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- PDB-6z9g: Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibri... -

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基本情報

登録情報
データベース: PDB / ID: 6z9g
タイトルStructure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Oxygen gas - structure G491A-O2
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 complex / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / cell envelope / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding ...cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase activity / anaerobic respiration / cell envelope / 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 / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / 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 / Nickel-dependent hydrogenases large subunit signature 1. / Nickel-dependent hydrogenases large subunit signature 2. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / 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 / Orthogonal Bundle / Mainly Alpha
類似検索 - ドメイン・相同性
oxygen-damaged SF4 / CARBONMONOXIDE-(DICYANO) IRON / : / HYDROSULFURIC ACID / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFe] hydrogenase large subunit / 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: 1.76 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3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
E: Periplasmic [NiFeSe] hydrogenase, small subunit
F: Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing
G: Periplasmic [NiFeSe] hydrogenase, small subunit
H: 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)341,54144
ポリマ－334,5078
非ポリマー7,03436
水17,042946
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)85,38511
ポリマ－83,6272
非ポリマー1,7599
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)85,38511
ポリマ－83,6272
非ポリマー1,7599
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Periplasmic [NiFeSe] hydrogenase, small subunit
F: 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)85,38511
ポリマ－83,6272
非ポリマー1,7599
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Periplasmic [NiFeSe] hydrogenase, small subunit
H: 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)85,38511
ポリマ－83,6272
非ポリマー1,7599
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)120.306, 93.815, 126.951
Angle α, β, γ (deg.)90.000, 105.201, 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 7 through 20 or resid 22...
d_2ens_1(chain "C" and (resid 7 through 20 or resid 22...
d_3ens_1(chain "E" and (resid 7 through 20 or resid 22...
d_4ens_1(chain "G" and (resid 7 through 20 or resid 22...
d_1ens_2(chain "B" and (resid 15 through 74 or resid 76...
d_2ens_2(chain "D" and (resid 15 through 74 or resid 76...
d_3ens_2(chain "F" and (resid 15 through 74 or resid 76...
d_4ens_2(chain "H" and (resid 15 through 74 or resid 76...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGGLYA1 - 14
d_12ens_1SERSERA17
d_13ens_1VALALAA20 - 54
d_14ens_1GLUILEA58 - 75
d_15ens_1GLYPROA78 - 241
d_16ens_1THRALAA245 - 285
d_17ens_1FS4FS4B
d_18ens_1FS4FS4C
d_21ens_1ARGGLYL1 - 14
d_22ens_1SERSERL17
d_23ens_1VALALAL20 - 54
d_24ens_1GLUILEL58 - 75
d_25ens_1GLYPROL78 - 241
d_26ens_1THRALAL245 - 285
d_27ens_1FS4FS4M
d_28ens_1FS4FS4N
d_31ens_1ARGGLYW1 - 14
d_32ens_1SERSERW17
d_33ens_1VALALAW20 - 54
d_34ens_1GLUILEW58 - 75
d_35ens_1GLYPROW78 - 241
d_36ens_1THRALAW245 - 285
d_37ens_1FS4FS4X
d_38ens_1FS4FS4Y
d_41ens_1ARGGLYG1 - 14
d_42ens_1SERSERG17
d_43ens_1VALALAG20 - 54
d_44ens_1GLUILEG58 - 75
d_45ens_1GLYPROG78 - 241
d_46ens_1THRALAG245 - 285
d_11ens_2GLYILEF1 - 60
d_12ens_2GLYGLYF63
d_13ens_2VALTYRF65 - 150
d_14ens_2GLUVALF154 - 194
d_15ens_2TYRASPF198 - 264
d_16ens_2PROTYRF268 - 378
d_17ens_2LEUPROF382 - 484
d_18ens_2LEULEUF488
d_19ens_2ALAHISF492 - 496
d_110ens_2FCOFCOG
d_111ens_2FE2FE2I
d_21ens_2GLYILEQ1 - 60
d_22ens_2GLYGLYQ63
d_23ens_2VALTYRQ65 - 150
d_24ens_2GLUVALQ154 - 194
d_25ens_2TYRASPQ196 - 262
d_26ens_2PROTYRQ266 - 376
d_27ens_2LEUPROQ380 - 482
d_28ens_2LEULEUQ486
d_29ens_2ALAHISQ490 - 494
d_31ens_2GLYILEF1 - 60
d_32ens_2GLYGLYF63
d_33ens_2VALTYRF65 - 150
d_34ens_2GLUVALF154 - 194
d_35ens_2TYRASPF198 - 264
d_36ens_2PROTYRF268 - 378
d_37ens_2LEUPROF382 - 484
d_38ens_2LEULEUF488
d_39ens_2ALAHISF492 - 496
d_41ens_2GLYILEH1 - 60
d_42ens_2GLYGLYH63
d_43ens_2VALTYRH65 - 150
d_44ens_2GLUVALH154 - 194
d_45ens_2TYRASPH196 - 262
d_46ens_2PROTYRH266 - 376
d_47ens_2LEUPROH380 - 482
d_48ens_2LEULEUH486
d_49ens_2ALAHISH490 - 494

