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- PDB-6wxp: De novo TIM barrel-ferredoxin fold fusion homodimer with 4-glutam... -

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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: 6wxp
タイトルDe novo TIM barrel-ferredoxin fold fusion homodimer with 4-glutamate centre TFD-EE
要素TFD-EE
キーワードDE NOVO PROTEIN / TIM barrel / ferredoxin fold / homodimeric fusion / symmetric fusion protein / metal binding
機能・相同性Ribosomal protein S10 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
機能・相同性情報
生物種synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.5 Å
データ登録者Caldwell, S.J. / Zeymer, C. / Haydon, I.C. / Huang, P. / Hilvert, D. / Baker, D.
資金援助 米国, スイス, 2件
組織認可番号
Defense Threat Reduction Agency (DTRA)HDTRA1-19-1-0003 米国
Swiss National Science Foundation スイス
引用ジャーナル: Proc.Natl.Acad.Sci.USA / : 2020
タイトル: Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion.
著者: Caldwell, S.J. / Haydon, I.C. / Piperidou, N. / Huang, P.S. / Bick, M.J. / Sjostrom, H.S. / Hilvert, D. / Baker, D. / Zeymer, C.
履歴
登録2020年5月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年11月25日Provider: repository / タイプ: Initial release
改定 1.12020年12月2日Group: Database references / カテゴリ: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22020年12月16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_author.identifier_ORCID
改定 1.32024年3月6日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.42024年4月3日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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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: TFD-EE
B: TFD-EE
C: TFD-EE
D: TFD-EE
E: TFD-EE
F: TFD-EE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)113,87421
ポリマ-113,0096
非ポリマー86515
1,02757
1
A: TFD-EE
B: TFD-EE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)38,33013
ポリマ-37,6702
非ポリマー66111
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-18 kcal/mol
Surface area15840 Å2
手法PISA
2
C: TFD-EE
D: TFD-EE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,8345
ポリマ-37,6702
非ポリマー1643
362
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-28 kcal/mol
Surface area16210 Å2
手法PISA
3
E: TFD-EE
F: TFD-EE
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)37,7103
ポリマ-37,6702
非ポリマー401
0
タイプ名称対称操作
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-32 kcal/mol
Surface area16810 Å2
手法PISA
単位格子
Length a, b, c (Å)43.910, 101.160, 117.730
Angle α, β, γ (deg.)90.000, 95.497, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 0 through 7 or resid 9...
d_2ens_1(chain "B" and (resid 0 through 7 or resid 9...
d_3ens_1(chain "F" and (resid 0 through 7 or resid 9...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYALAA2 - 9
d_12ens_1ASPLEUA11 - 16
d_13ens_1GLNARGA18 - 23
d_14ens_1LEUALAA25 - 27
d_15ens_1ILETRPA30 - 37
d_16ens_1ILELEUA39 - 44
d_17ens_1ASPALAA66 - 69
d_18ens_1ALAALAA73
d_19ens_1GLUASNA76 - 100
d_110ens_1GLUARGA106 - 109
d_111ens_1LEUALAA112 - 120
d_112ens_1GLUTHRA122 - 128
d_113ens_1METLEUA138 - 139
d_114ens_1GLNARGA141 - 146
d_115ens_1LEUALAA148 - 150
d_116ens_1GLNSERA152 - 157
d_117ens_1TRPTRPA160
d_118ens_1ILELEUA162 - 163
d_21ens_1GLYALAB2 - 9
d_22ens_1ASPLEUB11 - 16
d_23ens_1GLNARGB18 - 23
d_24ens_1LEUALAB25 - 27
d_25ens_1ILETRPB30 - 37
d_26ens_1ILELEUB39 - 44
d_27ens_1ASPALAB66 - 69
d_28ens_1ALAALAB73
d_29ens_1GLUASNB76 - 100
d_210ens_1GLUARGB106 - 109
d_211ens_1LEUALAB112 - 120
d_212ens_1GLUTHRB122 - 128
d_213ens_1METLEUB138 - 139
d_214ens_1GLNARGB141 - 146
d_215ens_1LEUALAB148 - 150
d_216ens_1GLNSERB152 - 157
d_217ens_1TRPTRPB160
d_218ens_1ILELEUB162 - 163
d_31ens_1GLYALAF1 - 8
d_32ens_1ASPLEUF10 - 15
d_33ens_1GLNARGF17 - 22
d_34ens_1LEUALAF24 - 26
d_35ens_1ILETRPF29 - 36
d_36ens_1ILELEUF38 - 43
