908471728788-0.243920897783-0.143330483294-1.35955743346-0.5877373337960.01969320539870.3241860707290.0797341629945-0.04123744395170.489776905231-0.02659265609830.284898569258-133.476297708103.59450758-7.49083380612
271.050348453830.4918083317021.005495427072.125441834210.3523043298341.06607106461-0.1139189276930.4783987757180.64908648690.5540261813890.1732193473950.1888429292440.0192843493587-0.231569952707-0.07571902769410.3021377596350.144632435790.04762410801110.527048598620.04795726297130.385289267607-135.57539503193.0864117016-4.45832870274
285.187438923020.515267978006-2.810289313811.05951821879-0.003747279529862.217507691690.425277746071-0.4934665693970.6902462552080.08155599011410.1769903814750.489611717744-0.181599120993-0.70619019535-0.4835564817520.3358361780870.182823570447-0.03952972734111.007644111630.2279261182290.383774368783-145.24414478396.2346707393-17.2203173009
291.3101413553-0.0844622467260.4281996388130.33169395904-0.6756273771974.657504940920.1482231828230.3989754605060.0919318833689-0.2978419077020.107132374452-0.1724498341380.432812775704-0.627186843646-0.1034151312570.3082166634830.3163639953250.06250127168740.214980359045-0.002877118315640.382524884724-137.2656057680.3010489621-12.0142279413
301.953531259490.3623595801790.9949414589381.72492551688-0.152714090642.064586425430.2274988472560.127660681003-0.242740072036-0.1519653684220.169279807171-0.05407423002460.526908043283-0.379507825725-0.2331727467120.412789453923-0.0340787267978-0.2161490774320.5233294197150.1600390773630.296988420878-142.97621044279.8449977015-8.10296976593
312.76489580959-0.286136996452-1.208882165384.25274618893-1.309905794553.5203743450.02892415579250.0870917639226-0.113656972955-0.5230089673240.01688308142130.4276925505650.942649100795-0.195257440632-0.03555123123950.631704242108-0.03421338602390.0009326772376050.392595177506-0.07646733619010.328955143306-142.78094708971.1502827023-8.5340432582
324.148823213120.1682819018543.274412040362.30446963151-1.273247043194.00432993202-0.151261523547-0.777159280545-0.1399233850330.2399640525290.1221925228590.07056168886610.240925287123-0.535747355268-0.001183092385980.392187693369-0.03169119509050.08607295853480.257402676367-0.02852631043920.263809953601-125.60621321433.863668878815.8118128632
331.6336418719-0.6061472607210.4947808876110.411259031891-0.674008985741.3576283274-0.02795219023310.06121319679030.151251938960.121371037966-0.0869632465039-0.0967370887233-0.213735943490.06501565465530.1461407138810.301547720746-0.145270579960.04236894849450.272230605498-0.05707771079940.287082329107-112.42363216750.29370875510.627361042654
344.251291886090.03228845053060.2469007404161.197575993790.2395867713392.53637334814-0.0368025526091-0.29608972184-0.1268924561950.130627081445-0.09508711416620.1147755628250.3094571616580.09376826539690.1269486260560.2750307413-0.09421602617540.05164391469490.3041854570470.04777593885110.236350587705-116.51788502137.46291539122.23952366372
351.67557281887-0.9656001482950.1535267742641.24322527284-0.8748963334761.268777604270.500145908719-0.237915429647-0.275817616319-0.092889010769-0.09091112579820.03369242021660.115883625921-0.184765419621-0.4207084322030.318271617427-0.120766960697-0.02281750558090.277295586142-0.02070712597860.281536555533-122.12820431633.19098672075.97994179323
