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- PDB-6ztw: Crystal Structure of catalase HPII from Escherichia coli (serendi... -

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基本情報

登録情報
データベース: PDB / ID: 6ztw
タイトルCrystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized)
要素Catalase HPII
キーワードOXIDOREDUCTASE / catalase / hydrogen-peroxide / heme / iron / oxidative stress / artifact crystallization / impurities / contaminations
機能・相同性
機能・相同性情報


catalase / hyperosmotic response / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / iron ion binding / DNA damage response / heme binding / identical protein binding / cytosol / cytoplasm
類似検索 - 分子機能
Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain ...Large catalase, C-terminal domain / C-terminal domain found in long catalases / Catalase, mono-functional, haem-containing, clade 2 / Catalase, mono-functional, haem-containing, clade 2, helical domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily / Class I glutamine amidotransferase-like
類似検索 - ドメイン・相同性
CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / Catalase HPII
類似検索 - 構成要素
生物種Escherichia coli K-12 (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.84 Å
データ登録者Grzechowiak, M. / Sekula, B. / Ruszkowski, M.
資金援助 ポーランド, 米国, 3件
組織認可番号国
Polish National Science CentreSONATA 2018/31/D/NZ1/03630 ポーランド
Polish National Science CentreSYMFONIA 2016/20/W/ST5/00478 ポーランド
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program 米国
引用ジャーナル: Acta Biochim.Pol. / 年: 2021
タイトル: Serendipitous crystallization of E. coli HPII catalase, a sequel to "the tale usually not told".
著者: Grzechowiak, M. / Sekula, B. / Jaskolski, M. / Ruszkowski, M.
履歴
登録2020年7月20日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年10月7日Provider: repository / タイプ: Initial release
改定 1.12021年2月10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_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
改定 1.22021年2月24日Group: Database references / カテゴリ: citation / Item: _citation.title
改定 1.32021年3月3日Group: Database references / カテゴリ: citation / Item: _citation.title
改定 1.42021年3月31日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.52024年1月31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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Catalase HPII
B: Catalase HPII
C: Catalase HPII
D: Catalase HPII
E: Catalase HPII
F: Catalase HPII
G: Catalase HPII
H: Catalase HPII
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)682,03639
ポリマ－674,7728
非ポリマー7,26431
水84,5804695
1
A: Catalase HPII
B: Catalase HPII
C: Catalase HPII
D: Catalase HPII
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)341,13921
ポリマ－337,3864
非ポリマー3,75317
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: Catalase HPII
F: Catalase HPII
G: Catalase HPII
H: Catalase HPII
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)340,89718
ポリマ－337,3864
非ポリマー3,51114
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)121.188, 168.071, 137.982
Angle α, β, γ (deg.)90.000, 105.239, 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

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要素

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タンパク質 , 1種, 8分子 ABCDEFGH

#1: タンパク質
Catalase HPII / Hydroxyperoxidase II


分子量: 84346.477 Da / 分子数: 8 / 変異: S99N / 由来タイプ: 天然 / 由来: (天然) Escherichia coli K-12 (大腸菌) / 参照: UniProt: P21179, catalase

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非ポリマー , 6種, 4726分子

#2: 化合物
ChemComp-HDD / CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE / HEME


分子量: 632.487 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C34H32FeN4O5 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / トリス(ヒドロキシメチル)メチルアンモニウム


分子量: 122.143 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C4H12NO3 / コメント: pH緩衝剤*YM
#4: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C3H8O3
#5: 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
#6: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C2H6O2
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 4695 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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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: 2.09 Å3/Da / 溶媒含有率: 41.01 %
結晶化温度: 292 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5 / 詳細: 0.1 M Tris pH 7.5, 20% w/v PEG 4000