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.994268599537, -0.106529527578, -0.00902284477874), (0.106786185731, 0.993641298596, 0.0356886573341), (0.00516357539729, -0.0364476265253, 0.999322224315)43.6514406623, 8.86111628448, 62.018994567
2given(0.991138853673, -0.112062862342, 0.0713140071967), (0.106361238448, 0.991162015892, 0.0792789077122), (-0.0795679564561, -0.0709913595862, 0.994298329059)-7.89222256592, 13.521029641, 57.3504343573
3given(0.973249880701, -0.221145698909, 0.0622836220024), (0.214351159034, 0.971594018424, 0.10029279128), (-0.0826937140065, -0.0842593805836, 0.993006599398)68.3435070572, 21.4227746779, -4.03878454569
4given(0.994387660406, -0.105723650206, -0.00396113873801), (0.105794426133, 0.993958811312, 0.0292133670661), (0.000848664950427, -0.029468478129, 0.999565349822)44.1483641572, 8.14377975763, 61.7855365001
5given(0.991318952371, -0.107980803671, 0.0750125370153), (0.102253613417, 0.991819576757, 0.0764076285716), (-0.0826494598538, -0.0680740273473, 0.994250971127)-7.61032652436, 12.9832628313, 57.1497952946
6given(0.973964689103, -0.215234750104, 0.0711813650305), (0.207748448363, 0.973081588242, 0.0997637450565), (-0.0907379004737, -0.0823785468003, 0.992461791932)69.3734293801, 20.9745638649, -4.49728044302

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要素

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Periplasmic [NiFeSe] hydrogenase, ... , 2種, 8分子 ACEGBDFH

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


分子量: 30261.568 Da / 分子数: 4 / 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)
株: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / 遺伝子: hysB, DVU_1917
発現宿主: Desulfovibrio vulgaris str. Hildenborough (バクテリア)
参照: UniProt: Q72AS4, ferredoxin hydrogenase
#2: タンパク質
Periplasmic [NiFeSe] hydrogenase, large subunit, selenocysteine-containing


分子量: 53365.086 Da / 分子数: 4 / Mutation: G491A / 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)
株: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / 遺伝子: hysA, DVU_1918
発現宿主: Desulfovibrio vulgaris str. Hildenborough (バクテリア)
参照: UniProt: Q72AS3, ferredoxin hydrogenase

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非ポリマー , 8種, 982分子

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


分子量: 351.640 Da / 分子数: 12 / 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: 4 / 由来タイプ: 合成 / 式: Fe4O2S4
#5: 化合物
ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


分子量: 135.890 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C3FeN2O
#6: 化合物
ChemComp-NI / NICKEL (II) ION


分子量: 58.693 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Ni
#7: 化合物
ChemComp-FE2 / FE (II) ION


分子量: 55.845 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Fe
#8: 化合物
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / 硫化水素


分子量: 34.081 Da / 分子数: 4 / 由来タイプ: 合成 / 式: H2S
#9: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Cl
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 946 / 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N

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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→74.48 Å / Num. obs: 189459 / % possible obs: 70.4 % / 冗長度: 4.5 % / Biso Wilson estimate: 25.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.06 / Net I/σ(I): 7.4
反射 シェル解像度: 1.76→1.93 Å / 冗長度: 3.9 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8187 / CC1/2: 0.676 / Rpim(I) all: 0.459 / % possible all: 12.7

