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- PDB-8rja: Crystal structure of the F420-reducing formylmethanofuran dehydro... -

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基本情報

登録情報
データベース: PDB / ID: 8rja
タイトルCrystal structure of the F420-reducing formylmethanofuran dehydrogenase complex from the ethanotroph Candidatus Ethanoperedens thermophilum
要素
  • (Formylmethanofuran dehydrogenase subunit ...) x 3
  • Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
  • NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
  • formylmethanofuran dehydrogenase
キーワードOXIDOREDUCTASE / Anaerobic oxidoreductase / Formylmethanofuran dehydrogenase / F420 reductase / Anaerobic ethane oxidation / formate dehydrogenase / tungstopterin / CO2 / gas channel / metalloprotein.
機能・相同性
機能・相同性情報


NADH dehydrogenase (quinone) / allantoinase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / allantoinase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / methanogenesis, from carbon dioxide / methanogenesis / molybdopterin cofactor binding / transition metal ion binding ...NADH dehydrogenase (quinone) / allantoinase / formylmethanofuran dehydrogenase / formylmethanofuran dehydrogenase activity / allantoinase activity / oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor / methanogenesis, from carbon dioxide / methanogenesis / molybdopterin cofactor binding / transition metal ion binding / iron-sulfur cluster binding / oxidoreductase activity
類似検索 - 分子機能
Formylmethanofuran dehydrogenase, subunit D / Formylmethanofuran dehydrogenase, subunit B / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus ...Formylmethanofuran dehydrogenase, subunit D / Formylmethanofuran dehydrogenase, subunit B / Formylmethanofuran dehydrogenase, subunit A / Formylmethanofuran dehydrogenase subunit C / Glutamate synthase, alpha subunit, C-terminal domain superfamily / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal / Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal / Oxidoreductase FRHB/FDHB/HCAR-like / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Amidohydrolase 3 / Amidohydrolase family / : / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Metal-dependent hydrolase, composite domain superfamily / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Metal-dependent hydrolase / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
類似検索 - ドメイン・相同性
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / Chem-MGD / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / : / Formylmethanofuran dehydrogenase subunit A / formylmethanofuran dehydrogenase / NAD(P)H-quinone oxidoreductase subunit I, chloroplastic ...ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / Chem-MGD / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / : / Formylmethanofuran dehydrogenase subunit A / formylmethanofuran dehydrogenase / NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus / Formylmethanofuran dehydrogenase subunit B / Formylmethanofuran dehydrogenase subunit D
類似検索 - 構成要素
生物種Candidatus Methanoperedenaceae archaeon GB50 (古細菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.97 Å
データ登録者Lemaire, O.N. / Wagner, T.
資金援助 ドイツ, 2件
組織認可番号国
Max Planck Society ドイツ
German Research Foundation (DFG)WA 4053/2-1 ドイツ
引用ジャーナル: Nat Commun / 年: 2024
タイトル: Ethane-oxidising archaea couple CO 2 generation to F 420 reduction.
著者: Lemaire, O.N. / Wegener, G. / Wagner, T.
履歴
登録2023年12月20日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年10月2日Provider: repository / タイプ: Initial release
改定 1.12025年4月16日Group: Database references / Structure summary
カテゴリ: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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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: Formylmethanofuran dehydrogenase subunit A
B: Formylmethanofuran dehydrogenase subunit B
C: formylmethanofuran dehydrogenase
D: Formylmethanofuran dehydrogenase subunit D
E: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
F: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
G: Formylmethanofuran dehydrogenase subunit A
H: Formylmethanofuran dehydrogenase subunit B
I: formylmethanofuran dehydrogenase
J: Formylmethanofuran dehydrogenase subunit D
K: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
L: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)412,53679
ポリマ－399,49512
非ポリマー13,04167
水41,1102282
1
A: Formylmethanofuran dehydrogenase subunit A
B: Formylmethanofuran dehydrogenase subunit B
C: formylmethanofuran dehydrogenase
J: Formylmethanofuran dehydrogenase subunit D
K: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
L: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)206,18137
ポリマ－199,7486
非ポリマー6,43331
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area29430 Å2
ΔGint-325 kcal/mol
Surface area58890 Å2
手法PISA
2
D: Formylmethanofuran dehydrogenase subunit D
E: Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
F: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
G: Formylmethanofuran dehydrogenase subunit A
H: Formylmethanofuran dehydrogenase subunit B
I: formylmethanofuran dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)206,35542
ポリマ－199,7486
非ポリマー6,60836
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area30430 Å2
ΔGint-325 kcal/mol
Surface area58100 Å2
手法PISA
単位格子
Length a, b, c (Å)107.627, 135.636, 149.902
Angle α, β, γ (deg.)90.00, 90.49, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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Formylmethanofuran dehydrogenase subunit ... , 3種, 6分子 AGBHDJ

#1: タンパク質 Formylmethanofuran dehydrogenase subunit A


分子量: 62582.125 Da / 分子数: 2 / 由来タイプ: 天然
詳細: The lysine at position 180 is modified into carboxylysine, as in other homologs.
由来: (天然) Candidatus Methanoperedenaceae archaeon GB50 (古細菌)
参照: UniProt: A0A7R9MYH2, allantoinase
#2: タンパク質 Formylmethanofuran dehydrogenase subunit B


