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- PDB-8glc: A1 AncAla: Adenylation domain 1 core construct from ancestral rec... -

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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: 8glc
タイトルA1 AncAla: Adenylation domain 1 core construct from ancestral reconstruction of glycopeptide antibiotic biosynthesis, alanine selection pocket
要素
  • MbtH-like short polypeptide
  • Non-ribosomal peptide synthetase
キーワードLIGASE (リガーゼ) / AMP-binding enzyme / NRPS / Adenylation domain (アデニリル化)
機能・相同性MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / siderophore biosynthetic process / 細胞質基質 / MbtH-like short polypeptide
機能・相同性情報
生物種Actinoplanes (アクチノプラネス属)
Actinoplanes teichomyceticus (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.12 Å
データ登録者Hansen, M.H. / Cryle, M.J.
資金援助 オーストラリア, 2件
組織認可番号国
Australian Research Council (ARC)DP190101272 オーストラリア
Australian Research Council (ARC)DP210101752 オーストラリア
引用ジャーナル: Nat Commun / 年: 2023
タイトル: Resurrecting ancestral antibiotics: unveiling the origins of modern lipid II targeting glycopeptides.
著者: Hansen, M.H. / Adamek, M. / Iftime, D. / Petras, D. / Schuseil, F. / Grond, S. / Stegmann, E. / Cryle, M.J. / Ziemert, N.
履歴
登録2023年3月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年12月6日Provider: repository / タイプ: Initial release
改定 1.12023年12月13日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
B: Non-ribosomal peptide synthetase
D: MbtH-like short polypeptide
A: Non-ribosomal peptide synthetase
C: MbtH-like short polypeptide


分子量 (理論値)分子数
合計 (水以外)100,6004
ポリマ－100,6004
非ポリマー00
水0
1
B: Non-ribosomal peptide synthetase
D: MbtH-like short polypeptide


分子量 (理論値)分子数
合計 (水以外)50,3002
ポリマ－50,3002
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
A: Non-ribosomal peptide synthetase
C: MbtH-like short polypeptide


分子量 (理論値)分子数
合計 (水以外)50,3002
ポリマ－50,3002
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)261.925, 261.925, 261.925
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Space group name HallI4bd2c3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+1/4,z+3/4,-y+3/4
#4: z+1/4,y+3/4,-x+3/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y,-z+1/2,x
#11: z,-x,-y+1/2
#12: -y+1/2,z,-x
#13: -z,-x+1/2,y
#14: -z+1/2,x,-y
#15: y,-z,-x+1/2
#16: x,-y,-z+1/2
#17: -x+1/2,y,-z
#18: -x,-y+1/2,z
#19: y+1/4,x+3/4,-z+3/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x+1/2,y+1/2,z+1/2
#26: x+3/4,-z+3/4,y+5/4
#27: x+3/4,z+5/4,-y+5/4
#28: z+3/4,y+5/4,-x+5/4
#29: -z+3/4,y+5/4,x+3/4
#30: -y+3/4,x+5/4,z+3/4
#31: y+3/4,-x+3/4,z+5/4
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1,x+1/2
#35: z+1/2,-x+1/2,-y+1
#36: -y+1,z+1/2,-x+1/2
#37: -z+1/2,-x+1,y+1/2
#38: -z+1,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1
#40: x+1/2,-y+1/2,-z+1
#41: -x+1,y+1/2,-z+1/2
#42: -x+1/2,-y+1,z+1/2
#43: y+3/4,x+5/4,-z+5/4
#44: -y+3/4,-x+3/4,-z+3/4
#45: z+3/4,-y+3/4,x+5/4
#46: -z+3/4,-y+3/4,-x+3/4
#47: -x+3/4,z+5/4,y+3/4
#48: -x+3/4,-z+3/4,-y+3/4
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 1 through 22 or resid 24...
d_2ens_1(chain "B" and (resid 1 through 22 or resid 24...
d_1ens_2(chain "C" and (resid 3 through 59 or resid 61 through 65))
d_2ens_2(chain "D" and (resid 3 through 59 or resid 61 through 65))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METGLYC1 - 22
d_12ens_1ARGTYRC24 - 28
d_13ens_1GLNALAC30 - 76
d_14ens_1VALALAC78 - 135
d_15ens_1VALMETC137 - 167
d_16ens_1ALAALAC169 - 188
d_17ens_1VALGLYC190 - 194
d_18ens_1GLYALAC196 - 200
d_19ens_1ARGPHEC202 - 221
d_110ens_1ALAALAC223 - 225
d_111ens_1SERTYRC228 - 266
d_112ens_1PROGLUC268 - 281
d_113ens_1VALGLYC284 - 292
d_114ens_1ALAALAC294 - 363
d_21ens_1METGLYA1 - 22
d_22ens_1ARGTYRA24 - 28
d_23ens_1GLNALAA30 - 76
d_24ens_1VALALAA78 - 122
d_25ens_1ASPALAA124 - 136
d_26ens_1VALMETA138 - 168
d_27ens_1ALAALAA170 - 189
d_28ens_1VALGLYA191 - 195
d_29ens_1GLYALAA197 - 201
d_210ens_1ARGPHEA203 - 222
d_211ens_1ALAALAA224 - 226
d_212ens_1SERTYRA229 - 267
d_213ens_1PROGLUA269 - 282
d_214ens_1VALGLYA284 - 292
d_215ens_1ALAALAA295 - 364
d_11ens_2THRLEUD1 - 57
d_12ens_2PROILED59 - 63
d_21ens_2THRLEUB1 - 57
d_22ens_2PROILEB59 - 63