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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: PETRA III, EMBL c/o DESY / ビームライン: P13 (MX1) / 波長: 1.0332 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2019年10月16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: 1.0332 Å / 相対比: 1
反射解像度: 1.84→80 Å / Num. obs: 452364 / % possible obs: 98.4 % / 冗長度: 4.66 % / Biso Wilson estimate: 18.21 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.14 / Net I/σ(I): 9.85
反射 シェル解像度: 1.84→1.95 Å / 冗長度: 4.53 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 72060 / CC1/2: 0.714 / Rrim(I) all: 0.776 / % possible all: 97.1

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解析

ソフトウェア
名称バージョン分類
PHENIX1.16_3549精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1gge

1gge


解像度: 1.84→78.25 Å / SU ML: 0.184 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 18.6405
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.1839 2260 -
Rwork0.1443 449992 -
obs0.1445 452252 98.39 %
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: 22.17 Å2
精密化ステップサイクル: LAST / 解像度: 1.84→78.25 Å
タンパク質核酸リガンド溶媒全体
原子数45952 0 496 4695 51143
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006947940
X-RAY DIFFRACTIONf_angle_d1.086365355
X-RAY DIFFRACTIONf_chiral_restr0.0546863
X-RAY DIFFRACTIONf_plane_restr0.00578720
X-RAY DIFFRACTIONf_dihedral_angle_d17.649628741
LS精密化 シェル解像度: 1.84→1.88 Å
Rfactor反射数%反射
Rfree0.2784 138 -
Rwork0.2428 --
obs--96.41 %
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)
11.91809649897-0.9370290119720.07573571390750.554776958674-0.03846042548670.00328095058230.03089856771450.2328259535750.248835398169-0.175985794619-0.0283349532211-0.111377073051-0.0649481187270.0527779224642-0.003279425215460.224724830167-0.02012912154510.0166266005970.2195880196030.02878322591440.13453018245726.307856628528.999170811238.9408116024
20.2233904911-0.009775870301340.03831340460960.2141362547850.0211923255870.08881733875310.0009518957136390.0636032865997-0.0445400090513-0.04934386419040.01295693928-0.05614717502090.0301892403730.0301341193725-0.01505909717540.1445236613060.002295817092020.01235586448830.145793741387-0.01724624946640.14174369259431.98658039427.1825409863356.5459861788
30.6415608072680.0636672723169-0.2777472583470.6500404377390.3847181701610.6392153441670.0301593861419-0.0587048819022-0.0153653224780.06317518506840.0304571089894-0.1802105926030.02150896861490.110641125272-0.07442511377290.1277726739330.0266155634546-0.03225489937130.160647826866-0.01095615184270.20394977168853.53485712397.7793329917476.5510926043
40.457483225928-0.664995119708-0.05073261034661.99738519648-0.04344949413670.01512257926280.07859322237450.01419342030270.0587496529262-0.1024278568490.0250276422335-0.1803459530310.204957188810.192786306765-0.08350967207050.0725675272189-0.0120116371284-0.005314335845240.161790708449-0.04340519708460.24555046379958.14864863733.7449192386868.045808611
52.633255500130.854076414131-0.5128481856021.97036996035-0.4182944946792.259616980010.02613990530750.3475605377460.249786657481-0.5018240853740.0702657989083-0.288033341207-0.2586780036170.201823879869-0.09626082840140.263209671539-0.02313497060920.08914651810740.2403097196980.03612649742280.22440205295556.722443282138.021920337644.4308196085
62.322076032520.8348103940360.045089774852.08700000755-0.0325457971840.563563624489-0.003329266422670.06857199620650.139461002204-0.1354132883730.108030700695-0.363190479199-0.04283310754670.17877113807-0.09060413136870.137121618166-0.01663105867640.05745059310570.219864689822-0.03657993213940.3031636414465.166680914830.930136136155.611510435
