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- PDB-6ui1: Crystal structure of BoNT/A-LCHn domain in complex with VHH ciA-D... -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 6ui1
タイトルCrystal structure of BoNT/A-LCHn domain in complex with VHH ciA-D12, ciA-B5, and ciA-H7
要素
  • BoNT/A
  • ciA-B5
  • ciA-D12
  • ciA-H7
キーワードTOXIN/ANTITOXIN / Botulinum neurotoxin (BoNT) / VHH / receptor-binding domain / TOXIN / ANTITOXIN / TOXIN-ANTITOXIN complex
機能・相同性
機能・相同性情報


bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / extracellular region ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane
類似検索 - 分子機能
Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor-binding C-terminal ...Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Botulinum neurotoxin type A / Bontoxilysin-A
類似検索 - 構成要素
生物種Clostridium botulinum (ボツリヌス菌)
Vicugna pacos (アルパカ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.20000858936 Å
データ登録者Lam, K. / Jin, R.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 米国
National Institutes of Health/National Cancer Institute (NIH/NCI) 米国
引用ジャーナル: Cell Rep / 年: 2020
タイトル: Structural Insights into Rational Design of Single-Domain Antibody-Based Antitoxins against Botulinum Neurotoxins
著者: Lam, K. / Tremblay, J.M. / Vazquez-Cintron, E. / Perry, K. / Ondeck, C. / Webb, R. / McNutt, P.M. / Shoemaker, C.B. / Jin, R.
履歴
登録2019年9月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年3月4日Provider: repository / タイプ: Initial release
改定 1.12023年10月11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
改定 1.22024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: BoNT/A
B: ciA-H7
C: ciA-D12
D: ciA-B5


分子量 (理論値)分子数
合計 (水以外)141,7554
ポリマ－141,7554
非ポリマー00
水9,440524
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: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-15 kcal/mol
Surface area49380 Å2
手法PISA
単位格子
Length a, b, c (Å)141.04, 89.36, 143.69
Angle α, β, γ (deg.)90.0, 118.93, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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要素

#1: タンパク質 BoNT/A / BoNT/A1 neurotoxin / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT / ...BoNT/A1 neurotoxin / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT / Neurotoxin type A / Peptidase M27


分子量: 100030.023 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Clostridium botulinum (ボツリヌス菌)
遺伝子: a, A, boNT, bont, bonta, ACP52_06670 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q7B8V4, UniProt: P0DPI1*PLUS, bontoxilysin
#2: 抗体 ciA-H7


分子量: 13133.512 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli (大腸菌)
#3: 抗体 ciA-D12


分子量: 14404.154 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli (大腸菌)
#4: タンパク質 ciA-B5


分子量: 14186.932 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli (大腸菌)
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 524 / 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: 2.91 Å3/Da / 溶媒含有率: 57.74 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.4 / 詳細: 11 % PEG 20,000 and 0.1 M sodium cacodylate

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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: SSRL / ビームライン: BL7-1 / 波長: 1.12709 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2014年5月1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: 1.12709 Å / 相対比: 1
反射解像度: 2.2→37.74 Å / Num. obs: 75271 / % possible obs: 95 % / 冗長度: 2.6 % / Biso Wilson estimate: 29.5981913921 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.049 / Rrim(I) all: 0.069 / Net I/σ(I): 10.2
反射 シェル解像度: 2.2→2.25 Å / Rmerge(I) obs: 0.208 / Num. unique obs: 4576 / CC1/2: 0.965 / Rpim(I) all: 0.207

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
PHENIX1.9_1692精密化
Blu-Iceデータ収集
SCALAデータスケーリング
PHASER位相決定
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: 3V0A