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.0901188119229, -0.953795525851, -0.286622913605), (-0.952889427562, -0.166267884433, 0.25368628155), (-0.289621025787, 0.250258037777, -0.923845536846)2.72261374218, -0.779302458866, -0.962723858902
2given(0.130093709847, -0.941966880396, -0.309473783859), (-0.937866256916, -0.218176029103, 0.269826063352), (-0.321686976419, 0.255142345687, -0.911822281281)1.59724213502, -1.4034867708, -0.0960568917174

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要素

#1: タンパク質 Non-ribosomal peptide synthetase


分子量: 42663.441 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: Twist Bioscience DNA
由来: (組換発現) Actinoplanes (アクチノプラネス属)
発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#2: タンパク質 MbtH-like short polypeptide


分子量: 7636.309 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Actinoplanes teichomyceticus (バクテリア)
遺伝子: tcp13 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q70AZ5

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.72 Å3/Da / 溶媒含有率: 66.95 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5 / 詳細: 1.6 M Magnesium sulfate, 100 mM MES; pH 6.5

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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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.9536 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年10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: 0.9536 Å / 相対比: 1
反射解像度: 3.12→44.82 Å / Num. obs: 27241 / % possible obs: 99.39 % / 冗長度: 2 % / Biso Wilson estimate: 97.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02528 / Rpim(I) all: 0.02528 / Net I/σ(I): 13.92
反射 シェル解像度: 3.12→3.236 Å / 冗長度: 2 % / Num. unique obs: 2636 / CC1/2: 0.865

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
Aimless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: 8GIC