362.22979247567-0.7357662214820.2346683040531.175235032121.565989131062.95660126304-0.2785026195580.178755617675-0.5503153969980.3351748035830.296270972846-0.3612624919270.9538730768050.25429436511-0.06726208951090.9334917434690.1745619354550.2282626269120.245978550547-0.2620438623360.181931921602-122.30228170726.0141814646-34.5726984037
370.790941556434-1.10168681192-0.09724447189071.56796506439-0.2724711083443.36927287227-0.0107596943095-0.0367880265353-0.4889444812480.01519966926620.115053361228-0.1508884628220.2041109937320.209775944967-0.06975376469960.317569603605-0.05807694773130.04674328653870.2479871974420.01976251859240.364211243633-121.03243257333.9818041382-32.288563656
381.842562484690.125591722885-0.05811783062740.853318029939-1.034827659961.280919466570.1972348286950.1414109259-0.371371716175-0.376513607148-0.1021376902550.0261885118781-0.218931000139-0.871075945426-0.1052176171370.4120523177260.002826079818810.09584541317820.706043895967-0.1000096187760.265561571372-135.80570525142.0783426826-27.8182858411
392.753305138860.620059554048-0.3244103730151.39741990451-0.15152603692.416632515780.241786710044-0.651645646210.08352143638940.120112906449-0.2929853954750.231990727505-0.265319436841-0.8989165297420.02879029679690.291483312076-0.03785120124560.0741840706740.579426099279-0.07884048187870.333934702099-144.56190768241.3714767429-10.7745979701
402.036017002780.503798466736-1.159283906471.601445712770.9965250256113.413405313420.09248174581270.2402363455370.312969338765-0.237805028847-0.01518330451510.022902423716-0.460857162781-0.936101931209-0.02622255323440.2861593038170.0607570226082-0.01476467606020.606068172658-0.01426074281240.228556350474-143.32758118649.6712846792-26.3480917465
415.92797532041.872438605232.841048531972.232757699791.018319824921.90230902392-0.2356056829450.3559687613810.0210632382416-0.4172066481920.2160528979960.035091356636-0.2053575020330.413279805027-0.04792750175980.252551238543-0.04133193566150.058927856870.293946155982-0.04584996590430.23943165446-132.89759144443.7187176422-29.2394249315
421.69723405258-0.374617825729-0.2986820349051.915830523890.1885033956661.09912633588-0.1787708379060.2942800834640.561034103122-0.257122489738-0.00069287997304-0.204542414461-0.6203958800140.2232750793130.02326041757880.391440673967-0.140545196304-0.07837415805570.137576894012-0.03447447992130.519518401589-128.91042953752.0200725305-17.6229112368
432.32430644962-0.006935965776180.8317868222321.6381305368-0.2913135590540.75244906919-0.0554524881192-0.0435333924243-0.3866570263390.00862935622884-0.05403138471720.08432530408450.0229339308994-0.1305808977620.08757834821760.240185610229-0.1155132944480.08808043964210.479253966904-0.06954020973630.288469498964-131.30737775434.6746517671-21.7826900977
442.983246210690.468665428176-0.3197807236162.986393943581.130894371423.499763843820.2491847297550.0242878889314-0.2437920202560.186753557851-0.3152968960820.2500549561370.422619645555-0.190873075549-0.01600053795480.378862782481-0.01764340760810.02774897622850.269454349757-0.07756194258980.256789034827-125.15475238129.3596932445-24.3957493933
452.583984854090.1569485244540.8090476057331.359002142930.04413098516613.417514872890.2902923981320.0121344884591-0.205010852571-0.1562671952720.0153301758721-0.02111305677380.681270519847-0.596030695832-0.3012411139530.550366775020.0113192197502-0.1831282534710.7752202706370.1762760596810.360470859134-153.43621057580.0018912245-39.6483465376
