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- PDB-6z7r: Structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hil... -

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基本情報

登録情報
データベース: PDB / ID: 6z7r
タイトルStructure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hildenborough pressurized with Krypton gas - structure wtKr1
要素(Periplasmic [NiFeSe] hydrogenase, ...) x 2
キーワードOXIDOREDUCTASE / Hydrogenase / Selenium / gas channels / high-pressure derivatization
機能・相同性
機能・相同性情報


cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / cell envelope / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / cell envelope / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / metal ion binding / membrane
類似検索 - 分子機能
: / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / : / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenase, large subunit, nickel binding site ...: / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / : / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
類似検索 - ドメイン・相同性
oxygen-damaged SF4 / CARBONMONOXIDE-(DICYANO) IRON / : / HYDROSULFURIC ACID / KRYPTON / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing / cytochrome-c3 hydrogenase
類似検索 - 構成要素
生物種Desulfovibrio vulgaris (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: 1.77 Å
データ登録者Zacarias, S. / Temporao, A. / Carpentier, P. / van der Linden, P. / Pereira, I.A.C. / Matias, P.M.
資金援助 ポルトガル, 2件
組織認可番号国
Fundacao para a Ciencia e a TecnologiaPTDC/BBB-BEP/2885/2014 ポルトガル
Fundacao para a Ciencia e a TecnologiaLISBOA-01-0145-FEDER-007660 ポルトガル
引用ジャーナル: J.Biol.Inorg.Chem. / 年: 2020
タイトル: Exploring the gas access routes in a [NiFeSe] hydrogenase using crystals pressurized with krypton and oxygen.
著者: Zacarias, S. / Temporao, A. / Carpentier, P. / van der Linden, P. / Pereira, I.A.C. / Matias, P.M.
履歴
登録2020年6月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年9月9日Provider: repository / タイプ: Initial release
改定 1.12020年9月16日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
改定 1.22020年9月30日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32024年1月24日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Periplasmic [NiFeSe] hydrogenase, small subunit
B: Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
C: Periplasmic [NiFeSe] hydrogenase, small subunit
D: Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)174,07461
ポリマ－167,2894
非ポリマー6,78557
水4,432246
1
A: Periplasmic [NiFeSe] hydrogenase, small subunit
B: Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)86,99530
ポリマ－83,6452
非ポリマー3,35128
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Periplasmic [NiFeSe] hydrogenase, small subunit
D: Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)87,07931
ポリマ－83,6452
非ポリマー3,43429
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)75.125, 93.686, 98.433
Angle α, β, γ (deg.)90.000, 93.264, 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 5 through 20 or resid 22...
d_2ens_1(chain "C" and (resid 5 through 20 or resid 22...
d_1ens_2(chain "B" and (resid 15 through 47 or resid 49...
d_2ens_2(chain "D" and (resid 15 through 47 or resid 49...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYGLYA1 - 16
d_12ens_1SERSERA19
d_13ens_1VALGLYA22 - 53
d_14ens_1HISPROA57 - 242
d_15ens_1THRALAA246 - 286
d_21ens_1GLYGLYL1 - 16
d_22ens_1SERSERL19
d_23ens_1VALGLYL22 - 53
d_24ens_1HISPROL57 - 242
d_25ens_1THRALAL246 - 286
d_11ens_2GLYLEUF2 - 34
d_12ens_2GLYILEF38 - 63
d_13ens_2GLYASPF67 - 245
d_14ens_2SERASPF247 - 263
d_15ens_2PROTYRF267 - 377
d_16ens_2LEUPROF381 - 483
d_17ens_2LEULEUF487
d_18ens_2GLYHISF491 - 495
d_21ens_2GLYLEUQ1 - 33
d_22ens_2GLYILEQ37 - 62
d_23ens_2GLYASPQ66 - 244
d_24ens_2SERASPQ248 - 264
d_25ens_2PROTYRQ268 - 378
d_26ens_2LEUPROQ382 - 484
d_27ens_2LEULEUQ488
d_28ens_2GLYHISQ492 - 496

