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- PDB-9dvh: A1 Tei + D-Hpg: Adenylation Domain 1 Core Construct from Teicopla... -

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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: 9dvh
タイトルA1 Tei + D-Hpg: Adenylation Domain 1 Core Construct from Teicoplanin Biosynthesis with D-4-Hydroxyphenylglycine
要素
  • MbtH-like short polypeptide
  • Non-ribosomal peptide synthetase
キーワードLIGASE / AMP-binding enzyme / NRPS / Adenylation domain
機能・相同性
機能・相同性情報


siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / catalytic activity / phosphopantetheine binding / cytosol
類似検索 - 分子機能
MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain ...MbtH-like protein / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
類似検索 - ドメイン・相同性
BORIC ACID / (2R)-amino(4-hydroxyphenyl)ethanoic acid / MbtH-like short polypeptide / Non-ribosomal peptide synthetase
類似検索 - 構成要素
生物種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: 1.656 Å
データ登録者Hansen, M.H. / Cryle, M.J. / Ratnayake, M.S.
資金援助 オーストラリア, 2件
組織認可番号
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: Biochemistry / : 2025
タイトル: Teicoplanin Nonribosomal Peptide Synthetase Is Unable to Incorporate Alpha-Ketoacid Building Blocks.
著者: Ratnayake, M.S. / Jian, X. / Tailhades, J. / Challis, G.L. / Hansen, M.H. / Lewandowski, J.R. / Cryle, M.J.
履歴
登録2024年10月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年8月13日Provider: repository / タイプ: Initial release

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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: Non-ribosomal peptide synthetase
B: Non-ribosomal peptide synthetase
C: MbtH-like short polypeptide
D: MbtH-like short polypeptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,36810
ポリマ-99,4424
非ポリマー9266
12,611700
1
A: Non-ribosomal peptide synthetase
D: MbtH-like short polypeptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,0554
ポリマ-49,7212
非ポリマー3342
362
タイプ名称対称操作
identity operation1_555x,y,z1
2
B: Non-ribosomal peptide synthetase
C: MbtH-like short polypeptide
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,3126
ポリマ-49,7212
非ポリマー5914
362
タイプ名称対称操作
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)42.253, 123.488, 176.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
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 9 through 41 or resid 43...
d_2ens_1(chain "B" and (resid 9 through 41 or resid 43...
d_1ens_2(chain "C" and (resid 3 through 15 or resid 17...
d_2ens_2(chain "D" and (resid 3 through 15 or resid 17...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERASPASPAA9 - 412 - 34
d_12ens_1LEULEUASPASPAA43 - 6036 - 53
d_13ens_1VALVALASPASPAA62 - 7155 - 64
d_14ens_1VALVALARGARGAA73 - 10966 - 102
d_15ens_1VALVALASPASPAA111 - 131104 - 124
d_16ens_1GLUGLUASPASPAA136 - 146129 - 139
d_17ens_1ALAALAVALVALAA148 - 150141 - 143
d_18ens_1TYRTYRTHRTHRAA152 - 153145 - 146
d_19ens_1GLYGLYSERSERAA155 - 156148 - 149
d_110ens_1GLYGLYGLYGLYAA158151
d_111ens_1PROPROHISHISAA160 - 167153 - 160
d_112ens_1SERSERGLYGLYAA169 - 210162 - 203
d_113ens_1VALVALALAALAAA212 - 222205 - 215
d_114ens_1ARGARGGLYGLYAA224 - 241217 - 234
d_115ens_1PHEPHELEULEUAA243 - 257236 - 250
d_116ens_1GLUGLUARGARGAA259 - 276252 - 269
d_117ens_1ALAALAPROPROAA278 - 280271 - 273
d_118ens_1ARGARGGLUGLUAA283 - 307276 - 300
d_119ens_1PROPROPROPROAA310303
d_120ens_1LEULEULEULEUAA312 - 330305 - 323
d_121ens_1ALAALAARGARGAA332 - 354325 - 347
d_122ens_1ALAALAGLUGLUAA356 - 361349 - 354
d_123ens_1PHEPHEGLYGLYAA363 - 393356 - 386
d_124ens_1ALAALAALAALAAA395388
d_21ens_1SERSERASPASPBB9 - 412 - 34
d_22ens_1LEULEUASPASPBB43 - 6036 - 53
d_23ens_1VALVALASPASPBB62 - 7155 - 64
d_24ens_1VALVALARGARGBB73 - 10966 - 102
d_25ens_1VALVALASPASPBB111 - 131104 - 124
d_26ens_1GLUGLUASPASPBB136 - 146129 - 139
d_27ens_1ALAALAVALVALBB148 - 150141 - 143
d_28ens_1TYRTYRTHRTHRBB152 - 153145 - 146
d_29ens_1GLYGLYSERSERBB155 - 156148 - 149
d_210ens_1GLYGLYGLYGLYBB158151
d_211ens_1PROPROHISHISBB160 - 167153 - 160
d_212ens_1SERSERGLYGLYBB169 - 210162 - 203
d_213ens_1VALVALALAALABB212 - 222205 - 215
d_214ens_1ARGARGGLYGLYBB224 - 241217 - 234
d_215ens_1PHEPHELEULEUBB243 - 257236 - 250
d_216ens_1GLUGLUARGARGBB259 - 276252 - 269
d_217ens_1ALAALAPROPROBB278 - 280271 - 273
d_218ens_1ARGARGGLUGLUBB283 - 307276 - 300
d_219ens_1PROPROPROPROBB310303
d_220ens_1LEULEULEULEUBB312 - 330305 - 323
d_221ens_1ALAALAARGARGBB332 - 354325 - 347
d_222ens_1ALAALAGLUGLUBB356 - 361349 - 354
d_223ens_1PHEPHEGLYGLYBB363 - 393356 - 386
d_224ens_1ALAALAALAALABB395388
d_11ens_2ASNASNLEULEUCC3 - 153 - 15
d_12ens_2ASNASNPROPROCC17 - 3217 - 32
d_13ens_2GLYGLYGLUGLUCC34 - 5234 - 52
d_14ens_2ASNASNASPASPCC54 - 5754 - 57
d_15ens_2PROPROLYSLYSCC60 - 6160 - 61
d_21ens_2ASNASNLEULEUDD3 - 153 - 15
d_22ens_2ASNASNPROPRODD17 - 3217 - 32
d_23ens_2GLYGLYGLUGLUDD34 - 5234 - 52
d_24ens_2ASNASNASPASPDD54 - 5754 - 57
d_25ens_2PROPROLYSLYSDD60 - 6160 - 61