3v0a


解像度: 2.20000858936→37.1635590417 Å / SU ML: 0.233539670702 / 交差検証法: FREE R-VALUE / σ(F): 1.33647799258 / 位相誤差: 22.8444478048
Rfactor反射数%反射
Rfree0.228599973817 3774 5.01608229884 %
Rwork0.180585060409 --
obs0.182987256077 75238 94.7832550171 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 34.9171563415 Å2
精密化ステップサイクル: LAST / 解像度: 2.20000858936→37.1635590417 Å
タンパク質核酸リガンド溶媒全体
原子数9564 0 0 524 10088
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.008489196766199769
X-RAY DIFFRACTIONf_angle_d1.0875066326613228
X-RAY DIFFRACTIONf_chiral_restr0.04592758542071459
X-RAY DIFFRACTIONf_plane_restr0.004712043378831707
X-RAY DIFFRACTIONf_dihedral_angle_d13.80501766313573
LS精密化 シェル解像度: 2.20000858936→2.2279 Å
Rfactor反射数%反射
Rfree0.274725339152 145 -
Rwork0.217003227929 2721 -
obs--97.5825672455 %
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)
11.535023440630.05612071847680.382751877750.9944983867660.1734766402910.740870239770.00146797978230.189642089509-0.0747119078867-0.1270055630710.0948877737814-0.04515525127770.1676555952310.1309629757250.003405818320160.2867426643530.006171160899570.0380661167090.191359838175-0.009070637672510.14905435246-31.6178022619-42.547310925319.6305463822
20.906241422566-0.2263067104310.09647223830590.659998828393-0.6257659231120.884232534443-0.07310294531660.02159207086420.0573257014073-0.07580727259540.0828100255527-0.0532577530438-0.0384050341250.1027300674360.002952989296310.1967677533190.01384692619680.02874535227470.190098572087-0.01336162551130.18173771872-30.1291436365-33.529285338323.6758595563
30.3076128622030.04891694220110.3358037438930.322575296501-0.1978900953280.339327398234-0.1349738979710.07754053959460.180674828971-0.09196619248680.0917251997442-0.0709442027673-0.03258737975490.198605049642.15287066919E-70.234752414123-0.01895300638140.01500097131650.251267346824-0.001325594120260.286867275042-29.9721564257-14.85486236222.5020400388
40.897668312122-0.2147691997320.5034188271880.771584918754-0.315501683510.860568610081-0.0479726749725-0.0294224564340.07922928957140.02036623769170.06304440807060.04432322309270.0249965267965-0.07751139678027.38761284026E-60.181695821540.007323778338080.03592908067640.1795421436730.004440741275010.146642301824-38.6829354758-30.375950123129.1564534224
50.607272177943-0.333074995439-0.3160915373970.7776973739480.2804471484040.604932523633-0.03983982744220.2516031431820.0857716294566-0.0872650472504-0.0363106555456-0.0352174827328-0.1458889919220.0159416366113-0.001170363933610.305830905697-0.0427116724523-0.0002474822573020.2988860636670.04518773358510.324268043431-19.7913755033-7.203183533323.2544336278
60.4526129637520.006118031243040.7645780565290.212272986840.4420891616680.721275114804-0.1106875906090.1415501078220.0580574243517-0.2444231050250.1162609013950.05811170445680.00548891759458-0.132114347331-0.003654568357440.3897913368560.007919463720340.04916288904560.2748764357840.02844756722750.315680115589-36.3551053758-28.383427977821.6259743067
70.7331742466550.2630555727710.05423531890350.681603737946-0.5732713805630.812667698699-0.01464203278680.1333364513670.004006929777850.0756019946268-0.120963385885-0.166896370662-0.08635639045590.350717759327.47329929367E-80.226321643235-0.04324851665320.01796572620640.303498698960.0364871501640.3591311362053.29227690724-9.7638383257439.3888374528
80.6447151322620.189002272587-0.3230031612820.7320491625240.3951935371440.893177382512-0.06355512185710.02269818127890.5084241944030.0940222809372-0.165941341062-0.223202659569-0.340736585481-0.124928501694-0.002546581284830.248001713901-0.0171044341521-0.01655866700650.295901820384-0.01648695771880.343979182917-7.6686681846-6.4872756896850.0830073928
90.562226272644-0.593872106874-0.4548743708930.8471702828450.2993442454250.3227137252250.155837698370.2540129995450.1412573267050.110491211418-0.100954720873-0.0419765714056-0.01247566267520.0140248235974-0.0001693029193750.3851173796270.00900662572004-0.02670972930710.2998040530890.00157929843490.386671808585-41.63036065021.7499242206833.5208567259