70.297405670020.01548617432730.1501610802881.08284926838-0.0496815954020.2961585331740.0101298385929-0.09473390969940.02095756452540.148499857825-0.0161511447940.165268179970.00951546323525-0.0966136501004-0.01443712421660.0948087131564-0.009422409677820.02491252840520.144711193014-0.01706283557980.131634306721-6.630823348423.432391362479.1293404792
80.2726147578370.0558864428370.01364256017470.1792581544060.02581811916550.1328551895630.0142637153876-0.0428703954006-0.07797014775930.045531394316-0.01686844308750.01520069896620.0815249749508-0.02068509037020.001536999119850.176143065488-0.01545989386660.004711971053090.1361784977280.002897720603370.1601076784063.48367162117-6.255209701275.8348901652
90.500647042524-0.088240071357-0.2011161259630.2582583798780.1156919243330.4119978691560.00108876916430.00210207371825-0.08993362119860.0328256268799-0.03288076370650.1069197947850.0911485728594-0.1085371289390.0517805238810.173600036942-0.05377311058370.006585971308870.159142589802-0.02251845531650.235601212418-26.453806545-11.908693642570.60244541
100.2863890057990.02967877519010.05386657316820.2654547600780.008170692973780.128172515814-0.003869939081540.06672163121740.0242286019916-0.0958611156325-0.007519371180740.0677654756091-4.26262328748E-5-0.02313121381440.00569390507070.124027586713-0.00359072483914-0.01678831401590.121647198474-0.001703099515830.10442371899-5.6508377423321.22167207149.9266829633
110.270502956966-0.05038403997560.1335002189030.7789516656950.1393020136620.61637499580.02723467676780.0210890795926-0.0338966958872-0.0969906086212-0.03642173859320.2123346901460.0921212600017-0.1328852287830.03147793824490.125207866084-0.0298884030303-0.03566240431540.185934393057-0.01802030186050.24314278276-32.798095143310.562617862153.6702307452
126.979226893182.647395879250.3612526933713.66643408591-0.4966162294671.527285633770.0299537358902-0.1196221721940.0407958842896-0.140941902389-0.03853184560.5421479315290.113542495871-0.230373778390.01079649786750.1386377251580.0179009553716-0.07565781852640.1775745367-0.02273423022270.352359991598-41.89037404774.879421955645.6687487717
130.3391986439110.09228028839380.07707050673381.230665087890.1814187529430.1971173104620.0207752908508-0.0703373745353-0.05760254193660.1999363543370.000746976352317-0.05261450886330.07816572164230.0110450144623-0.02666218364340.1094310397490.00171727642472-0.001841709579590.1163653231330.00873781730950.093103157474426.308093426911.796086330683.3248103983
140.912577311273-0.5181715489740.06669436432181.006865669480.04357988131710.346202006777-0.125205864654-0.1912799610160.0471133078790.1797355274490.07953147195390.124755765175-0.0191231814545-0.01001577847220.008805192640330.159987627501-0.005543654901150.01173315414730.140509112077-0.02364295122960.14789766723515.94333369142.955339473287.5552406838
150.2040117733860.01497771929240.02311427918310.2507241001010.04742385212410.129129876402-0.0123248015748-0.001236926582370.06553183771-0.0017081230021-0.0001905113720880.0238796579106-0.0195912674527-0.01489119706010.01507945156830.1156753646910.0002255459221170.0009275571249180.1159470713120.002027587541550.1366012865817.736319106640.125713083472.5527441606
160.329475465323-0.03289773268180.001574966949810.4962477242840.1438959716390.365479592712-0.02358702627440.06942028936740.100589881631-0.1107395449560.0111847917223-0.107298411813-0.05412293685280.05121927657260.0007793114239370.165390820717-0.01920546961250.004330346117430.1537115496820.0356920152920.2032735703336.129657859952.744851676256.6154246416