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.99168119705, 0.0950442798575, 0.0868043102805), (0.0965545732339, 0.995238029228, 0.0133596245026), (-0.0851211948021, 0.0216298415529, -0.996135800054)25.5149720438, 45.9123330845, 147.922813218
2given(-0.991545753914, 0.0947079503269, 0.088698489504), (0.0957671532765, 0.995373565829, 0.00775350257077), (-0.0875538134449, 0.0161823543917, -0.996028343551)25.4034427681, 46.3382587435, 147.698194333

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要素

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Periplasmic [NiFeSe] hydrogenase, ... , 2種, 4分子 ACBD

#1: タンパク質 Periplasmic [NiFeSe] hydrogenase, small subunit


分子量: 30261.568 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (バクテリア)
遺伝子: hysB, DVU_1917 / 細胞株 (発現宿主): alpha-select Silver Efficiency / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q72AS4, ferredoxin hydrogenase
#2: タンパク質 Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing


分子量: 53383.059 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: CYS 75 oxidized to Cysteine sulfinic acid
由来: (組換発現) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (バクテリア)
遺伝子: hysA, DVU_1918 / 細胞株 (発現宿主): alpha-select Silver Efficiency / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q72AS3, ferredoxin hydrogenase

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非ポリマー , 9種, 303分子

#3: 化合物
ChemComp-SF4 / IRON/SULFUR CLUSTER


分子量: 351.640 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Fe4S4
#4: 化合物 ChemComp-6ML / oxygen-damaged SF4


分子量: 383.639 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe4O2S4
#5: 化合物...
ChemComp-KR / KRYPTON


分子量: 83.798 Da / 分子数: 39 / 由来タイプ: 合成 / 式: Kr / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物 ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


分子量: 135.890 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3FeN2O
#7: 化合物 ChemComp-NI / NICKEL (II) ION


分子量: 58.693 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Ni
#8: 化合物 ChemComp-FE2 / FE (II) ION


分子量: 55.845 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe
#9: 化合物 ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / 硫化水素


分子量: 34.081 Da / 分子数: 2 / 由来タイプ: 合成 / 式: H2S
#10: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cl
#11: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 246 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 1.75 Å3/Da / 溶媒含有率: 29.6 % / 解説: Thin plate
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.6 / 詳細: 20% PEG 1500 (w/v) and 0.1 mM Tris-HCl pH 7.6.

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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: ESRF / ビームライン: ID30B / 波長: 0.9677 Å
検出器タイプ: DECTRIS EIGER X 4M / 検出器: PIXEL / 日付: 2017年9月27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: 0.9677 Å / 相対比: 1
反射解像度: 1.76→67.8 Å / Num. obs: 101087 / % possible obs: 75.6 % / 冗長度: 4.3 % / Biso Wilson estimate: 22.04 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.056 / Net I/σ(I): 9
反射 シェル解像度: 1.76→1.92 Å / 冗長度: 3.7 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5055 / CC1/2: 0.5 / Rpim(I) all: 0.467 / % possible all: 17

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解析

ソフトウェア
名称バージョン分類
PHENIX1.18.2_3874精密化
XDSデータ削減
STARANISO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: 5JSK