d_37ens_1ASPALAF62 - 65
d_38ens_1ALAALAF67
d_39ens_1GLUARGF69 - 97
d_310ens_1LEUALAF100 - 108
d_311ens_1GLUTHRF110 - 116
d_312ens_1METLEUF118 - 119
d_313ens_1GLNARGF121 - 126
d_314ens_1LEUALAF128 - 130
d_315ens_1GLNTRPF132 - 138
d_316ens_1ILELEUF140 - 141

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要素

#1: タンパク質
TFD-EE


分子量: 18834.840 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) synthetic construct (人工物) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
#2: 化合物 ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 3 / 由来タイプ: 合成 / : Ca / タイプ: SUBJECT OF INVESTIGATION
#3: 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: 12 / 由来タイプ: 合成 / : C2H6O2
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 57 / 由来タイプ: 天然 / : H2O
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: 2.31 Å3/Da / 溶媒含有率: 46.76 %
結晶化温度: 277 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 HEPES pH 7.5, 10-15 % PEG 4000, and 5-10 % iso-propanol

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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: SLS / ビームライン: X06SA / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年3月18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 Å / 相対比: 1
反射解像度: 2.5→46.44 Å / Num. obs: 34814 / % possible obs: 97.88 % / 冗長度: 3.1 % / Biso Wilson estimate: 56.35 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0524 / Rpim(I) all: 0.03466 / Rrim(I) all: 0.06303 / Net I/σ(I): 14.17
反射 シェル解像度: 2.5→2.589 Å / 冗長度: 2.9 % / Rmerge(I) obs: 0.5054 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3455 / CC1/2: 0.776 / CC star: 0.935 / Rpim(I) all: 0.3465 / Rrim(I) all: 0.6156 / % possible all: 96.05

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18rc2_3793精密化
XDSデータ削減
PHASER位相決定
Cootモデル構築
Aimlessデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: Rosetta model of TFD broken into TIM and FD fragments and searched independently

解像度: 2.5→46.44 Å / SU ML: 0.3632 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 29.3068
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2808 1736 4.99 %
Rwork0.2271 33063 -
obs0.2298 34799 97.9 %
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: 85.4 Å2
精密化ステップサイクル: LAST / 解像度: 2.5→46.44 Å
タンパク質核酸リガンド溶媒全体
原子数7200 0 51 57 7308
拘束条件
Refine-IDタイプDev ideal
X-RAY DIFFRACTIONf_bond_d0.00227265
X-RAY DIFFRACTIONf_angle_d0.45579709
X-RAY DIFFRACTIONf_chiral_restr0.04181186
X-RAY DIFFRACTIONf_plane_restr0.00241229
X-RAY DIFFRACTIONf_dihedral_angle_d16.97642793
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.881324501187
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.14728998735
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.37831430.28812717X-RAY DIFFRACTION95.94
2.57-2.660.34971400.26662715X-RAY DIFFRACTION98.52
2.66-2.750.31581500.24822822X-RAY DIFFRACTION99.33
2.75-2.860.30481430.24082734X-RAY DIFFRACTION98.97
2.86-2.990.27751460.23692769X-RAY DIFFRACTION98.58
2.99-3.150.2951480.22512802X-RAY DIFFRACTION99.06
3.15-3.350.2631440.22422764X-RAY DIFFRACTION98.64
3.35-3.610.271450.21292742X-RAY DIFFRACTION97.53
3.61-3.970.28741430.22362685X-RAY DIFFRACTION95.61
3.97-4.540.2771460.22182761X-RAY DIFFRACTION98.74
4.54-5.720.25551410.22512781X-RAY DIFFRACTION98.02
5.72-46.440.27631470.22172771X-RAY DIFFRACTION96.02
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)
17.503768319250.3261372466881.066461033172.460411489090.1859177661335.115947431790.133909461395-0.487761196723-0.01185268972140.441780628223-0.2856726245470.398428966669-0.242753706307-0.5885113270630.08822710661860.372448667187-0.02789635895690.03792730306190.394061791265-0.03740745671590.425329594748-7.679198804395.9415073401835.2106781655