8gic


解像度: 3.12→44.82 Å / SU ML: 0.4647 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 26.8468
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2664 2000 7.34 %
Rwork0.2288 25234 -
obs0.2315 27234 99.44 %
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: 88.44 Å2
精密化ステップサイクル: LAST / 解像度: 3.12→44.82 Å
タンパク質核酸リガンド溶媒全体
原子数6444 0 0 0 6444
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00376585
X-RAY DIFFRACTIONf_angle_d0.68258970
X-RAY DIFFRACTIONf_chiral_restr0.04741008
X-RAY DIFFRACTIONf_plane_restr0.00521176
X-RAY DIFFRACTIONf_dihedral_angle_d11.7152354
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS1.01693002603
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.501727663783
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.20.39641380.40841732X-RAY DIFFRACTION97.19
3.2-3.290.36741410.32481785X-RAY DIFFRACTION100
3.29-3.380.33421400.30011764X-RAY DIFFRACTION99.63
3.39-3.490.29161410.27261793X-RAY DIFFRACTION99.95
3.5-3.620.31381410.26271776X-RAY DIFFRACTION100
3.62-3.760.29841420.25931785X-RAY DIFFRACTION100
3.76-3.940.30041430.27081799X-RAY DIFFRACTION100
3.94-4.140.27361420.24651793X-RAY DIFFRACTION99.95
4.14-4.40.22381420.19461800X-RAY DIFFRACTION100
4.4-4.740.20731420.18391802X-RAY DIFFRACTION99.95
4.74-5.220.25821430.1971802X-RAY DIFFRACTION98.88
5.22-5.970.26551470.21991840X-RAY DIFFRACTION99.75
5.97-7.520.24581450.22991848X-RAY DIFFRACTION99.5
7.53-44.820.25441530.19791915X-RAY DIFFRACTION97.55
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)
12.80014059739-1.674531037310.2096015012542.782497390594.467233443146.5950648088-0.78486698267-0.0930771390526-0.3520697744450.578250932782-0.1658505128761.086528274560.367809866688-0.9040097707150.8602450845510.9347104394270.03049356099310.1969960835980.659058646984-0.1196015724760.69393036190631.925-22.337-22.476
22.1949709372-0.732808728814-3.089254448967.122804685860.1580641816349.47216367799-0.152868483577-0.182419105033-0.620958688224-0.125120411539-0.268143136276-0.7797677477171.501153677941.48211362460.4842902194520.4830604250890.1327668233150.03511115819340.6733121421870.02899875889160.63607352136744.552-23.889-17.732
38.83798557762-1.325843333032.451123394818.839453963816.032955694438.40827931263-0.220789543843-0.488250358540.612099853119-0.1585803208420.339799593715-0.764290925649-0.534029868080.576241123224-0.07805030948520.4743918591060.1448218627910.03445268156120.8296235328960.006240430376020.65966735408245.365-12.621-6.614
46.990620903872.913476508291.837011862742.361018156842.681120613576.69915373472-0.1063435491450.8976855327120.06475068060930.1322638713450.670055962008-1.80553591960.4762655061941.25460443436-0.9090948156870.8281836601610.249640317936-0.05154871123221.38567202752-0.1420414764090.94349460571154.597-17.792-6.235
54.71027059625.93547490152-0.7151207348847.958750332872.824464520063.91787921032-0.406178462242-0.3453706978330.613440878433-0.0517827317239-0.0483791955896-0.011875224875-0.063349278583-0.4888885437320.4653894886120.6416391535590.294147758954-0.04554923831070.8074128302270.002563249497550.7748408096233.163-10.466-7.393
66.59997664238-0.0148283072872-3.671002711128.08377924692-4.038787508822.85984848601-0.0362576637789-0.1043777739120.9645382015310.6632576545720.0371496818432-0.00525498086236-1.0303662261-0.968932849433-0.02714138507250.6373443602850.2158264395780.09466356255060.7072650591080.02669432735260.72864407276338.276-9.542-23.8
74.81375943427-0.7862266264593.305945619396.52709166387-3.257569426178.64567841768-0.129579691443-0.001420264989670.5652274356680.315075237649-0.195550031384-0.556611941255-0.7585407668630.3419860848960.2856866655130.6475853487270.06730026972810.1218613640480.594352551761-0.01842379814920.76236415984140.3062.93-32.15