5jsk


解像度: 1.77→58.05 Å / SU ML: 0.2404 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 27.5817
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
詳細: HYDROGEN ATOMS WERE INCLUDED IN CALCULATED POSITIONS; SOLVENT MOLECULES WERE ADDED MANUALLY IN COOT USING 2|FO|-|FC| AND |FO|-| MAPS; OCCUPANCY FACTORS WERE REFINED FOR DISORDERED RESIDUES ...詳細: HYDROGEN ATOMS WERE INCLUDED IN CALCULATED POSITIONS; SOLVENT MOLECULES WERE ADDED MANUALLY IN COOT USING 2|FO|-|FC| AND |FO|-| MAPS; OCCUPANCY FACTORS WERE REFINED FOR DISORDERED RESIDUES AND THE KR ATOMS; NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS AND TLS RIGID BODY REFINEMENT OF ATOMIC DISPLACEMENT PARAMETERS WERE APPLIED.
Rfactor反射数%反射
Rfree0.2419 4804 4.75 %
Rwork0.1877 96271 -
obs0.1903 101075 75.66 %
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: 28.85 Å2
精密化ステップサイクル: LAST / 解像度: 1.77→58.05 Å
タンパク質核酸リガンド溶媒全体
原子数11669 0 129 246 12044
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.013212165
X-RAY DIFFRACTIONf_angle_d1.334716554
X-RAY DIFFRACTIONf_chiral_restr0.071799
X-RAY DIFFRACTIONf_plane_restr0.00882147
X-RAY DIFFRACTIONf_dihedral_angle_d15.33074534
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.384634548737
ens_2d_2AX-RAY DIFFRACTIONTorsion NCS0.406220206341
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.780.49270.3012120X-RAY DIFFRACTION2.88
1.79-1.810.4696110.3383216X-RAY DIFFRACTION5.18
1.81-1.830.2923180.3171372X-RAY DIFFRACTION8.85
1.83-1.850.3019250.2927632X-RAY DIFFRACTION14.87
1.85-1.880.328600.2891980X-RAY DIFFRACTION23.37
1.88-1.90.3211800.29481292X-RAY DIFFRACTION31.07
1.9-1.930.3234970.28281748X-RAY DIFFRACTION41.45
1.93-1.960.32151380.27172155X-RAY DIFFRACTION52.03
1.96-1.990.29931190.25442764X-RAY DIFFRACTION64.82
1.99-2.020.31691360.24413187X-RAY DIFFRACTION75.05
2.02-2.060.28862030.23973523X-RAY DIFFRACTION83.96
2.06-2.090.30761880.23553910X-RAY DIFFRACTION92.19
2.09-2.130.27662110.23424006X-RAY DIFFRACTION95.28
2.13-2.180.26872190.23244098X-RAY DIFFRACTION97.16
2.18-2.220.27792190.23444218X-RAY DIFFRACTION99.06
2.22-2.280.27232040.22734178X-RAY DIFFRACTION98.96
2.28-2.330.30152140.21974168X-RAY DIFFRACTION99.12
2.33-2.40.28471800.21034241X-RAY DIFFRACTION99.19
2.4-2.470.28241680.20324289X-RAY DIFFRACTION99.44
2.47-2.550.28551940.19954185X-RAY DIFFRACTION99.5
2.55-2.640.2871950.19974226X-RAY DIFFRACTION99.53
2.64-2.740.2432050.20074218X-RAY DIFFRACTION99.39
2.74-2.870.25932170.2024231X-RAY DIFFRACTION99.46
2.87-3.020.23892000.20084225X-RAY DIFFRACTION98.88
3.02-3.210.25832100.18744135X-RAY DIFFRACTION97.84
3.21-3.450.24972310.17933819X-RAY DIFFRACTION90.54
3.45-3.80.20262020.1584255X-RAY DIFFRACTION99.71
3.8-4.350.18711990.14024286X-RAY DIFFRACTION99.82
4.35-5.480.19162090.13554301X-RAY DIFFRACTION99.85
5.48-58.050.17962450.15074293X-RAY DIFFRACTION99.15
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)
10.00975505931258-0.00183513672404-0.01696701119640.01154584794030.002636988565170.02118029799520.0163167673227-0.08514526635240.02793010086870.002009513981260.000175373045830.0543883437752-0.09717806286890.179684836342-0.005951600045290.148856056375-0.02519168398280.009367116380750.129978801491-0.00809893998630.0968932539889-1.65160568332-29.725102933783.2068144227
20.00550641990693-0.00531477768858-0.008400473776270.005338519145750.008093264913480.01085577765340.0350043961767-0.0113887976852-0.0191527143711-0.0693465744546-0.05554549892110.0301863218128-0.0735837222444-0.0550601135558-0.007269960662550.167272954640.03261911364670.004036242082960.110008436533-0.005995149368060.139425215026-15.2858933228-27.741495490382.297323557