24.289125423920.8672514914440.8829070063992.955623509920.9634876602622.687810778260.293799449619-0.413726887013-0.3589926725910.723449062728-0.252172020490.4771413346830.457405992765-0.522290755128-0.03279421831820.624678595841-0.06460550108790.08549685105430.4808635352750.002469992711610.559473305387-9.6534843773-20.863863872528.622958444
34.09040508124-1.08028432489-2.57041351222.9685256220.1692773762572.66029796758-0.04878897670390.3168653068520.256840723634-0.0344865365411-0.00524872385240.2207513727080.0590480282919-0.09047752078320.09331724170070.364985749054-0.00641148782236-0.05162059383810.4870384173770.02202506305330.450678476391-11.9690773960.55047620409718.9369494896
44.21817883835-2.95570276162-1.757532641296.040313898031.922387059874.0291249316-0.222047963733-1.03383264161-0.824337793931-0.3437892738190.5173292699070.6809466445590.0576036852950.0393659621188-0.4989083047140.372656439017-0.0063944013682-0.01211481635960.4062324246660.07503124512620.4958203824380.25413030615-1.4097860655120.206246125
55.861229423740.4160090067311.705749378915.03426308846-1.170252844723.03579747352-0.103105047203-0.03856726593030.0323290559371-0.2767900901050.182071494779-0.2722237331730.14396024497-0.3921987765-0.1612994902860.3469866543820.02057849278340.04271625930670.4038868332260.0348666540020.4215085962163.69672014146-0.78452760552514.6484837692
62.50883170019-0.2514330864340.9449620832662.823608089930.976009283923.216820785110.05616593931780.0965263333066-0.0266171151397-0.0956106658364-0.0278433862014-0.455850109407-0.02050278583450.0378645109918-0.1800175349980.4272281347290.008521517435280.03736083765570.4744716480430.009936369082170.55136018442810.5120144461.4931198373221.7492597649
74.058695285640.154611597052-0.05195697131246.809564786830.3649835621592.477963412390.0476155301836-0.0286970534013-0.1862530463840.7446769303540.164115228837-0.5962236445821.01370547434-0.117924086552-0.1784661435810.714051337843-0.0136341215326-0.07470851038790.6586982447790.06288008491040.5333767857044.12664364814-18.076430805838.012696455
84.78100178854-1.69982200682-0.1842982196126.08710544722-0.538644433485.67745472220.0808897183101-1.29279494354-0.5831525290331.51444065259-0.190803809843-0.629276559801-0.0936020688386-0.299230357420.3274684408691.03742474347-0.0746611103088-0.2306557101311.07034220410.2305443449970.7673242773576.71503026952-16.316453500748.5846481811
92.868216272420.607006483317-1.044844754192.105486407851.236745547053.084084517540.145050425129-0.532400387297-0.6532232286192.177016728890.6723118281440.7128140923940.636481411557-0.371238191886-0.9990136362550.660742517871-0.0146843009727-0.07473954398491.00832757670.2810258675480.98182087289412.4752338027-18.072833797241.8640217871
104.522600097720.3852596347061.453771500711.28086152796-0.3191624023255.93018719377-0.0348616052073-0.6782836475830.2788365591440.253622044646-0.157747501622-0.0665224824290.02494812568660.4236976927190.2413474198220.3915838330170.0198371337867-0.02103026294420.517904611438-0.02689228580460.51364593857813.0522259665.7732303552930.8134124578
115.701383682851.699631235040.09383121077289.081970344512.039720895596.907080773150.136399987307-0.4019197319460.3082698435491.28685375607-0.431731821991-0.002265073858670.5385054833470.349954640740.6337628095140.683313584355-0.01681506917250.05281166153530.744484379851-0.0009909642631560.7466497689272.528823331072.7341930799443.0570974711
122.137256361390.487190549055-0.9584311135435.565076020780.02933976213823.642372770360.0700765588078-0.313907941522-0.03809139360070.0360212948676-0.0557487542869-0.4746809937410.1496684238010.198301024909-0.05729142419620.4161992177370.008726266958350.04077236177250.5009308758610.01347935459970.4294822962425.4969687814-23.7743509929-21.0871061175