100.4388186209750.3164669504350.1050498758281.109483274170.1588640434420.5953185366930.0278213343721-0.0140058191754-0.1894223835010.00789427358639-0.08110870271790.0332087173536-0.01670216743240.0665431307326-7.37113373845E-80.222447550135-0.0202483049780.02389738878930.2590443961240.01639455568830.268734761997-7.41848550605-16.468062647345.7034912827
110.9446839929860.795446516159-0.4765015322351.678998888850.03197209774041.17151306573-0.309888684913-0.2628118749060.2520043454850.5875579353180.103160812159-0.16001448220.0760495622306-0.0406158687504-4.40100378032E-80.4042810559820.02919392514010.02031850004170.350734610111-0.04611900226370.407108002336-51.26457977295.1102601391338.3347839787
120.1487951865770.3741802829930.1405683817230.9712806950680.3484887427540.128734374889-0.151908493771-0.08140029987910.1076727367040.147036068175-0.1552230776550.807577441026-0.0377470662981-0.449590976059-0.1051930406220.4443305003450.0522502656056-0.1033490008910.4577872139520.116808377590.469521649716-59.7256054681-7.67365288826.52592569899
130.376787671991-0.300688090614-0.1730648249340.3242975997350.1365118864440.08737493879390.01865383847720.0702662737749-0.361136152471-0.220731894297-0.1450371611490.321103923858-0.0206895738725-0.216934396297-0.004583463818640.566418593894-0.0246486391031-0.02245128169420.3800476358640.06716528890890.335258352759-49.0112185252-15.0656200663-13.3159491217
140.092637290490.04847681195490.06655133914230.03658713880360.01680648767440.0537710735193-0.2514723527830.3017560222580.295155109094-0.1993959553980.2535674928130.156400531143-0.381420787851-0.0113092808797-1.60107417841E-50.469820974916-0.0163628189139-0.06012925000430.3319627238960.06276566664010.251782153517-52.0457323565-7.322781025510.642623500519
150.00503618130979-0.0103720781772-0.003520273533060.0146747896986-0.007880879304130.01353351289190.0227607427255-0.2575397082330.2207615461850.127489860904-0.3367277948780.294633202084-0.872418530694-0.2656719718458.17855767838E-60.5371851916860.112929320347-0.1062350564050.3414958499830.05758881668770.411337291641-51.046050543-5.6879432357615.1632473679
160.355542393646-0.273888202714-0.04206501301290.358237717614-0.2487778016120.325241427277-0.1212658641440.2122844733810.138463459722-0.261390556650.202434740610.1857257975470.0590418483805-0.112579419444-1.67407417117E-70.323857409156-0.0474548893351-0.04781822054860.2777759837480.06932220318460.20082407249-48.4231655595-19.20985541685.00414871897
170.2194112388750.15281848340.1406705783940.184409098118-0.053034883110.238426025099-0.1575175398010.01874826827470.0865409501325-0.1818418325090.304694992361-0.113823421073-0.2834760079860.0959362428782-4.50292697868E-70.445973023462-0.0257556888991-0.01763333609190.3123246403330.0616364728630.278720531564-44.4860787094-11.10167033331.91887404146
180.1008205964520.0727858570148-0.001987500578480.177586136536-0.1062534236170.13246200967-0.173363706030.0662563641413-0.00406257250824-0.2925507341930.1490505696820.06254564579030.12216657433-0.08554384974850.001463245799520.440337696145-0.0699340435769-0.04963188887370.2689063019050.07866193111670.238599015775-49.9238060497-19.0598880655-3.01358481874
190.1151155049320.04753803743570.1744673310450.1035639329980.09987383504620.258298190571-0.131688057794-0.1724972793690.151529877072-0.2280248359970.01225616418360.38777073789-0.101976724871-0.493880251867-0.01504260024350.3454561768170.0296685973424-0.0480999917140.3495084562430.08067096600760.319030686328-57.2655354-14.439298713410.7881502612
200.09063611121060.0386180584070.02561798076920.0628370915661-0.04655410597610.07029723937810.01721263010430.329982580931-0.0654381082022-0.735693195947-0.0376722626644-0.2365374914350.3033275481540.12670688337-0.008742275210040.584226317362-0.0592229852396-0.07015595833420.399161880777-0.002165380233950.303435194385-53.6341245399-18.5909283496-11.0104250121