171.04279097451-1.147268119580.3275009090442.45454341005-0.3415051164920.0952709334573-0.02893510019-0.01165987925330.1123309817760.01170383066070.0672693705498-0.0655291538604-0.318430451544-0.0282521299381-0.02471132129170.104078676684-0.0741747787833-0.008761027535350.1180180680750.01513230428970.23586340545835.671345487358.217351691265.4485434402
181.22173302496-0.1668863961440.4107633850892.11341275627-0.7745907931871.64065628111-0.0319257199506-0.07848379958310.03074641270590.100978545446-0.0106744722959-0.1947740187350.01110399401750.1970469634020.0159206467460.09497918709090.00513176410817-0.01694032304140.149915103738-0.01696025966280.15569881025157.71765477235.076909453885.3602980975
191.88468223915-0.1202912933160.5047872085352.31318718857-0.4641017884451.91758070344-0.0472576054269-0.00428825827630.2359239519630.0305912765308-0.0371147607909-0.232139724988-0.1447288840370.2490165306170.0704118986980.107681081836-0.017201586902-0.007880460873080.1350411142160.002727587013190.23979508734356.759568982748.709275991879.9508864431
201.73585518687-0.534655629639-0.3285250255960.2160660456620.09646581687480.135323958170.03588657205750.2442876833730.269595097485-0.1107107883870.0141912050532-0.102328257464-0.04358989179880.0189793715594-0.04736841049550.164205583562-0.01923355082060.03250134740450.2392867395860.03083705097840.1638311858188.4584399838340.6618974884106.011988088
210.77040958687-0.0167535035078-0.126024351580.450829459262-0.07596232165180.173848529984-0.02674975558770.0184957823944-0.0687886931991-0.02973510683770.00286703572959-0.06153461877630.03680895269040.04034671349980.005415808205930.0871939336692-0.002893067820090.009889163718840.121577925654-0.01996860234320.095982012342113.410597147924.8540382123126.536713581
221.105792560880.313613383901-0.07827625042030.883109110591-0.03772382510970.409069997418-0.07510069624670.0657450309817-0.228474658732-0.1431763504820.0578816399125-0.1817462787510.05574572482530.03454952161540.005839441054870.1380133435740.01743854402650.02317044488080.145929748111-0.02753531504840.19463966809325.822418673413.6843443471120.891163218
230.7527766733640.0926197279896-0.06543804752940.515152626209-0.1280346911290.378470945947-0.0265591113023-0.01050024999-0.178192401762-0.05917009080770.0117113588189-0.10861084470.07270415799770.06949162330670.03012505001150.1125814016880.009378824103460.02882477733140.164215857046-0.02252000453570.19037042564827.275962292217.7760257465122.89569818
240.5977401575670.23605394017-0.02050152050590.939259544894-0.3805987419370.498191758111-0.01547427124310.0561033519712-0.132587856909-0.0541457489020.0025871539316-0.08253483700610.05724306244860.03405807158050.00835544728960.107527088549-0.007770885044320.008557389286780.134963709823-0.02604716983590.13299366281811.979917265117.0356095091120.366805128
250.6892211790460.2220833491990.1237956575920.3246250143660.003908742389840.316128623116-0.05572251677710.10988619475-0.207353199648-0.06009798468120.0777918848347-0.04659925358420.07982838535170.0319608956303-0.006985882420270.150551223669-0.01225316276980.02003234035520.150850202556-0.04054339250520.161797251747-1.881961246997.66611448256116.941395301