135.200775520450.08474565958192.024955798570.401282638220.8881277140562.52799774891-0.74258805951-0.367602881422-0.313868158789-0.222534088166-0.09956157237450.01860577517620.227477664547-0.9213955900820.7546017690640.5416968829760.04860431580360.01369059450770.255530724742-0.1422179979430.5493801374495.89620566506-15.9304068012-14.8459243755
143.722663662212.37544050448-1.115521547524.82663221457-0.9524801839752.54530953397-0.3341356485370.213086203655-0.2738309874270.1107186076730.382543073737-0.8611482884480.7415848008370.381841907272-0.07055434922060.4847102282130.0864417594294-0.1068423202950.551270022748-0.1563220548580.4485871702298.1424593958-29.38283397315.02443900464
153.11720375053-2.56902427255-2.595344611257.653921935610.8510921550553.02028912870.3883209927410.299282358589-0.3078084654290.335881186461-0.169443242416-0.8501267708030.6165159591031.35777990256-0.2673181679750.5822633859820.1456978856-0.1955744780150.665422337-0.1926326274610.58437555574912.6346897831-24.262617688113.4760890621
165.63470379116-2.545918038061.109501236753.39714706842.351601217979.757151784270.1306979717650.60301242065-1.337680332220.6231822957030.5870564498180.848426972631.833920736471.87028828344-0.2743926419620.490871143562-0.128721948202-0.02347859758490.853558116961-0.4775366018490.95206928310317.0547704439-24.23846154274.27086427515
175.84946239665-1.891839103720.02598628750925.38969339905-0.2986211578738.160206265910.311691735992-0.04217072930121.311195405140.453891209478-0.320324564208-0.7105089303230.0920635519275-0.9261588438820.1649990395430.696894463188-0.0944277382828-0.008692800546680.613748284284-0.06794415689670.97362072649711.252701703-10.8967188932-13.892392732
182.55080264219-0.9138859680360.08627597280551.692024043230.9901669263641.379842609910.110932987019-1.186528964370.2027405914280.7076534047050.0937815642838-0.487775434468-0.0058056300787-0.275929487492-0.430963754230.9615464210480.01794897769650.1612683982110.963757952137-0.1350233836660.923206771636-7.35230244025-7.23713380967-6.13657638157
194.14136801649-0.6859624268960.7927786172824.07487876787-0.8529318437265.26974432270.105690304512-0.1277005302590.4618976764370.6489624554730.222652017610.0183223998973-0.842934900807-0.480702202915-0.2942306511460.6927183768440.09346711292940.1204720978280.619940753356-0.01737074101690.784369779386-10.5576601713-12.2114610554-12.4405122914
203.4279976847-0.8495277464860.8347769731863.462088975182.552131804076.45355849812-0.0553219386387-0.100895281821-0.2313309178880.4466920938310.01370916714290.6167416652380.823112019679-0.3304069156140.04931943842610.493297631556-0.01555589166320.01988294007020.342716355998-0.01262007175770.516225083706-7.4961410462-34.75495846821.32569149207
212.64189261626-2.843645310841.109951826795.490802738961.267641019053.289485834660.5801165206952.33914553227-0.9053023437070.656219710519-1.512307578110.9593657581461.40771729382-0.2477218303750.06406306727390.769013792219-0.1998905881020.1275746371271.42265029554-0.2234720807090.987520395208-17.5283923047-19.3998715987-20.4713124789
226.22516854285-1.96067406956-0.8749826230536.87066497761-0.02117775461445.019700748410.09993099375851.78155667419-0.1057367978040.128079325854-0.1256405081950.5403799431910.239780403936-0.808289146202-0.03533824364980.5215079324940.03699702874270.1104130561130.9458483855470.1216149652780.636440175512-7.8378215171-22.9973168577-21.5535440726
232.45204966356-3.267170305852.146263757076.06576830739-0.8477090556984.21768519136-0.1148601161691.26158995990.6332454420120.875441126992-0.2102151858881.44255034607-0.952412924555-0.332595875544-0.01263973574521.57851663617-0.0711197280015-0.2534016947740.8257687923640.1666130874651.20343503829-4.954965355972.19708054514-55.5579853069