461.184376594680.13051339804-0.4230971950951.96717916167-0.8292164235454.96452498142-0.03033926248750.152735764863-0.207239198873-0.416918612217-0.08688914027950.1621900655940.798291483358-0.862847964366-0.07150958192790.539790255099-0.0188794588045-0.1168074187571.479907101390.3820303640720.186193024197-162.30421857281.6771935634-24.9405089557
472.76142119398-0.312755392461.375100215111.450948307130.5795392960223.533112085670.0896196855103-0.1113303204370.0853312628287-0.1011860058460.04169889880350.02261424008590.427549696216-0.624850664621-0.1690162025120.4547119117780.0899121027007-0.04630348224960.7887060455640.1644760419840.336091759198-153.42405938683.0501152099-38.5603961408
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 194 )
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 218 )
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 265 )
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 38 )
6X-RAY DIFFRACTION6chain 'B' and (resid 39 through 92 )
7X-RAY DIFFRACTION7chain 'B' and (resid 93 through 130 )
8X-RAY DIFFRACTION8chain 'B' and (resid 131 through 141 )
9X-RAY DIFFRACTION9chain 'B' and (resid 142 through 155 )
10X-RAY DIFFRACTION10chain 'B' and (resid 156 through 177 )
11X-RAY DIFFRACTION11chain 'B' and (resid 178 through 243 )
12X-RAY DIFFRACTION12chain 'B' and (resid 244 through 265 )
13X-RAY DIFFRACTION13chain 'C' and (resid 24 through 82 )
14X-RAY DIFFRACTION14chain 'C' and (resid 83 through 102 )
15X-RAY DIFFRACTION15chain 'C' and (resid 103 through 177 )
16X-RAY DIFFRACTION16chain 'C' and (resid 178 through 265 )
17X-RAY DIFFRACTION17chain 'D' and (resid 24 through 38 )
18X-RAY DIFFRACTION18chain 'D' and (resid 39 through 105 )
19X-RAY DIFFRACTION19chain 'D' and (resid 106 through 155 )
20X-RAY DIFFRACTION20chain 'D' and (resid 156 through 194 )
21X-RAY DIFFRACTION21chain 'D' and (resid 195 through 231 )
22X-RAY DIFFRACTION22chain 'D' and (resid 232 through 265 )
23X-RAY DIFFRACTION23chain 'E' and (resid 24 through 38 )
24X-RAY DIFFRACTION24chain 'E' and (resid 39 through 63 )
25X-RAY DIFFRACTION25chain 'E' and (resid 64 through 130 )
26X-RAY DIFFRACTION26chain 'E' and (resid 131 through 141 )
27X-RAY DIFFRACTION27chain 'E' and (resid 142 through 177 )
28X-RAY DIFFRACTION28chain 'E' and (resid 178 through 194 )
29X-RAY DIFFRACTION29chain 'E' and (resid 195 through 218 )
30X-RAY DIFFRACTION30chain 'E' and (resid 219 through 243 )
31X-RAY DIFFRACTION31chain 'E' and (resid 244 through 265 )
32X-RAY DIFFRACTION32chain 'F' and (resid 24 through 63 )
33X-RAY DIFFRACTION33chain 'F' and (resid 64 through 194 )
34X-RAY DIFFRACTION34chain 'F' and (resid 195 through 218 )
35X-RAY DIFFRACTION35chain 'F' and (resid 219 through 265 )
36X-RAY DIFFRACTION36chain 'G' and (resid 24 through 38 )
37X-RAY DIFFRACTION37chain 'G' and (resid 39 through 58 )
38X-RAY DIFFRACTION38chain 'G' and (resid 59 through 82 )
39X-RAY DIFFRACTION39chain 'G' and (resid 83 through 119 )
40X-RAY DIFFRACTION40chain 'G' and (resid 120 through 155 )
41X-RAY DIFFRACTION41chain 'G' and (resid 156 through 178 )
42X-RAY DIFFRACTION42chain 'G' and (resid 179 through 194 )
43X-RAY DIFFRACTION43chain 'G' and (resid 195 through 227 )
44X-RAY DIFFRACTION44chain 'G' and (resid 228 through 265 )
45X-RAY DIFFRACTION45chain 'H' and (resid 24 through 105 )
46X-RAY DIFFRACTION46chain 'H' and (resid 106 through 119 )
47X-RAY DIFFRACTION47chain 'H' and (resid 120 through 265 )

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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