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.999868593498, -0.00189497570551, -0.0160998386039), (-0.00124093212799, 0.999177246277, -0.0405375210154), (0.0161634100193, -0.0405122153146, -0.999048299426)-3.83175512323, 2.0206357757, 77.2546900469
2given(-0.997745408057, 0.0195685894308, 0.0641963473172), (0.014848638364, 0.997207189789, -0.0731938424406), (-0.0654493593545, -0.0720755918475, -0.995249461401)-9.11719459495, 3.60151480351, 77.8708199577

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要素

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タンパク質 , 2種, 4分子 ABCD

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


分子量: 42084.703 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: tcp9 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q70AZ9
#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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非ポリマー , 4種, 706分子

#3: 化合物
ChemComp-GHP / (2R)-amino(4-hydroxyphenyl)ethanoic acid


タイプ: D-peptide linking / 分子量: 167.162 Da / 分子数: 4 / 由来タイプ: 天然 / : C8H9NO3 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物 ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / 2-モルホリノエタンスルホン酸


分子量: 195.237 Da / 分子数: 1 / 由来タイプ: 天然 / : C6H13NO4S / コメント: pH緩衝剤*YM
#5: 化合物 ChemComp-BO3 / BORIC ACID / ほう酸


分子量: 61.833 Da / 分子数: 1 / 由来タイプ: 天然 / : BH3O3
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 700 / 由来タイプ: 天然 / : H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationN

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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: 2.32 Å3/Da / 溶媒含有率: 46.99 % / 解説: Cuboid
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
詳細: 0.1 M MMT (L-Malic acid, MES and Tris in a ratio of 1:2:2), pH 6 and 25% w/v PEG 1500