3-1.82745301986E-50.000382086927139-0.0001717157284190.00137753413454-0.0002278185256583.50088957104E-50.02789105845760.01272500148430.00942562630341-0.000330393658111-0.02323262671550.0133318820493-0.0183360447111-0.0077837137548.46411330328E-60.3020958119390.01424353424390.0761499645830.1072644759570.02319168761320.152700714229-14.3485747301-20.683713855281.9821766061
40.00119462292374-0.00581830227152-0.003658923241110.0181244028230.01322386351970.03720658179030.00474370403377-0.02532706818870.02372213605050.00377340580583-0.0326854614745-0.000782389219926-0.00782537805590.0253350362330.001048223362890.116244335479-0.00943333049944-0.02730770631120.366878665005-0.005568863919190.1050997309743.03640702275-29.768324617898.063559781
50.00266089403860.003208996047790.004289927068920.005003271650060.005725776677590.005624092414780.0220374316919-0.000758853275034-0.01132505840090.0161734104962-0.00289886129524-0.02287116692210.008730688303490.02436801785430.0125536360460.142574175504-0.0873070655307-0.06282362393580.495475098889-0.04137076553130.19090044019423.7780876543-31.402398251778.7142694817
60.0161677802059-0.0069170067190.007447645533480.025668717768-0.00284485160810.002808756756450.0194601499033-0.0398783189147-0.02784289493480.006259819624220.030686707325-0.01675939364240.00504690910690.06595779873580.1069915069080.0760971051711-0.0499840018574-0.03574063100450.448653250923-0.007741211414950.097340886826616.7363779398-32.642566133576.7845417275
70.0110357630827-0.00742606624333-0.003733766238850.005708418643040.001830654500420.001932747587810.0005038720292370.020352679063-0.00896995846207-0.01710300793980.007942489530270.04634413176310.00597215472183-0.0558930867948-0.004034612222310.05864686373020.0128114479047-0.04796289600180.218318269634-0.01642257264130.123816143792-24.454850954-35.104042674167.9256436045
80.09404618697940.0240615929397-0.1095631071040.154120938155-0.04034935766970.298913353204-0.06825377964240.058132609491-0.141687308578-0.0494771821154-0.0851737097196-0.01873025631030.15516830761-0.0398704464625-0.2725875082410.1092643168040.02888435818210.02730055230860.0503384702461-0.0131776158260.106618564806-5.33453560078-41.325333872968.3992314924
9-7.76681484073E-5-0.000858982175389-0.0004184598128410.005895303979630.004294702504270.00192218927836-0.00765901514290.0232461380285-0.05773387610390.00979452261163-0.02262132108940.026304456170.07606026728240.0660689632689-0.01154533025330.1772227490170.1238186527290.0627512886550.2015100785090.05659341479020.19534687622311.3077127927-51.157761252372.1525614554
100.01868859975920.005131472106560.0167678382980.04189333305-0.01412855079380.0253446524089-0.002467071624960.0222339496847-0.0455132547683-0.0211220654672-0.0217113781440.02105007867570.0868849076715-0.0324275736778-0.03505319771760.29963147667-0.06565235986430.09342549297250.179331084045-0.1129815405720.25426181081-9.23381523359-53.566931322761.7070253889
110.0194944449590.00920289564583-0.01778224406430.0168449091111-0.01499459337660.0194877253197-0.01687395560260.0934822993955-0.01798383703370.02472502045240.04485301795520.0247175164299-0.038995591573-0.1023861623890.01432245596820.1603487664080.0685753518855-0.03907535539650.293129108211-0.02150439143230.0995479503611-10.2182567389-33.047518802451.6610634432
120.0220389639603-0.007729654327430.009842502024690.0035035733973-0.004034033989760.0109877095587-0.0234210658040.00637561948484-0.0302940669238-0.0267924919424-0.03204461828630.02115162131180.0497088099227-0.0314735303495-0.04991296699090.297359814188-0.03597744648990.05495092472580.0975692454651-0.07394062544140.225096410094-8.38423402868-59.075145647861.8642923328