241.021198766110.8059201905760.4940224783950.7412952160330.4702917556420.2955942100040.697058838604-0.965854652753-1.136586309150.2756726074210.0513945488074-1.03429166977-0.09689312215390.581580386809-0.3362727977472.29720831315-0.6364449467940.282681654131.467136628130.02299098706481.45912200541-0.02666518523993.00925419296-63.9657489704
258.921458106730.453055948191.45972059850.02946161240650.09017310945753.408961508230.340828683-1.153115683581.34457573243-0.118072239364-0.3148979871240.8808789855810.313514800444-0.2968772028880.594480487781.512655611580.154548825234-0.08029046867640.423867429915-0.07583759493041.50259283548-5.38398815366.88144026881-57.1307184247
261.896382902312.12484237964-1.010124050342.44262880426-1.650987762364.43735284309-0.2978622920680.709700422102-0.645473012911-1.20790445897-0.142845610061-1.19582432245-2.089299812750.5763862797790.5000731536661.91173626193-0.1609182112150.118118149180.9064246267140.0618560801431.178609742223.267949930298.02280603105-53.24429785
273.608421356541.30488150657-0.3425278777691.946317385490.9128369466324.78232641961-0.288867413264-0.681390727976-2.38321800155-0.006307337243210.705694657351-0.6528674958860.4599430382131.16220402068-0.1237109744910.825595620215-0.01007944787080.2721863568741.085335931140.1260474877621.8002240093211.4742774416-16.9276069616-49.0111393534
282.104467310480.713033339887-1.95756865312.15340046848-1.974774062444.517626697611.04665479734-0.3977659791040.749878917283-0.327737881889-1.02977114377-1.04168657609-0.6952577694831.836765265770.1519106213771.27655732250.1910901290710.09837928845981.290594221310.1479746886741.058710624644.73271414238-20.8680490704-46.3276752516
290.590894434430.7171589600240.04082656582192.000557362872.233931831465.001172565330.4325402224870.0406605430725-0.558587256876-0.4265497787850.119078224318-0.609380445465-0.3649769960191.45775640184-0.4555206467850.8595552314070.2304548664030.1460392001081.317352327620.1517991008191.101782092399.51369858839-17.9592010313-40.6247949743
302.782005359681.423809517330.3192423760152.19723802331-1.169889831963.80139140291-0.1555905458120.1727202277440.979880433691-0.5136885090210.205890838582-0.540321167051.255450064660.327840839036-0.08811514396181.5301322254-0.2420977534780.00771899846481.785547066980.1357376481881.5975940543615.7381329572-9.55586248099-42.1829258657
317.519833396862.634945469260.5451829983182.54180869954-1.815273178512.495837246650.577309643386-1.658428200180.6838599251020.3601600666020.724925658044-2.288774619510.974118354037-0.742658575985-1.430293871771.74578243817-0.279423488219-0.06144162112911.21294089902-0.409404096491.223686137198.2958863973511.287039281-43.2862769994
324.79069110229-3.0057902502-1.366708596564.036179319994.294499171625.885981771471.34092966369-0.885880390971.379485982791.052394494441.772492686842.043025642470.57697959651-0.0255749145356-1.480999315521.35561110895-0.297812065919-0.0603571468170.9549826514460.1116381574281.43801844614-1.0215100306310.8428712704-46.0005396348
338.416293795750.944631130452-0.3750174280028.740758558721.643066531097.43184607223-0.384578671168-0.7100825828460.515331370255-0.3314802989250.1440366249860.3155752843010.04792580451880.3547283038980.693701507011.01904615625-0.1563629648920.1080451771520.996740977658-0.09644784168961.03800828112-0.56231707545-2.69510049123-34.8479490087
342.55164811371-0.328663738641-0.9237941844435.94674606280.5371730024893.256633418310.219818538312-0.1496258804610.07544491857411.16297864986-0.2977674865040.73476361236-0.661118318354-0.8441721910950.2467394544771.238582895560.114992450531-0.00685982219861.07009204774-0.07227496193250.92478138359-9.23026424076-0.653886041641-36.5313588382