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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: 0.9537 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年9月25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: 0.9537 Å / 相対比: 1
反射解像度: 1.656→44.02 Å / Num. obs: 110910 / % possible obs: 99.96 % / 冗長度: 6.8 % / Biso Wilson estimate: 23.86 Å2 / CC1/2: 0.976 / CC star: 0.994 / Rmerge(I) obs: 0.1989 / Rpim(I) all: 0.08363 / Net I/σ(I): 14.07
反射 シェル解像度: 1.656→1.715 Å / Rmerge(I) obs: 1.019 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 10934 / CC1/2: 0.756 / CC star: 0.928 / Rpim(I) all: 0.418 / % possible all: 99.96

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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: 1AMU
解像度: 1.656→44.02 Å / SU ML: 0.1889 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 20.0987
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.1924 5666 5.11 %
Rwork0.1683 105206 -
obs0.1695 110872 99.96 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 32.89 Å2
精密化ステップサイクル: LAST / 解像度: 1.656→44.02 Å
タンパク質核酸リガンド溶媒全体
原子数6717 0 64 700 7481
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00467112
X-RAY DIFFRACTIONf_angle_d0.83989730
X-RAY DIFFRACTIONf_chiral_restr0.05281084
X-RAY DIFFRACTIONf_plane_restr0.01031303
X-RAY DIFFRACTIONf_dihedral_angle_d11.14262569
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.664579622475
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS0.58272051946
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.670.31581780.33713480X-RAY DIFFRACTION100
1.67-1.690.34981870.32013508X-RAY DIFFRACTION99.97
1.69-1.710.33221900.29263387X-RAY DIFFRACTION99.97
1.71-1.740.29841940.27893461X-RAY DIFFRACTION99.92
1.74-1.760.24471830.25693510X-RAY DIFFRACTION100
1.76-1.780.26931980.24793402X-RAY DIFFRACTION100
1.78-1.810.24251950.23323464X-RAY DIFFRACTION99.86
1.81-1.840.25151670.21883521X-RAY DIFFRACTION99.92
1.84-1.860.21841560.21343460X-RAY DIFFRACTION100
1.86-1.90.25011920.22393454X-RAY DIFFRACTION99.92
1.9-1.930.27241780.22993496X-RAY DIFFRACTION99.92
1.93-1.960.25741730.20673442X-RAY DIFFRACTION100
1.96-20.21931730.18773529X-RAY DIFFRACTION100
2-2.040.19292010.1763459X-RAY DIFFRACTION99.97
2.04-2.090.22931810.17333486X-RAY DIFFRACTION100
2.09-2.130.19241760.15533515X-RAY DIFFRACTION99.95
2.13-2.190.18392000.14423457X-RAY DIFFRACTION99.97
2.19-2.250.18922110.15543485X-RAY DIFFRACTION100
2.25-2.310.21451940.15863469X-RAY DIFFRACTION99.97
2.31-2.390.17571880.15313494X-RAY DIFFRACTION100
2.39-2.470.1982050.15383509X-RAY DIFFRACTION99.92
2.47-2.570.18731790.16143511X-RAY DIFFRACTION99.97
2.57-2.690.17951890.15793514X-RAY DIFFRACTION99.97
2.69-2.830.18882000.15623535X-RAY DIFFRACTION100
2.83-3.010.192040.15923517X-RAY DIFFRACTION99.97
3.01-3.240.18972110.17443524X-RAY DIFFRACTION100
3.24-3.570.19191900.15963556X-RAY DIFFRACTION100
3.57-4.080.15341840.14333585X-RAY DIFFRACTION99.97
4.08-5.140.14421740.12683669X-RAY DIFFRACTION100
5.14-44.020.17452150.16993807X-RAY DIFFRACTION99.85
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.288643445382.23946346966-2.236261715749.57705566272-6.516308604425.068216278510.00982562718292-0.241069473231-0.03675905168560.173011014278-0.186702010887-0.611592815447-0.05565290517960.3370075241190.1562025266890.1669715524570.0150739483756-0.003637392405630.189803117409-0.02995197405750.22162258734111.23513.12425.074