260.9850326665420.0240936033516-0.5262009422320.761719068510.1764282045920.4580774731930.0225900418882-0.287331607419-0.13602891910.045139827948-0.0420788142861-0.1777341074070.05353467679410.1658118592260.01322889739080.1353680294080.0353324934744-0.03325190550580.260309754980.04549913843080.211836149735.337896938417.8485145468142.954802202
270.8431200964350.0524018512949-0.2833720571692.32975891608-0.8603406560820.627738487098-0.0244978947418-0.251800362758-0.2008151525340.0481677264903-0.0922039027037-0.3269169242760.1663570083050.1647783085670.1070897498420.1134732996410.0300537750194-0.02908316128620.2655221088570.04074457278560.32434617628640.011637972714.1787154137134.293926729
280.804451893151-0.147430992436-0.2229990083372.80387897128-0.5264648967571.272195734360.03771210120420.2109851443380.116677887967-0.150590363645-0.03315311104980.0239777191148-0.0853410480344-0.0215932121871-0.03195759181520.119649930087-0.01052161250150.005512669788540.212922899672-0.008811553038640.20192468459138.572127217849.3304824192111.75609026
292.296132575610.5039556451630.2533182392273.19629184729-0.5553645785740.910720723308-0.00280148277639-0.0671269394560.05204521069540.031208351568-0.0222190629173-0.0946847620203-0.05454658173350.1496580322530.02456702450730.083071176667-0.007370469806240.01515949595050.200639835736-0.04128362965460.18180615397447.09130338441.8145235158122.737231204
301.023543059440.0546315186804-0.4491413548271.91511255955-0.2050786139770.2982823712-0.00831654720572-0.197440126910.06929551249060.2081113274150.02732794642570.183720002161-0.00611048590753-0.0310984284671-0.0241270298390.197387090172-0.008834034442160.01973630453130.244529738058-0.04099567342610.143072324066-27.92381440829.6794874599153.796608011
310.5427557221040.0703488074887-0.06494704751190.32195555639-0.01540165597920.175203872372-0.00848344582597-0.0593531727902-0.07968705325390.03575580186580.011232306819-0.01615091556270.0689959748151-0.005044627543710.00220173843980.122945511433-0.01469765056440.0005023240851040.12472427750.006639782731480.109822142453-19.537398130411.9729735332135.737849104
320.5786342265240.14503705262-0.06617762698210.1754829998960.02751822482070.1616244864830.00067563647516-0.110859002917-0.1566833296650.0549842734815-0.0122557217167-0.04159679485820.07663268047510.02743604895530.008533068551330.168679661267-0.00102993032591-0.007226331634260.148221868370.03489468056630.149565533487-12.65148650984.24391983425143.530626502
330.6867679715190.116040874919-0.08086972474960.309337587033-0.3877248858230.489163126461-0.039136790990.108385784912-0.235675913302-0.0480627581753-0.00118044519460.05025011863630.172688350095-0.08061411765050.03651816107990.212320467137-0.04865200885540.01551233986810.154605256136-0.07018626664560.265528002331-29.712855207-10.1562516519121.605166433
340.781988715005-0.796668308486-0.2798343465581.91851110767-0.127716944720.33192305511-0.1075714236780.0650512132437-0.2870267747150.1030551934060.03373524319760.05447060185360.48753103454-0.01174997722190.1181252702380.205301670649-0.06784661346460.01109784646470.162742530944-0.03715616806080.386981758256-31.0293908282-14.7938210261130.83700388
351.56982546629-0.240908795328-0.3011777299822.42736403878-0.3058611514621.308640213130.0273782031861-0.0181187875695-0.1116982350830.1397171748030.02602001452290.2362986966520.0385449363048-0.264803624923-0.03615752149740.144694337906-0.05434113795590.02705069650240.2180003368710.02603186452010.186314757498-55.55614628896.1475475063142.624675524