210.1046478028770.2015429032660.1113303708390.4141365827440.1166772265770.180432540689-0.0352665086361-0.0814368096141-0.0002466456066810.2973475862-0.05959823876940.0386310092176-0.246226689785-0.3483912828860.00317543047630.3290174645950.0678073779433-0.01803713065770.5003422953580.04310988452440.385490798707-10.9054271654-54.787024648158.6827447247
220.0662793941103-0.056064602261-0.03233398909230.1596046782620.1518936511160.128467624245-0.4794355050480.00566175980762-0.5621876309690.1140494961030.2664343618740.2768950102680.045629854569-0.459122738161-0.0003323750353010.3437790610980.0124129563674-0.009124032478950.5436435425190.1172720480930.412398267798-23.414257181-59.418032677156.6714306857
230.122709955637-0.1272349617340.1005634155720.13877505291-0.0703913807620.285871619856-0.0280302308422-0.1230094924350.03016323809520.0432646470980.066222009515-0.0381371625351-0.01983766409150.137132744114-9.52466919125E-100.3040532892530.0488942814256-0.04003756644080.2738044244250.0433167869160.31094380757-14.9759114221-51.443438860347.8830209235
240.352903354992-0.4797425027590.09225527407350.481424202093-0.009815287488050.348843812694-0.0642245955414-0.0696367318273-0.470039200086-0.2010918044330.09035278792440.2788330462280.441884772701-0.0464835795566-5.60674294195E-50.3032576641150.0737354861559-0.05289429007620.3949404817270.05519935902820.380016861362-16.3053045651-63.375223186849.6827508315
250.105158487353-0.06144614111750.1672481310350.194988921996-0.0842254348610.140699968497-0.05250983805250.47332554830.01311315274120.101835301210.0240672669346-0.1761537994310.05059228655280.224925714282-1.13382708944E-60.2854011647050.058169527033-0.04889811181030.3502095197410.01004740993110.329883900397-9.4771352375-54.250545672150.7027652939
260.3957757936960.3208457543890.3457958766690.3094248843660.2393106644880.344465174284-0.0669998760123-0.416342551409-0.259534287321-0.9271540207860.04939306134090.265487217564-0.0104267318854-0.3412404525880.003434761152270.3691323007690.03984896582310.006366914526110.316716568482-0.003004211868360.301038230758-31.0370837773-51.895141169842.0047025356
270.07677363943010.18515308712-0.05914190450030.377828708309-0.2418721417290.2395032612240.0692130444438-0.2596411687680.3213944276750.229027948587-0.00881875369788-0.0158150368313-0.0467587409392-0.0905707015351-1.84936944988E-80.3133550825880.0856351744227-0.0007184137489660.3588261257390.01436186702690.3148793834-17.6126690834-49.018913519753.1883777972
280.04429368803260.0492319649332-0.01428981392840.0332141149845-0.0130472146161-0.0165327635528-0.0943522647606-0.0945928921915-0.09046746253770.09608141032070.0580475316443-0.2708215130490.1104095340850.0826321554363-7.64240575359E-60.486505125438-0.05069925207390.003944387122260.302999156690.0601720496470.381554001079-6.65159298788-37.247453893772.2462423408
290.04432949990980.0002351018269130.05853765895590.153457223489-0.07116513571820.0903939721364-0.146853587158-0.0161635648131-0.09520615554070.307798960932-0.0773696633624-0.129112642156-0.0264734216660.1802128135988.23766208063E-60.339601630121-0.0479408730972-0.01857929068630.4006303552860.007655896425870.246579196688-11.1283474252-31.772700895276.0095515736
30-0.000564038709074-0.00761563187357-0.005623262158350.01440491426710.01506578324720.0281641829479-0.466352477829-0.198560908214-0.3776460131990.124828884396-0.1752004584550.07265876381330.2633344821250.2318987903357.19887454602E-60.3993389504110.0413418673581-0.01455814908130.4102402714850.02763900699410.58413852345212.4553024414-32.731062309365.7492419135
310.147434185265-0.0806316181662-0.03861087714120.04010682960760.06797189211340.0135876919788-0.1555401617790.0802635408301-0.1125929328050.2005147987950.15131145849-0.1871803308930.184212468020.106272940925-7.90359529366E-80.239804022789-0.0746196651756-0.02072981795680.36817533974-0.02065583524050.375006635931-2.4395519579-28.195467337364.9425810384