22.4599765772-2.11498049896-1.887401527672.69975123655-0.3090281826055.57573470544-0.04455722489940.172372021424-0.285373650957-0.518484244740.0928855321111-0.001776368265580.604663507447-0.0786510100427-0.04920153809820.370309678176-0.02543507522950.01065395011210.141294338433-0.02628771528650.2286557394374.0775.7315.93
32.87067480406-0.682892695169-0.1747476742579.773785732180.5842606326082.02162128589-0.1404843873761.602656987430.019396019878-0.6556157512131.08577643195-0.5717410485131.105328361610.443481618536-0.7410342906230.7192539343860.07889835319610.2037569165160.495975905365-0.03035598882980.34502556713213.39512.045-0.337
42.787253611430.692001918856-0.5136895730913.55511988448-1.892211252042.93878330889-0.1290713727780.1527325428060.0428300040485-0.4568419783050.09954854643080.06464347378540.486927379077-0.2413208488640.02111901296390.349319612436-0.04387629464310.02173302291590.202231393409-0.04257756528650.2031598139272.52816.467.839
52.015802371974.109107344110.6403680845056.12508134773-0.7682850400185.214206669380.0334119196279-0.09194033852070.0368209334468-0.4030432748210.1627479655980.148566483514-0.676086398515-0.491541264115-0.2317188417010.512696398596-0.067932827743-0.04395214622080.3521814291380.02822523016520.255444791596-2.75125.194-2.762
66.903276240643.28082100064-1.239781022229.43679801284-1.717901469345.0517220185-0.05401170696890.688754411418-0.279933783398-0.9910899682550.1632490178070.5117877863140.515238516362-0.250050384433-0.1070552661270.633495738338-0.126970315997-0.02672240351580.344118177493-0.0723290827020.268439830273-1.00412.621-1.09
72.01658792694-2.854067626643.499150491383.3016950548-2.288188435087.736296125640.3780301650611.75759331743-1.05818009254-0.923941396061-0.128939548745-0.2153435622580.8704347906230.151411801705-0.3370643557251.01321645678-0.305520698886-0.04643651163480.651207790949-0.0763495706250.37231753385-0.02114.858-6.912
82.01217962237-4.42800797647-2.758011612088.80638807282.552791651372.01281834822-0.381028425836-0.171346339169-1.672153198050.576621074881-0.09331756843220.2116677160132.93465512646-0.368591804770.298180711760.990260013271-0.09374074065470.03048736343010.380322984984-0.06537894764390.4808279598450.695.7471.969
9-0.00142359093326-0.001949191299650.00499707434774-0.00161240340360.00457037673375-0.00432674588874-0.186409792153-0.376413028551-1.02076584422.672760126220.902078826474-1.17447184350.1935586128740.183748101349-0.8005819665481.019688290690.144928199739-0.1585578496110.414312098014-0.09850116658990.71102047160712.3460.8236.32
104.54092626266-0.9447926573711.138023854024.74002068983-0.4627882464392.97344695466-0.14738771649-0.128124950176-0.1357901772-0.4386734581990.0660040479999-0.3536581695910.212205832922-0.002475961747290.1071119422680.255371968283-0.0100374858940.08177580277290.21552677607-0.005528284073650.22073710720710.11922.6059.629
117.095821167123.855947804964.923493264485.80505473556-1.265839777997.605929462090.4675420031480.6643477299372.28118597862-0.281605558139-0.4124067788171.81570819038-2.82916947071-2.89656534271-0.02783067982970.8177193698850.352396768181-0.1297720179460.8276002633720.1650604503641.20449478593-4.55136.3173.294