361.738527930961.492311738910.4419978118584.610549525040.2192288323821.33105850525-0.1723475788080.351267857484-0.237681171253-0.5915476438730.174601881844-0.1500729608020.139758400273-0.03564075840170.01548529716350.180622027289-0.03635574294870.02492789205720.303767491278-0.06111803638560.150874634213-21.606987179213.1683634032101.528539548
370.70327698596-0.0805354020795-0.09391670855870.337086874811-0.001838058533670.1639982569770.002188541670050.1419322923150.0536198802196-0.04709830040830.002399352591410.01309818688840.0120605129301-0.045155687188-0.007760186289890.0880955632134-0.0220309179466-0.009127959833160.1283122603630.008827290282670.0797153645497-22.927696360626.8133663929120.925917791
380.7052396485820.091496217156-0.08515917773110.2520385946560.05608034733870.2551865169410.01053647035940.1733570814290.169297180911-0.05308401942770.02070016402680.0542323214745-0.0302857392004-0.0733002484784-0.02950807037910.117320444586-0.00987575757397-0.004089033319510.1849179949840.04931551384290.142611817971-32.247446422937.1460494089115.203294075
390.8045137756520.0855407410192-0.1315335202060.1308578731160.03422777661920.164663436050.01777169230780.08838339641850.209591762819-0.02099679592770.01788444543820.0435906466044-0.020171478062-0.0386345176-0.04445960924620.111441817765-0.00419042755172-0.00234910147610.1301786638110.02827396576550.159350958912-27.488594492941.5680747458123.575310527
400.612673639302-0.2490489250110.3235238901851.577714741860.1350070959450.4994980845370.02989493607360.03709756280270.163091444483-0.05538627011210.01293541076750.153288714418-0.239143351381-0.233806191536-0.007823568433190.07762171006580.009611368019640.003759131946290.2295666930410.02139899440010.274962194593-52.582112978139.9022998643123.658665649
411.50484005722-0.4615403449510.4077580277720.40317061626-0.2028931984770.9230200297380.00181433643130.212980852801-0.173752516952-0.0776100460528-0.008209364899210.09673353754350.329475041029-0.2226252610020.002679334819950.201888209347-0.09384326341-0.009210115379510.271670447424-0.04378954395780.165321340405-50.53943504465.1543019256108.350475219
423.186484109840.5777299743980.7417818116872.845707218540.06592285193640.6127277802160.0873566643817-0.0393434242885-0.08969794893680.0979865371325-0.1057287196530.2931068730860.064636404739-0.2249861193060.007658147596590.104840132729-0.0577231023563-0.003722928576210.271332946811-0.001799821608810.213382878581-59.76934325916.1905783266111.329131858
430.3713915043380.4128570756340.07593306525751.877470980720.1862146406090.2152289454190.0303336711632-0.277371426406-0.04575118400010.228697670018-0.0143896402726-0.1524194276390.0367228879750.168281661191-0.01592356602110.186871728423-0.0331773683928-0.01704844357530.3345623542160.007397687871370.1303103443969.214831845525.780579737158.089582484
440.5697125682670.0391397200754-0.1278457874670.179691170163-0.00610092775620.150961265860.0554704027404-0.1426865809660.1978242339240.05368784091730.00607491323372-0.00839581516265-0.04556823882390.0480094481187-0.06067870339070.118633766965-0.02061613914360.0163817136670.157338130466-0.05381909141290.1754563452471.2731061480846.2705833839141.320560529
450.7123496216540.060309620293-0.1812123154810.4458006633060.1098152019670.3288305200210.0817040102195-0.04820116150430.35042288349-0.01027730357140.0219684197169-0.014367577334-0.06516039788940.0357524882778-0.1091806332250.147522224582-0.01388634234440.05391135709140.143140169678-0.01799319634150.3551638052546.4234387368962.1398584861128.355936568