80.5159414238773.78224196459-2.084700969751.950888517812.06158631668.541955757781.691097254521.63880908174-2.81690038388-1.45893755402-1.755817681922.63783653875-0.885200596874-0.394216877339-0.009936498339161.982023056540.847364681688-0.2307761795261.92615047061-0.3605835543780.97714174186732.1612.114-11.989
97.71616527656.530488474421.609627110489.35167371620.21021108829.01841069863-0.0903279713766-0.459621120243-0.0411536357927-0.2514793711630.1093952993350.651150376682-0.05898863738182.12568677628-0.04325292247380.9064692307040.3440295455260.2709220978570.9615988138750.119303044720.82740272490826.5529.745-26.439
102.00122406231.995010941151.998495084391.999156970291.997674352852.00325656417-2.18421884881-4.271534438832.891731731591.51439324563-0.7748994296081.754842793561.839398781121.262933356512.506087264071.555267902460.787907498149-0.4934028880391.440845197010.1530562579851.0775147839516.9780.447-12.953
115.9350088918-1.74636509329-2.633693188158.183171290011.217737981779.094960699540.4483508472140.7696613845210.1606518547110.0311329405016-0.05857494066210.522169797609-0.600677366874-0.250670126245-0.3634459646850.4181252039740.01555159580590.0786959124860.49755441131-0.0005607434382450.43949923367223.5726.749-4.54
128.20656340203-3.7511221254-0.6493253236848.67207371338-0.3678376239797.469744738870.9687611360391.880334182640.290153946082-2.27941978655-0.8853056108060.088660467881-0.3672506781320.460218295113-0.3669961261670.9350045908270.254618325940.04025169464070.9179682962610.02861349968460.57418160538723.36310.009-13.72
135.9255580543-0.1959803584341.587442648220.412220411491-2.619138152819.028439526210.06188966462790.36614553899-0.194384149130.0588963328131-0.730598543497-0.26226319014-0.4019453764140.8448998385710.6417201756940.8049122373710.144307600429-0.003215126652170.6171077536770.2123098584910.70528804666733.024-39.192-2.366
149.083945410221.454959801245.752505152730.854500632827-0.1555100563985.616711765750.1842663678230.117558597067-0.995965177083-0.315767007906-0.1513766497440.08491886244860.63803575504-0.0119233153315-0.002242133265460.8031180788010.1967078610940.02966150955160.581019162667-0.0973352100620.68875144299120.067-44.782-10.25
158.915882843022.94531168722-0.7675182130912.876990767872.378626971834.39255538517-0.7345774558470.070971067168-1.55188152907-0.05321253921070.185694287268-0.608337286150.7377588749210.8506546006960.294310561320.9471789517850.253101246126-0.07764098087720.797671325753-0.09962289477460.98943016882728.034-46.458-14.959
169.034373389435.344570743194.703798888826.73450840079-0.8635361312095.121325370270.704325647749-0.34507457199-0.452999884137-0.228356732052-0.677094695814-0.2541384649190.4546963778110.03247000227450.02332604687130.5891170162480.223792735624-0.0127989820490.642488209071-0.06616483806010.63573400154515.278-33.028-6.409
177.29913814419-3.07416240394-0.05498760054997.3842871396-1.827751613829.40520482122-0.3196142610022.060201715790.0725181342990.667289553486-0.3841481002921.17207882769-1.20403433710.2892283006650.7894314022230.8503937367210.161247658276-0.02534656309770.8942701005970.1331321221980.96331820268822.972-40.88211.347
182.039307912061.96594220187.422107228542.013608664322.142992513051.96344858801-0.318605972149-2.756456548290.619035155737-1.18330566608-2.848602840833.718753606380.432577452107-2.465484387433.512508476371.32113060260.1325224851910.04651748661031.16203548605-0.3555034909481.343425374314.757-43.0471.075
197.902138242055.4318245173-3.376450342246.0250175168-6.291445448429.70235688164-0.101537101467-0.343036798012-0.9618500957480.281185037717-0.337819348688-0.2893456181260.05178174472750.02632328785650.2998144295850.6626135245250.1517670651150.1829672408310.6213516577230.1306483392680.70187784945822.594-47.31413.085
208.63660389633-2.04823681602-3.055374343347.923650094284.068428766297.754860835010.2148413659060.300564174013-0.801110308842-0.20718390322-0.6367240646270.206278366891-0.186416402831-1.216047829890.3298839037950.7543845676520.1201640564490.01823969244320.8102822283990.1007134621430.6721770157989.762-46.09919.283