130.00484633229227-0.0055411397532-0.01224297400510.006212410513820.01335399520770.0257588213184-0.02291592281670.0215241578529-0.0101729756295-0.0192328408069-0.03290055213630.01094716286710.04081592050020.0601835894451-0.002509125073180.096455171794-0.00198533188440.009363159744340.134474548111-0.01021646279930.11986200139710.9252741379-38.657028268256.2391282165
140.08941959508060.009344167129860.0299412860650.0102959394390.01890207075840.04848988814440.1029503958350.1225624548070.06022430673760.009918926602650.00505630921396-0.0304342047491-0.05053961490230.005803032995850.03931435287080.1368307814380.02075503378720.02271836426630.0987719364428-0.001555786891010.097525384060931.567818654317.312266893764.5621920528
150.01439103341090.001194012326480.003048920302480.01658994051870.002975506866130.01289362637720.08407458470230.02797004323070.05038039876330.012845543777-0.0284567794482-0.0120717780902-0.05497456710940.05362183363890.01304826886840.1073451756670.01258078334660.03981109705040.1386168413590.0011915803250.13391198042745.223498476717.904289692366.667235751
16-3.44978607525E-57.01301482144E-5-0.0001155970630520.0005171742970094.26810898538E-56.18129484443E-50.0138849444967-0.01272394570750.00304438121141-0.00118249937741-0.0158870567419-0.00826960287527-0.004410863274930.01460677934074.93724919429E-60.267030841701-0.03214998679930.1201094604040.211930861425-0.07068272976770.24318865885844.9492448924.992722504866.9510997548
170.00300887333830.00385698381214-0.006832203472510.00523904562474-0.006784113544880.0191250165425-0.01015244352260.02290461359270.0171145060391-0.0117708325945-0.0170818787771-0.00117454543174-0.01648193135960.00200506991588-0.001674043011050.1285205098710.037085780881-0.02259684109290.265960821743-0.0007404562305360.078182587782528.073541556117.898391611449.3577658518
180.00422852972136-0.006911339010290.003694577220770.0114978203792-0.003762525103590.004713945666630.0110510838980.04592193391870.0141501024584-0.0264698000937-0.008585380636120.0374696446981-0.00619729647626-0.0352701798367-0.004232559191850.1499335333160.0553760348459-0.0365716687790.3283641934290.05011105619740.1857074868535.7819611572217.973566742666.7456492817
190.01448211638460.00597090573109-0.005836357093970.007259528601960.001148364817150.00701087688010.07527024593010.100146773560.00302926220535-0.00350975143790.0525656392580.021169315477-0.0123663826417-0.06553431710060.02732406427080.1254653149140.0329051344286-0.02134856718180.2123114666050.01491953303780.11335518341612.461886514216.04491771869.3011539223
200.01017292010240.003526177329660.01212529833220.0009362593368630.004599681799740.0136453072055-0.0017377739183-0.0393987207114-0.003775078383860.0173175963182-0.00325685630818-0.0251530364110.004829575410360.03891751154560.001787865412090.0941322251760.0553377133092-0.03673879254050.325815102905-0.003031887895410.17172720235651.98958858569.3839156152481.3610371025
210.0122531919257-0.00977780204992-0.01451372671640.0821144195658-0.02057886856280.0919373345443-0.02639451209678.90514032931E-5-0.138916744823-0.0211571960573-0.0563992949524-0.04189695411550.1640396604250.125175849412-0.3051969460730.0912119338120.09034110808590.0512815022025-0.0854325055636-0.05137609620810.1051812364132.85005377835.2140062564379.3648076913
220.003150854254770.0025237770827-0.004371250927280.0102107392748-0.00656060730650.007408137127120.003883050193080.0206449677398-0.0520095233152-0.01896799643070.00923141788888-0.00338347994440.0709546600592-0.005693357339370.027972495970.171448116631-0.0156020616565-0.00201814432750.0654194398811-0.07702000448260.17775534893715.796969436-2.9375394885274.0540547003