460.666316604276-0.7330848449180.06429368167481.532478620780.1211537383220.05133282368130.127040936521-0.05747172665370.37922444604-0.05725592367730.0576226770352-0.0785210542629-0.2779726875970.0948733553636-0.1812565930770.17449462718-0.07928461795740.06324623661630.201275910411-0.07510650984780.5052569493619.168236708168.2666311174130.921843821
470.5719852971710.2742109760160.1116743398631.162974514440.4209144494980.7170100691470.0354370743525-0.3928081085360.2401938093180.215358453020.120091326494-0.424620344110.03165339797280.429555923435-0.09900262539850.196597821258-0.0128666804083-0.04511727255180.520000728273-0.2072143987480.40603937542839.25648221749.347838848151.252496219
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 498 )
3X-RAY DIFFRACTION3chain 'A' and (resid 499 through 562 )
4X-RAY DIFFRACTION4chain 'A' and (resid 563 through 601 )
5X-RAY DIFFRACTION5chain 'A' and (resid 602 through 658 )
6X-RAY DIFFRACTION6chain 'A' and (resid 659 through 753 )
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 130 )
8X-RAY DIFFRACTION8chain 'B' and (resid 131 through 498 )
9X-RAY DIFFRACTION9chain 'B' and (resid 499 through 753 )
10X-RAY DIFFRACTION10chain 'C' and (resid 28 through 498 )
11X-RAY DIFFRACTION11chain 'C' and (resid 499 through 708 )
12X-RAY DIFFRACTION12chain 'C' and (resid 709 through 753 )
13X-RAY DIFFRACTION13chain 'D' and (resid 28 through 130 )
14X-RAY DIFFRACTION14chain 'D' and (resid 131 through 167 )
15X-RAY DIFFRACTION15chain 'D' and (resid 168 through 498 )
16X-RAY DIFFRACTION16chain 'D' and (resid 499 through 562 )
17X-RAY DIFFRACTION17chain 'D' and (resid 563 through 601 )
18X-RAY DIFFRACTION18chain 'D' and (resid 602 through 706 )
19X-RAY DIFFRACTION19chain 'D' and (resid 707 through 753 )
20X-RAY DIFFRACTION20chain 'E' and (resid 28 through 90 )
21X-RAY DIFFRACTION21chain 'E' and (resid 91 through 257 )
22X-RAY DIFFRACTION22chain 'E' and (resid 258 through 303 )
23X-RAY DIFFRACTION23chain 'E' and (resid 304 through 367 )
24X-RAY DIFFRACTION24chain 'E' and (resid 368 through 422 )
25X-RAY DIFFRACTION25chain 'E' and (resid 423 through 498 )
26X-RAY DIFFRACTION26chain 'E' and (resid 499 through 562 )
27X-RAY DIFFRACTION27chain 'E' and (resid 563 through 601 )
28X-RAY DIFFRACTION28chain 'E' and (resid 602 through 658 )
29X-RAY DIFFRACTION29chain 'E' and (resid 659 through 753 )
30X-RAY DIFFRACTION30chain 'F' and (resid 28 through 91 )
31X-RAY DIFFRACTION31chain 'F' and (resid 92 through 257 )
32X-RAY DIFFRACTION32chain 'F' and (resid 258 through 498 )
33X-RAY DIFFRACTION33chain 'F' and (resid 499 through 562 )
34X-RAY DIFFRACTION34chain 'F' and (resid 563 through 601 )
35X-RAY DIFFRACTION35chain 'F' and (resid 602 through 753 )
36X-RAY DIFFRACTION36chain 'G' and (resid 27 through 70 )
37X-RAY DIFFRACTION37chain 'G' and (resid 71 through 257 )
38X-RAY DIFFRACTION38chain 'G' and (resid 258 through 422 )
39X-RAY DIFFRACTION39chain 'G' and (resid 423 through 562 )
40X-RAY DIFFRACTION40chain 'G' and (resid 563 through 601 )
41X-RAY DIFFRACTION41chain 'G' and (resid 602 through 706 )
42X-RAY DIFFRACTION42chain 'G' and (resid 707 through 753 )
43X-RAY DIFFRACTION43chain 'H' and (resid 28 through 90 )
44X-RAY DIFFRACTION44chain 'H' and (resid 91 through 474 )
45X-RAY DIFFRACTION45chain 'H' and (resid 475 through 550 )
46X-RAY DIFFRACTION46chain 'H' and (resid 551 through 601 )
47X-RAY DIFFRACTION47chain 'H' and (resid 602 through 753 )

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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://pdbjlc1.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