215.219271728061.44756935759-1.910662016080.160994889362-1.563111576759.2811552031-1.986891094160.407895359727-3.402874527291.011329044871.874191218940.69365868480.260418617425-1.61877068755-0.01036448040511.444213762250.9874235330440.4561746273171.225302337010.34721771141.283022022517.96-36.1685.626
222.116977773421.79605757878-2.600251508757.403938821851.927908409978.086076738460.118621506238-0.205219574581-0.1220606004691.413652187590.759382535149-0.0429063369522.306748603371.22586979072-0.3879068052431.226777183760.330194773589-0.01007865058321.010298994830.1190053572310.6590295770011.95-34.02819.388
232.02666466401-6.68710158754-3.176395471732.00269353515-8.588265566959.32107800869-3.13667863857-0.09766798122112.10011348369-0.9344107167173.12078124677-2.10434445020.748373250092-0.896647490184-0.1028546346011.136175370870.05396413561890.1398058697790.934061392440.00898754036441.529906193527.7-20.2628.754
2410.68053153541.042157831-3.579389923954.32459770429-0.9121231942489.565451490320.025117733324-0.7062909209030.1805306678660.7687189893850.237337293456-0.0464214975360.4048631361770.209493039827-0.3138886213270.6313317011040.134560782834-0.06782290511720.39217620829-0.01440939519860.471135831353-0.531-26.7351.251
258.682193040562.01561887135-6.698027547182.00259048191-9.894541810542.00659892180.343133029738-1.765261707122.79217758336-0.9993154015320.163570833595-3.35340488248-0.3237033894455.32456301428-0.1447959317680.704005817789-0.4997426162880.1124016381790.912371975543-0.3677607150941.3055609050926.20415.0120.76
262.03337931535-6.91942524565-7.804221923769.265028200414.729122422422.00862105625-2.06319878248-2.728978144563.23169619564-1.839267890462.79762568563-2.14667131717-3.004594013583.5696091641-0.8773020349761.40807050277-0.3402779063820.1829668597061.25900984425-0.3011295980971.1908272116326.31718.2428.804
272.057993446660.3776085890931.395389140572.008748316020.6998574462686.738863352190.294796996996-1.75049820659-1.673429972610.633137871982-1.35011383213-0.671249350086-0.636423774233-0.6016462390690.990581601370.553088734499-0.1788174326250.1135973699340.8894703989820.006910044307530.51449134999920.7436.139.253
282.017497152730.302706512498-1.86582234422.00415534511-7.018689378191.99459596625-1.60971325010.768041151441-0.790478458318-2.65616169225-0.509269967731-0.2758889302413.070046125570.9092270964051.937485723681.02525266346-0.09365210270420.114841594870.8381942091660.1763084206330.85343422653820.181-6.3624.608
293.18338848304-4.36683530028-1.234155248942.140028688981.995146485584.172914218620.486074469713-0.4191605309090.2986064646670.05662600021410.1794437980360.2675585300930.437921730074-0.338339981688-0.5168885041940.494592009752-0.111645000001-0.01383762180270.5305846242850.04669913054870.6963674792320.6436.8445.518
305.29126285028-3.67900848530.02624304943982.026479948236.809882094888.34674096460.571123341507-1.07064141732-1.89407514034-1.57452195474-0.633548648151.97166450738-0.271244666146-1.655863515580.02945864318310.7041658242580.115877196597-0.2379232319070.8714965265740.05200148447440.85372363066611.9625.3953.746
312.026247604722.203203467581.967779150489.5432772445-3.27433117432.00285396683-0.2406040277920.0661006428371-1.097838123690.3256262209240.6390792708141.478665741890.3373082130920.277375142788-0.5519037005040.5335301701070.121407139598-0.1157550169470.4714333582520.05551822255750.71189344692916.8130.8738.443
322.135351335136.1712129256-9.163100104192.00952907459-4.963673149898.532513788280.443933527335-2.16819507332-1.04968515716-0.544551198701-0.695598020439-0.221208254004-1.396788868242.109391666620.5561737098180.8951694048670.0236952299150.01329633948120.826978654028-0.1080303642851.0002373583125.26510.77913.308