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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: 1.76→61.2 Å / SU ML: 0.2234 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 27.7786
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|-|Fc| maps and occupancy factors were refined for disordered ...詳細: Hydrogen atoms were included in calculated positions, solvent molecules were added manually in COOT using 2|Fo|-|Fc| and |Fo|-|Fc| maps and occupancy factors were refined for disordered residues; TLS rigid body refinement of atomic displacement parameters were refined; Non-crystallographic symmetry restraints were used and weight optimization was applied to lower the gap between the R-factor and the R-free.
Rfactor反射数%反射
Rfree0.2397 9477 5.01 %
Rwork0.192 179842 -
obs0.1944 189319 70.29 %
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: 26.77 Å2
精密化ステップサイクル: LAST / 解像度: 1.76→61.2 Å
タンパク質核酸リガンド溶媒全体
原子数23300 0 180 946 24426
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.005824342
X-RAY DIFFRACTIONf_angle_d0.945533146
X-RAY DIFFRACTIONf_chiral_restr0.05463610
X-RAY DIFFRACTIONf_plane_restr0.00574296
X-RAY DIFFRACTIONf_dihedral_angle_d13.97079082
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.369083439744
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.360289792437
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.452066575521
ens_2d_2FX-RAY DIFFRACTIONTorsion NCS0.37736445159
ens_2d_3FX-RAY DIFFRACTIONTorsion NCS0.326626159852
ens_2d_4FX-RAY DIFFRACTIONTorsion NCS0.417596874406
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.3998200.3657272X-RAY DIFFRACTION3.28
1.78-1.80.2184200.3498406X-RAY DIFFRACTION4.78
1.8-1.820.3381190.3207541X-RAY DIFFRACTION6.24
1.82-1.850.3877430.301777X-RAY DIFFRACTION9.19
1.85-1.870.3685520.31051253X-RAY DIFFRACTION14.58
1.87-1.90.2977810.29111714X-RAY DIFFRACTION20.15
1.9-1.920.32191240.29292274X-RAY DIFFRACTION26.66
1.92-1.950.28941600.28973010X-RAY DIFFRACTION35.48
1.95-1.980.30621900.27073637X-RAY DIFFRACTION42.92
1.98-2.010.29962370.26884455X-RAY DIFFRACTION52.54
2.01-2.050.30212680.25345394X-RAY DIFFRACTION63.25
2.05-2.090.29652930.25016206X-RAY DIFFRACTION72.23
2.09-2.130.27953440.2447033X-RAY DIFFRACTION82.92
2.13-2.170.28354090.23477897X-RAY DIFFRACTION92.79
2.17-2.220.30434530.22848400X-RAY DIFFRACTION98.61
2.22-2.270.27624510.21798508X-RAY DIFFRACTION99.53
2.27-2.330.27914230.21488441X-RAY DIFFRACTION99.76
2.33-2.390.2574470.21148531X-RAY DIFFRACTION99.67
2.39-2.460.24664750.20648459X-RAY DIFFRACTION99.7
2.46-2.540.25255110.19698435X-RAY DIFFRACTION99.61
2.54-2.630.25064690.18948449X-RAY DIFFRACTION99.52
2.63-2.730.25624850.19368454X-RAY DIFFRACTION99.52
2.73-2.860.24534330.19538496X-RAY DIFFRACTION99.43
2.86-3.010.23434650.19488463X-RAY DIFFRACTION99.16
3.01-3.20.26274110.19358422X-RAY DIFFRACTION98.62
3.2-3.440.2233890.18257905X-RAY DIFFRACTION91.77
3.44-3.790.22024810.16228147X-RAY DIFFRACTION95.95
3.79-4.340.18594360.1458599X-RAY DIFFRACTION99.88
4.34-5.470.18324450.14298661X-RAY DIFFRACTION99.89
5.47-61.20.21034430.17928603X-RAY DIFFRACTION98.07
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)
10.103057480970.04225061820170.03504723228520.05931352081090.03607244622320.230335515026-0.0275439953247-0.0720093001565-0.03402226394740.0370564804199-0.0560873864364-0.04026102467940.316115706408-0.106147021021-0.351355511060.205687997136-0.03066810386780.009348146243060.08354947521850.02042093630240.103780570084-51.21889559557.0576777589-98.6946260454
20.06901977499550.01501624358120.007516422606020.07770637771120.02831180452210.00876377457180.01276566443-0.008881406942450.01356755805690.0510453391921-0.0527983737660.1065687668770.102381372586-0.191385071236-0.1319247102920.0556318299564-0.1604712481020.03903993096430.3370138237720.003466106096940.106355092605-64.989083026311.038808196-117.64030553