355.364350702531.43774967745-0.8406722686964.2391102445-0.7329301033897.005390159090.134289029639-1.0675457627-0.423013904320.797095569498-0.05908057637270.428305625843-1.24982857843-1.356562154260.1743946543441.19068669740.0976541096248-0.2140527039551.06127348178-0.03768632510280.98268812015-16.5101521592-2.85457439356-43.1642190737
364.222455092410.1466578413770.851621469551.48012694654-1.358235701252.74108457886-0.5855129925820.7994169265230.25798654585-1.513502431960.3432890811630.4280325780470.7077145430080.2541612552270.08227000022811.690281122240.486389122466-0.0374727080171.26082242945-0.08206690129930.714105971749-3.84937854699-23.7991619193-55.1668714453
373.122733193191.141588905671.499482257991.346894582990.06369432489710.926273070652-0.2657392895720.5943525898010.110820866136-0.805046215810.04645211644240.1395640967240.204397022594-0.4980807664850.009082385811851.628118613460.0991457417630.02253508551561.305778540630.09119451288791.17894138504-10.9259453143-16.5877260559-56.2740206037
386.403531800631.455557045964.16825082386.6513408501-1.467380563566.07637455308-1.511266077540.06512930663560.860067556949-0.05789559926-0.0922540831229-0.2657275586340.936503645455-0.7491239601661.877024827851.30246930080.022777304431-0.05065075276150.8636287801350.02394135073361.01210050808-10.265138142-0.845647164722-59.4252910988
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 52 )AA0 - 522 - 54
22chain 'A' and (resid 53 through 132 )AA53 - 13255 - 134
33chain 'A' and (resid 133 through 165 )AA133 - 165135 - 167
44chain 'B' and (resid 0 through 9 )BB0 - 92 - 11
55chain 'B' and (resid 10 through 34 )BB10 - 3412 - 36
66chain 'B' and (resid 35 through 52 )BB35 - 5237 - 54
77chain 'B' and (resid 53 through 103 )BB53 - 10355 - 105
88chain 'B' and (resid 104 through 120 )BB104 - 120106 - 122
99chain 'B' and (resid 121 through 129 )BB121 - 129123 - 131
1010chain 'B' and (resid 130 through 154 )BB130 - 154132 - 156
1111chain 'B' and (resid 155 through 163 )BB155 - 163157 - 165
1212chain 'C' and (resid 0 through 44 )CC0 - 442 - 46
1313chain 'C' and (resid 45 through 55 )CC45 - 5547 - 57
1414chain 'C' and (resid 56 through 103 )CC56 - 10358 - 105
1515chain 'C' and (resid 104 through 121 )CC104 - 121106 - 123
1616chain 'C' and (resid 122 through 133 )CC122 - 133124 - 131
1717chain 'C' and (resid 134 through 156 )CC134 - 156132 - 154
1818chain 'D' and (resid 0 through 22 )DD0 - 221 - 23
1919chain 'D' and (resid 23 through 55 )DD23 - 5524 - 54
2020chain 'D' and (resid 56 through 134 )DD56 - 13455 - 128
2121chain 'D' and (resid 135 through 145 )DD135 - 145129 - 139
2222chain 'D' and (resid 146 through 166 )DD146 - 166140 - 160
2323chain 'E' and (resid 1 through 10 )EE1 - 101 - 8
2424chain 'E' and (resid 11 through 20 )EE11 - 209 - 18
2525chain 'E' and (resid 21 through 32 )EE21 - 3219 - 26
2626chain 'E' and (resid 33 through 51 )EE33 - 5127 - 40
2727chain 'E' and (resid 52 through 66 )EE52 - 6641 - 51
2828chain 'E' and (resid 67 through 91 )EE67 - 9152 - 76
2929chain 'E' and (resid 92 through 121 )EE92 - 12177 - 106
3030chain 'E' and (resid 122 through 135 )EE122 - 135107 - 115
3131chain 'E' and (resid 136 through 146 )EE136 - 146116 - 126
3232chain 'E' and (resid 147 through 153 )EE147 - 153127 - 133
3333chain 'E' and (resid 154 through 162 )EE154 - 162134 - 142
3434chain 'F' and (resid 0 through 34 )FF0 - 341 - 35
3535chain 'F' and (resid 35 through 52 )FF35 - 5236 - 51
3636chain 'F' and (resid 53 through 82 )FF53 - 8252 - 77
3737chain 'F' and (resid 83 through 149 )FF83 - 14978 - 131
3838chain 'F' and (resid 150 through 164 )FF150 - 164132 - 144

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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