332.05838311358-0.883519013671-5.638169494718.54108188443-2.828175341757.59966798918-1.10690245997-0.1554276962952.19357312096-0.2835025653231.61683792958-0.5067513423380.840816653388-0.492287885129-0.7456814051850.423450681644-0.09126467748820.02117640300250.786237300389-0.01736551609220.7153712494827.6765.4213.34
342.154539118897.522967989322.449081751232.080336891046.990771992912.027113327451.32908168627-0.687676890005-0.8176097269260.8664463877710.636074989027-2.819602760491.139641122741.73792559544-1.123109376280.775580635280.220456869331-0.1988792106581.09838219632-0.3037148757280.99800162654929.975-2.09712.133
352.027737521366.562637994215.53965917711.99924715076-1.660870872672.041751753361.464270215320.667381563485-0.3328321385772.67812289037-0.113928849564-1.13937756121-0.562453322502-0.755238177423-1.761242697531.183410023610.185886637541-0.01142198087770.9340614811920.1649907483341.0993695709129.033-9.4064.983
361.9490468001-2.62197250618-2.506926768032.027256179921.447387170799.74421765781.493322060360.5404979999440.111527403189-1.93060871496-0.3312115727440.5836073775110.7934543649782.68365608091-0.413440827741.172126171140.2554775934350.04039970133721.365122483760.204738216030.73862390636423.412-14.6584.103
372.039296271998.449188530113.590176143022.026706438994.77557599512.056988674092.63617052375-1.69062579796-1.25678260374-0.874238036459-0.6070918607332.940874880443.53373865198-0.0488411398909-2.052490360670.940522049989-0.0695341163874-0.09899217296910.5406011142310.2036189491411.53701709709-9.352-28.389-4.918
382.00053544556-3.335388863347.428382092612.0299809657-2.501094125449.423406657661.438947776070.157896855299-0.373915428297-0.440816430618-0.2574110409411.413832599460.362562711293-0.702842429154-1.641017540761.06344583806-0.391827338328-0.1083137994291.25673210470.1401530852340.993955250042-13.784-29.47-10.78
392.045592588029.69995132556-2.323064104124.271584208810.7896686637643.94043843058-0.7835198514030.9523105937121.89530816011-0.5184437097570.8777741292540.6564313659150.170050945578-0.828025050874-0.03744940778350.7208933908130.1502207747780.02701885871940.7256116312330.1248344027920.500932035441-5.639-19.9-13.651
406.14441657143-4.545136826627.646837652786.169146926711.17105411812.00417473795-0.8389944938710.0875932351992.451508084451.73303602451-1.15462243092.361292594970.703904022682.078893372641.715480074090.6641632231-0.1937056308550.226805948920.790799995577-0.03968262165680.7613756827578.799-17.583-12.52
417.20596643998-0.566481956127-1.881137245777.91204990299-0.6290716676038.108134754940.639545417932-0.0373548866434-0.110813557779-0.372768301044-0.3809243281060.568989351416-2.02290034165-0.156444056633-0.5053260056180.6664246581980.0657966667470.09410168972830.3883229677760.1168187762060.481659011675-4.594-19.534-9.171
422.016225053361.991472042711.923583498242.016304294113.024940625832.01158699281-1.61701936698-0.9681693493271.729542009642.301792002382.118473285640.465920963121.04555751148-0.426572359635-0.5423367199180.743955307670.138823065266-0.0005387634599760.6490433126920.01481751858270.701869899197-0.518-12.474-6.225
432.09793641937-3.109508739534.775385588799.24336209923-6.150413157222.0742468686-0.8241281967441.636078564790.3344873774190.343765077126-0.0558234438786-0.429538853208-1.046128149120.2664079029731.077104583640.4883770639780.1216307970130.02206498248750.685562517110.007387525247660.500150771011-1.209-15.982-14.696
442.067084604571.041609834635.518882332579.74542395024-6.320134595872.06692258115-0.4963309723651.69953614434-0.43444190646-1.2943550498-0.535086569076-0.711565274811.564084709390.8633035934431.427915110430.769477000493-0.05437432660890.1478674664060.920389586282-0.06004193152290.907418775289-10.517-23.47-16.552
452.13412729103-8.164634677172.085889638272.00284160119-3.197655553842.146321082510.385947747288-0.624350918343-2.06469827237-0.295412589876-0.4959446339241.577331423280.0384525511211-0.723519050702-0.6263206412690.846284395153-0.08531180033750.1304430689220.727039059038-0.0462014406880.842874189597-5.598-25.895-19.701