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460.006062033987870.010090449987-0.01556311704480.0172604501612-0.02580623115460.03944045904830.0327758472591-0.02445127595390.00831678571374-0.0219328000699-0.0440746997149-0.0180012709096-0.1317720364630.1061924440380.01124550666590.152557939533-0.0175117554691-0.00995462491370.1016135575160.01428516076290.06566122408317.016286844416.4726992842-130.982584333
470.045493447803-0.02344116986480.05666732647270.0517094853021-0.01988501208920.06607931924130.0470418618206-0.06815137224340.01895376737810.0903791761551-0.11743346623-0.0271961056756-0.1366264319090.250781917472-0.06639421093180.203314157243-0.126462032217-0.01354711657710.2622306013920.02018056738220.10868131478128.269666888517.8428748672-107.972656266
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 7 through 147 )AA7 - 1471 - 147
22chain 'A' and (resid 148 through 283 )AA148 - 283148 - 285
33chain 'B' and (resid 15 through 219 )BF15 - 2191 - 211
44chain 'B' and (resid 220 through 252 )BF220 - 252212 - 244
55chain 'B' and (resid 253 through 305 )BF253 - 305245 - 299
66chain 'B' and (resid 306 through 495 )BF306 - 495300 - 496
77chain 'C' and (resid 7 through 46 )CL7 - 461 - 43
88chain 'C' and (resid 47 through 96 )CL47 - 9644 - 96
99chain 'C' and (resid 97 through 111 )CL97 - 11197 - 111
1010chain 'C' and (resid 112 through 162 )CL112 - 162112 - 162
1111chain 'C' and (resid 163 through 192 )CL163 - 192163 - 192
1212chain 'C' and (resid 193 through 283 )CL193 - 283193 - 285
1313chain 'D' and (resid 15 through 151 )DQ15 - 1511 - 139
1414chain 'D' and (resid 152 through 219 )DQ152 - 219140 - 209
1515chain 'D' and (resid 220 through 262 )DQ220 - 262210 - 252
1616chain 'D' and (resid 263 through 329 )DQ263 - 329253 - 321
1717chain 'D' and (resid 330 through 432 )DQ330 - 432322 - 426
1818chain 'D' and (resid 433 through 495 )DQ433 - 495427 - 494
1919chain 'E' and (resid 7 through 46 )EW7 - 461 - 43
2020chain 'E' and (resid 47 through 67 )EW47 - 6744 - 66
2121chain 'E' and (resid 68 through 111 )EW68 - 11167 - 111
2222chain 'E' and (resid 112 through 162 )EW112 - 162112 - 162
2323chain 'E' and (resid 163 through 192 )EW163 - 192163 - 192
2424chain 'E' and (resid 193 through 258 )EW193 - 258193 - 260
2525chain 'E' and (resid 259 through 283 )EW259 - 283261 - 285
2626chain 'F' and (resid 15 through 49 )FF15 - 491 - 35
2727chain 'F' and (resid 50 through 252 )FF50 - 25236 - 244
2828chain 'F' and (resid 253 through 305 )FF253 - 305245 - 299
2929chain 'F' and (resid 306 through 395 )FF306 - 395300 - 391
3030chain 'F' and (resid 396 through 432 )FF396 - 432392 - 428
3131chain 'F' and (resid 433 through 495 )FF433 - 495429 - 496
3232chain 'G' and (resid 7 through 46 )GG7 - 461 - 43
3333chain 'G' and (resid 47 through 67 )GG47 - 6744 - 66
3434chain 'G' and (resid 68 through 96 )GG68 - 9667 - 96
3535chain 'G' and (resid 97 through 162 )GG97 - 16297 - 162
3636chain 'G' and (resid 163 through 192 )GG163 - 192163 - 192
3737chain 'G' and (resid 193 through 262 )GG193 - 262193 - 264
3838chain 'G' and (resid 263 through 283 )GG263 - 283265 - 285
3939chain 'H' and (resid 15 through 49 )HH15 - 491 - 35
4040chain 'H' and (resid 50 through 124 )HH50 - 12436 - 112
4141chain 'H' and (resid 125 through 180 )HH125 - 180113 - 170
4242chain 'H' and (resid 181 through 219 )HH181 - 219171 - 209
4343chain 'H' and (resid 220 through 252 )HH220 - 252210 - 242
4444chain 'H' and (resid 253 through 329 )HH253 - 329243 - 321
4545chain 'H' and (resid 330 through 395 )HH330 - 395322 - 389
4646chain 'H' and (resid 396 through 432 )HH396 - 432390 - 426
4747chain 'H' and (resid 433 through 495 )HH433 - 495427 - 494

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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