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622.00809519028-9.78050277181.115632866972.0107340732-2.597482078929.936649418110.222984566617-1.349541115240.7875278069630.9699370957260.0645463189207-0.889910124129-0.5282935160960.282477981456-0.3504736788990.643104468629-0.16504343759-0.07912130554360.374275118537-0.008917532563390.42486883613114.64556.47513.4
638.018571423962.790527200982.805474320918.700774350976.352001096327.270549494530.0714305948924-1.050509089460.572531390021.19362747318-0.66109415382-0.825194738378-0.9595312226550.7741021869250.498862305020.445604031143-0.196054006445-0.1157271287690.4395997395510.00788386333450.40531186736719.59647.57614.65
648.28453787087-1.984782635645.813232632782.01180498615-7.972370950572.01359034323-0.4872202996640.247096354130.7566004714620.0751915763958-0.484665781025-1.28381057468-0.2341728675660.6587299322621.005069821920.320129283053-0.0549444783713-0.004377568260560.3649751188840.04303853626670.41466171456219.6751.9343.066
658.959968404630.9575509892254.870797129228.285312928543.930949047247.98556635081-0.1720799744480.1208638630990.3161928502690.216061189506-0.2355788879570.2950070719720.2042063818410.2272599456250.3962832811680.2562822488130.03471149579830.01047092499850.1700120351430.01690886256730.2095255445868.16452.501-1.136
666.71049508198-3.718292423910.05664583053989.124787722437.383581751087.788070523820.002944633858830.4744501892880.219594645032-0.5751888590240.0329145878836-0.409552914229-0.5284716974720.319789338479-0.03211796302040.2924093636010.01032767688050.02579911955340.2304581388450.03328966203250.19822646916411.60549.042-2.326
677.508527208840.9017033105-2.965696097138.83681516324-0.3348781984818.91324910705-0.01540553643160.0437725409521-0.294379412377-0.239755974544-0.01317642779460.055943837263-0.06565366066550.1514679031130.1060587873490.1903401306230.04927977934640.02821864044640.2215539259830.003211597339650.20907340204415.17643.524-3.007
682.018740752724.92410822368-5.612041477342.00485485113-9.133211186142.01229120212-0.05471113618240.0706744574933-0.87950191985-0.450823045584-0.7064321531-1.108184949490.9946883986760.8454189223630.7599175810920.3921731194630.04170574854950.009595606465160.3285204253980.01463811173010.4380802822816.97837.5070.511
697.821353537722.130864352084.465283582259.02706252373-1.106619507612.02010528022-0.5667933858470.0408113541876-0.814075516141-0.20891202056-0.300894191474-2.160460209610.4352654208381.462318227850.8998376262120.4224292473950.09270851129040.05658748775640.6129687301060.1277659033440.7656296754218.6432.6647.265
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:25 )A9 - 25
2X-RAY DIFFRACTION2( CHAIN A AND RESID 26:53 )A26 - 53
3X-RAY DIFFRACTION3( CHAIN A AND RESID 54:57 )A54 - 57
4X-RAY DIFFRACTION4( CHAIN A AND RESID 58:93 )A58 - 93
5X-RAY DIFFRACTION5( CHAIN A AND RESID 94:105 )A94 - 105
6X-RAY DIFFRACTION6( CHAIN A AND RESID 106:118 )A106 - 118
7X-RAY DIFFRACTION7( CHAIN A AND RESID 119:125 )A119 - 125
8X-RAY DIFFRACTION8( CHAIN A AND RESID 126:131 )A126 - 131
9X-RAY DIFFRACTION9( CHAIN A AND RESID 134:137 )A134 - 137
10X-RAY DIFFRACTION10( CHAIN A AND RESID 138:152 )A138 - 152
11X-RAY DIFFRACTION11( CHAIN A AND RESID 153:161 )A153 - 161
12X-RAY DIFFRACTION12( CHAIN A AND RESID 162:178 )A162 - 178
13X-RAY DIFFRACTION13( CHAIN A AND RESID 179:267 )A179 - 267
14X-RAY DIFFRACTION14( CHAIN A AND RESID 268:307 )A268 - 307