462.023898873855.72001367285-2.233637129181.98718657413-4.95599095412.087563288560.5315087065532.09730325727-2.98783649492-0.1311235592320.370743638808-0.824277556893-1.12674354262-2.13688297135-1.146686376260.8600562540950.1749421398360.1423874460370.8009989676430.01633227718791.173813227981.302-26.126-22.304
472.003256377472.24258691517-5.316161638072.040927506468.365110827822.10953715679-2.140044558682.13516871949-1.601299000411.701591313782.48439813256-2.203792758381.890603341251.711868162370.4076844352260.9257534108820.3179715813110.186051275530.8084804675010.1527300242411.3849791316110.195-25.798-17.606
482.024065337453.469412869256.986706561042.002355969782.734014343022.00485201850.7546037070481.310177493551.296267099890.971145399577-2.201574433050.076706311935-0.3501042514591.163283967151.650436281540.7330891698850.07959923831890.1899809227931.070101111020.1954427322781.0525406386416.573-19.902-14.682
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:18 )A1 - 18
2X-RAY DIFFRACTION2( CHAIN A AND RESID 19:46 )A19 - 46
3X-RAY DIFFRACTION3( CHAIN A AND RESID 47:102 )A47 - 102
4X-RAY DIFFRACTION4( CHAIN A AND RESID 103:130 )A103 - 130
5X-RAY DIFFRACTION5( CHAIN A AND RESID 131:169 )A131 - 169
6X-RAY DIFFRACTION6( CHAIN A AND RESID 174:208 )A174 - 208
7X-RAY DIFFRACTION7( CHAIN A AND RESID 209:281 )A209 - 281
8X-RAY DIFFRACTION8( CHAIN A AND RESID 282:289 )A282 - 289
9X-RAY DIFFRACTION9( CHAIN A AND RESID 290:309 )A290 - 309
10X-RAY DIFFRACTION10( CHAIN A AND RESID 316:316 )A316
11X-RAY DIFFRACTION11( CHAIN A AND RESID 317:365 )A317 - 365
12X-RAY DIFFRACTION12( CHAIN A AND RESID 366:386 )A366 - 386
13X-RAY DIFFRACTION13( CHAIN B AND RESID 1:52 )B1 - 52
14X-RAY DIFFRACTION14( CHAIN B AND RESID 53:99 )B53 - 99
15X-RAY DIFFRACTION15( CHAIN B AND RESID 100:136 )B100 - 136
16X-RAY DIFFRACTION16( CHAIN B AND RESID 137:167 )B137 - 167
17X-RAY DIFFRACTION17( CHAIN B AND RESID 168:186 )B168 - 186
18X-RAY DIFFRACTION18( CHAIN B AND RESID 187:195 )B187 - 195
19X-RAY DIFFRACTION19( CHAIN B AND RESID 196:229 )B196 - 229
20X-RAY DIFFRACTION20( CHAIN B AND RESID 230:279 )B230 - 279
21X-RAY DIFFRACTION21( CHAIN B AND RESID 280:292 )B280 - 292
22X-RAY DIFFRACTION22( CHAIN B AND RESID 293:308 )B293 - 308
23X-RAY DIFFRACTION23( CHAIN B AND RESID 309:316 )B309 - 316
24X-RAY DIFFRACTION24( CHAIN B AND RESID 317:386 )B317 - 386
25X-RAY DIFFRACTION25( CHAIN C AND RESID 3:7 )C3 - 7
26X-RAY DIFFRACTION26( CHAIN C AND RESID 8:12 )C8 - 12
27X-RAY DIFFRACTION27( CHAIN C AND RESID 13:17 )C13 - 17
28X-RAY DIFFRACTION28( CHAIN C AND RESID 18:21 )C18 - 21
29X-RAY DIFFRACTION29( CHAIN C AND RESID 22:29 )C22 - 29
30X-RAY DIFFRACTION30( CHAIN C AND RESID 30:35 )C30 - 35
31X-RAY DIFFRACTION31( CHAIN C AND RESID 36:39 )C36 - 39
32X-RAY DIFFRACTION32( CHAIN C AND RESID 40:46 )C40 - 46
33X-RAY DIFFRACTION33( CHAIN C AND RESID 47:52 )C47 - 52
34X-RAY DIFFRACTION34( CHAIN C AND RESID 53:57 )C53 - 57
35X-RAY DIFFRACTION35( CHAIN C AND RESID 58:61 )C58 - 61
36X-RAY DIFFRACTION36( CHAIN C AND RESID 62:65 )C62 - 65
37X-RAY DIFFRACTION37( CHAIN D AND RESID 3:6 )D3 - 6
38X-RAY DIFFRACTION38( CHAIN D AND RESID 7:11 )D7 - 11
39X-RAY DIFFRACTION39( CHAIN D AND RESID 12:17 )D12 - 17
40X-RAY DIFFRACTION40( CHAIN D AND RESID 18:21 )D18 - 21
41X-RAY DIFFRACTION41( CHAIN D AND RESID 22:31 )D22 - 31
42X-RAY DIFFRACTION42( CHAIN D AND RESID 32:35 )D32 - 35
43X-RAY DIFFRACTION43( CHAIN D AND RESID 36:40 )D36 - 40
44X-RAY DIFFRACTION44( CHAIN D AND RESID 41:45 )D41 - 45
45X-RAY DIFFRACTION45( CHAIN D AND RESID 46:51 )D46 - 51
46X-RAY DIFFRACTION46( CHAIN D AND RESID 52:55 )D52 - 55
47X-RAY DIFFRACTION47( CHAIN D AND RESID 56:60 )D56 - 60
48X-RAY DIFFRACTION48( CHAIN D AND RESID 61:65 )D61 - 65

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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