320.102918626859-0.0707023887050.05345657595350.0331724066987-0.03561234470660.15389309025-0.0402867424168-0.0795360029562-0.0180203053388-0.130500102144-0.06040848501460.167697848903-0.05938974573660.1028870776513.5728323492E-70.300312677373-0.114964784642-0.009181161324910.3936267215890.01587517155860.289963412635-9.59704785285-25.340829798262.685379858
330.1530310368330.0223976639222-0.1541790570180.2186044071740.101802918080.174446086321-0.2050958994530.1060530571370.2468245518070.3056223475860.01388046835110.138204589158-0.4764946664840.1716521603492.08072133599E-60.264620781577-0.0116788615619-0.002164264977770.3709779220970.0426677154590.354714505565-10.9443258194-22.309261384470.7265055166
340.2287932348830.204633960618-0.2241226394850.576968479009-0.06199937105860.2217844534220.0377513940044-0.1074753226080.08006101809720.359153246425-0.198343542786-0.07983525846670.07074699160890.001329169444341.38361927191E-70.374268298464-0.0916679293323-0.01252125373680.3620659281620.008806175909630.307833757952-9.51120203431-29.813804364571.1582082286
350.0832445342511-0.103104476657-0.0432642134260.09306670504180.06038538538240.0621412553439-0.152023094028-0.0521294762114-0.4793995256350.4353437494840.1310978581760.04943591581720.06690712813580.139527006218-1.96883903972E-70.23531910063-0.0469589812912-0.003829716252320.3281357351560.05625270418590.416571024741-0.0481925216974-32.465566199260.3209666047
360.0420480444437-0.05562665215430.05363585768060.0983662667099-0.07330546666390.05493494530440.0311551861503-0.438965929192-0.2308065786510.06561678485530.07550680828210.628179411610.435351758023-0.12553132115-8.86754210088E-70.373686887822-0.06710718431740.05495907691510.462927330780.0919397289480.463710349428-22.0952531702-38.568321532773.8360444406
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 232 )
3X-RAY DIFFRACTION3chain 'A' and (resid 233 through 275 )
4X-RAY DIFFRACTION4chain 'A' and (resid 276 through 416 )
5X-RAY DIFFRACTION5chain 'A' and (resid 417 through 485 )
6X-RAY DIFFRACTION6chain 'A' and (resid 486 through 546 )
7X-RAY DIFFRACTION7chain 'A' and (resid 547 through 599 )
8X-RAY DIFFRACTION8chain 'A' and (resid 600 through 648 )
9X-RAY DIFFRACTION9chain 'A' and (resid 649 through 720 )
10X-RAY DIFFRACTION10chain 'A' and (resid 721 through 799 )
11X-RAY DIFFRACTION11chain 'A' and (resid 800 through 866 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 7 )
13X-RAY DIFFRACTION13chain 'B' and (resid 8 through 17 )
14X-RAY DIFFRACTION14chain 'B' and (resid 18 through 25 )
15X-RAY DIFFRACTION15chain 'B' and (resid 26 through 33 )
16X-RAY DIFFRACTION16chain 'B' and (resid 34 through 59 )
17X-RAY DIFFRACTION17chain 'B' and (resid 60 through 82 )
18X-RAY DIFFRACTION18chain 'B' and (resid 83 through 97 )
19X-RAY DIFFRACTION19chain 'B' and (resid 98 through 107 )
20X-RAY DIFFRACTION20chain 'B' and (resid 108 through 114 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1 through 17 )
22X-RAY DIFFRACTION22chain 'C' and (resid 18 through 32 )
23X-RAY DIFFRACTION23chain 'C' and (resid 33 through 51 )
24X-RAY DIFFRACTION24chain 'C' and (resid 52 through 82 )
25X-RAY DIFFRACTION25chain 'C' and (resid 83 through 98 )
26X-RAY DIFFRACTION26chain 'C' and (resid 99 through 108 )
27X-RAY DIFFRACTION27chain 'C' and (resid 109 through 123 )
28X-RAY DIFFRACTION28chain 'D' and (resid 3 through 12 )
29X-RAY DIFFRACTION29chain 'D' and (resid 13 through 24 )
30X-RAY DIFFRACTION30chain 'D' and (resid 25 through 34 )
31X-RAY DIFFRACTION31chain 'D' and (resid 35 through 45 )
32X-RAY DIFFRACTION32chain 'D' and (resid 46 through 63 )
33X-RAY DIFFRACTION33chain 'D' and (resid 64 through 76 )
34X-RAY DIFFRACTION34chain 'D' and (resid 77 through 101 )
35X-RAY DIFFRACTION35chain 'D' and (resid 102 through 110 )
36X-RAY DIFFRACTION36chain 'D' and (resid 111 through 120 )

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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