230.006230776013360.006351543676040.006492172379330.01286303636240.003685702279340.01024616275890.0156905107587-0.00562189523854-0.0626582402096-0.002398500993940.00253424191197-0.04367971751940.04215985417570.02723406261830.001861017485680.2433427730570.1374989514180.04043177735440.1883296754170.07494439388790.28501039004534.5377105973-7.2487389770986.250642991
240.0257766570204-0.0144216273616-0.006438470537240.0152769497010.01938247266450.0355936474470.0123915440289-0.138732012865-0.04125295966120.02496384489230.0732142387246-0.05300669693960.01449194294640.1074203859130.02177760294110.1507615163070.00917445840668-0.04773828946510.336835336607-0.01503648380620.16417178139537.004008529912.851411830696.6091528919
250.006966501283870.00795781728601-0.002444348938230.0174977108347-0.007579813318870.00167673504071-0.0382988762822-0.0133296602236-0.0202623933-5.18568561517E-5-0.0176648594718-0.01376949874990.04630380368270.048881223682-0.06088199747780.2969825004720.1418463468680.05382414563440.1267128070110.09555343960520.3276989597533.5526871892-12.700483119585.8947618445
260.002605955529620.0037281672528-0.006323256649750.00747076172553-0.01282797713360.01865027681110.0412842013522-0.0357327174748-0.02082964653450.0638517210869-0.01347409600070.06095002246790.01270535529580.04569946026411.36164811747E-50.1472865770620.0196240577074-0.001555833284320.128591308313-0.0001053445937180.10720706648715.85325550289.288663708590.1026992945
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 5 through 46 ) or (resid 112 through 162 ) or (resid 286 through 287))AA - E5 - 461
22chain 'A' and (resid 47 through 96 )AA47 - 9646 - 97
33chain 'A' and (resid 97 through 111 )AA97 - 11198 - 112
44chain 'A' and (resid 163 through 192 )AA163 - 192164 - 193
55chain 'A' and (resid 193 through 242 )AA193 - 242194 - 245
66chain 'A' and ((resid 243 through 283 ) or (resid 284 through 285))AA - C243 - 283246
77chain 'B' and (resid 14 through 49 )BF14 - 491 - 38
88chain 'B' and ((resid 50 through 180 ) or (resid 433 through 495 ) or (resid 500 through 504))BF - K50 - 18039
99chain 'B' and (resid 181 through 219 )BF181 - 219172 - 210
1010chain 'B' and (resid 220 through 262 )BF220 - 262211 - 253
1111chain 'B' and (resid 263 through 329 )BF263 - 329254 - 322
1212chain 'B' and (resid 330 through 395 )BF330 - 395323 - 390
1313chain 'B' and (resid 396 through 432 )BF396 - 432391 - 427
1414chain 'C' and ((resid 5 through 46 ) or (resid 112 through 162 ) or (resid 286 through 287))CL - P5 - 461
1515chain 'C' and (resid 47 through 96 )CL47 - 9646 - 97
1616chain 'C' and (resid 97 through 111 )CL97 - 11198 - 112
1717chain 'C' and (resid 163 through 192 )CL163 - 192164 - 193
1818chain 'C' and (resid 193 through 242 )CL193 - 242194 - 245
1919chain 'C' and ((resid 243 through 283 ) or (resid 284 through 285))CL - N243 - 283246
2020chain 'D' and (resid 15 through 49 )DQ15 - 491 - 37
2121chain 'D' and ((resid 50 through 180 ) or (resid 433 through 495 ) or (resid 500 through 504))DQ - V50 - 18038
2222chain 'D' and (resid 181 through 219 )DQ181 - 219171 - 209
2323chain 'D' and (resid 220 through 262 )DQ220 - 262210 - 254
2424chain 'D' and (resid 263 through 329 )DQ263 - 329255 - 323
2525chain 'D' and (resid 330 through 395 )DQ330 - 395324 - 391
2626chain 'D' and (resid 396 through 432 )DQ396 - 432392 - 428

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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