15X-RAY DIFFRACTION15( CHAIN A AND RESID 308:316 )A308 - 316
16X-RAY DIFFRACTION16( CHAIN A AND RESID 317:356 )A317 - 356
17X-RAY DIFFRACTION17( CHAIN A AND RESID 357:366 )A357 - 366
18X-RAY DIFFRACTION18( CHAIN A AND RESID 367:388 )A367 - 388
19X-RAY DIFFRACTION19( CHAIN A AND RESID 389:397 )A389 - 397
20X-RAY DIFFRACTION20( CHAIN B AND RESID 9:20 )B9 - 20
21X-RAY DIFFRACTION21( CHAIN B AND RESID 21:30 )B21 - 30
22X-RAY DIFFRACTION22( CHAIN B AND RESID 31:39 )B31 - 39
23X-RAY DIFFRACTION23( CHAIN B AND RESID 40:56 )B40 - 56
24X-RAY DIFFRACTION24( CHAIN B AND RESID 57:92 )B57 - 92
25X-RAY DIFFRACTION25( CHAIN B AND RESID 93:97 )B93 - 97
26X-RAY DIFFRACTION26( CHAIN B AND RESID 98:134 )B98 - 134
27X-RAY DIFFRACTION27( CHAIN B AND RESID 135:138 )B135 - 138
28X-RAY DIFFRACTION28( CHAIN B AND RESID 139:147 )B139 - 147
29X-RAY DIFFRACTION29( CHAIN B AND RESID 148:169 )B148 - 169
30X-RAY DIFFRACTION30( CHAIN B AND RESID 170:213 )B170 - 213
31X-RAY DIFFRACTION31( CHAIN B AND RESID 214:220 )B214 - 220
32X-RAY DIFFRACTION32( CHAIN B AND RESID 221:237 )B221 - 237
33X-RAY DIFFRACTION33( CHAIN B AND RESID 238:251 )B238 - 251
34X-RAY DIFFRACTION34( CHAIN B AND RESID 252:286 )B252 - 286
35X-RAY DIFFRACTION35( CHAIN B AND RESID 287:315 )B287 - 315
36X-RAY DIFFRACTION36( CHAIN B AND RESID 316:331 )B316 - 331
37X-RAY DIFFRACTION37( CHAIN B AND RESID 332:360 )B332 - 360
38X-RAY DIFFRACTION38( CHAIN B AND RESID 361:386 )B361 - 386
39X-RAY DIFFRACTION39( CHAIN B AND RESID 387:395 )B387 - 395
40X-RAY DIFFRACTION40( CHAIN C AND RESID 2:5 )C2 - 5
41X-RAY DIFFRACTION41( CHAIN C AND RESID 6:9 )C6 - 9
42X-RAY DIFFRACTION42( CHAIN C AND RESID 10:15 )C10 - 15
43X-RAY DIFFRACTION43( CHAIN C AND RESID 16:19 )C16 - 19
44X-RAY DIFFRACTION44( CHAIN C AND RESID 20:23 )C20 - 23
45X-RAY DIFFRACTION45( CHAIN C AND RESID 24:28 )C24 - 28
46X-RAY DIFFRACTION46( CHAIN C AND RESID 29:32 )C29 - 32
47X-RAY DIFFRACTION47( CHAIN C AND RESID 33:36 )C33 - 36
48X-RAY DIFFRACTION48( CHAIN C AND RESID 37:40 )C37 - 40
49X-RAY DIFFRACTION49( CHAIN C AND RESID 41:44 )C41 - 44
50X-RAY DIFFRACTION50( CHAIN C AND RESID 45:48 )C45 - 48
51X-RAY DIFFRACTION51( CHAIN C AND RESID 49:52 )C49 - 52
52X-RAY DIFFRACTION52( CHAIN C AND RESID 53:56 )C53 - 56
53X-RAY DIFFRACTION53( CHAIN C AND RESID 57:61 )C57 - 61
54X-RAY DIFFRACTION54( CHAIN C AND RESID 62:65 )C62 - 65
55X-RAY DIFFRACTION55( CHAIN C AND RESID 66:69 )C66 - 69
56X-RAY DIFFRACTION56( CHAIN D AND RESID 2:5 )D2 - 5
57X-RAY DIFFRACTION57( CHAIN D AND RESID 6:9 )D6 - 9
58X-RAY DIFFRACTION58( CHAIN D AND RESID 10:15 )D10 - 15
59X-RAY DIFFRACTION59( CHAIN D AND RESID 16:19 )D16 - 19
60X-RAY DIFFRACTION60( CHAIN D AND RESID 20:23 )D20 - 23
61X-RAY DIFFRACTION61( CHAIN D AND RESID 24:27 )D24 - 27
62X-RAY DIFFRACTION62( CHAIN D AND RESID 28:31 )D28 - 31
63X-RAY DIFFRACTION63( CHAIN D AND RESID 32:35 )D32 - 35
64X-RAY DIFFRACTION64( CHAIN D AND RESID 36:41 )D36 - 41
65X-RAY DIFFRACTION65( CHAIN D AND RESID 42:45 )D42 - 45
66X-RAY DIFFRACTION66( CHAIN D AND RESID 46:49 )D46 - 49
67X-RAY DIFFRACTION67( CHAIN D AND RESID 50:53 )D50 - 53
68X-RAY DIFFRACTION68( CHAIN D AND RESID 54:57 )D54 - 57
69X-RAY DIFFRACTION69( CHAIN D AND RESID 58:61 )D58 - 61

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万見について

-
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