分子量: 47081.023 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Candidatus Methanoperedenaceae archaeon GB50 (古細菌)
参照: UniProt: A0A7R9R4U5
#4: タンパク質 Formylmethanofuran dehydrogenase subunit D


分子量: 13536.473 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Candidatus Methanoperedenaceae archaeon GB50 (古細菌)
参照: UniProt: A0A7R9R4V6, formylmethanofuran dehydrogenase

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タンパク質 , 3種, 6分子 CIEKFL

#3: タンパク質 formylmethanofuran dehydrogenase


分子量: 27015.598 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Candidatus Methanoperedenaceae archaeon GB50 (古細菌)
参照: UniProt: A0A7R9MYM1, formylmethanofuran dehydrogenase
#5: タンパク質 Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus


分子量: 40467.078 Da / 分子数: 2 / 由来タイプ: 天然
詳細: The 8 last residues cannot be reliably modeled in the density.
由来: (天然) Candidatus Methanoperedenaceae archaeon GB50 (古細菌)
参照: UniProt: A0A7R9N9K9
#6: タンパク質 NAD(P)H-quinone oxidoreductase subunit I, chloroplastic


分子量: 9065.233 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Candidatus Methanoperedenaceae archaeon GB50 (古細菌)
参照: UniProt: A0A7R9MZV2, NADH dehydrogenase (quinone)

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非ポリマー , 15種, 2349分子

#7: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn / タイプ: SUBJECT OF INVESTIGATION
#8: 化合物 ChemComp-PEG / DI(HYDROXYETHYL)ETHER


分子量: 106.120 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C4H10O3
#9: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C3H8O3
#10: 化合物
ChemComp-ACT / ACETATE ION


分子量: 59.044 Da / 分子数: 5 / 由来タイプ: 合成 / 式: C2H3O2
#11: 化合物 ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


分子量: 354.436 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C16H34O8 / コメント: 沈殿剤*YM
#12: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


分子量: 62.068 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C2H6O2
#13: 化合物
ChemComp-CL / CHLORIDE ION


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Cl
#14: 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 / タイプ: SUBJECT OF INVESTIGATION
#15: 化合物 ChemComp-W / TUNGSTEN ION


分子量: 183.840 Da / 分子数: 2 / 由来タイプ: 合成 / 式: W / タイプ: SUBJECT OF INVESTIGATION
#16: 化合物
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


分子量: 740.557 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C20H26N10O13P2S2 / タイプ: SUBJECT OF INVESTIGATION
#17: 化合物 ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


分子量: 34.081 Da / 分子数: 2 / 由来タイプ: 合成 / 式: H2S / タイプ: SUBJECT OF INVESTIGATION
#18: 化合物 ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


分子量: 785.550 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C27H33N9O15P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: FAD*YM
#19: 化合物
ChemComp-NA / SODIUM ION


分子量: 22.990 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Na
#20: 化合物 ChemComp-PG4 / TETRAETHYLENE GLYCOL


分子量: 194.226 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H18O5 / コメント: 沈殿剤*YM
#21: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2282 / 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
Has protein modificationY

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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: 2.97 Å3/Da / 溶媒含有率: 58.67 % / 解説: Brown brick
結晶化温度: 293.15 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: Crystals were obtained by initial screening at 20 degrees Celsius using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The crystallization ...詳細: Crystals were obtained by initial screening at 20 degrees Celsius using the sitting drop method on a 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 ul of mother liquor, the crystallization drop contained a mixture of 0.6 ul protein at 4.64 mg.ml-1 and 0.6 ul precipitant. The protein was in 25 mM Tris/HCl buffer pH 7.6, 10 % (v/v) glycerol, 2 mM DTT, 1 mM FAD and 1 mM FMN. The crystal was obtained in a Coy tent under an N2/H2 atmosphere (96:4 %). The crystallization reservoir contained 200 mM sodium acetate trihydrate, 100 mM sodium cacodylate, pH 6.5, and 18 % (w/v) polyethylene glycol 8,000. The crystal was soaked in the crystallization solution supplemented with 30 % (v/v) glycerol before freezing in liquid nitrogen.

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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: X06DA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2020年3月21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: 1.97→57.38 Å / Num. obs: 167948 / % possible obs: 93 % / 冗長度: 7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.101 / Rrim(I) all: 0.271 / Net I/σ(I): 7.2
反射 シェル解像度: 1.973→2.187 Å / 冗長度: 6.9 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8397 / CC1/2: 0.621 / Rpim(I) all: 0.486 / Rrim(I) all: 1.296 / % possible all: 64.3

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.20.1_4487: ???)精密化
autoPROCデータ削減
autoPROCデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 1.97→57.38 Å / SU ML: 0.2 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 22.73 / 立体化学のターゲット値: ML
詳細: The last refinement steps were performed by refining with a translation libration screw (TLS) with hydrogens modelled in the riding position. Hydrogens were omitted in the final deposited model.
Rfactor反射数%反射
Rfree0.21 8349 4.97 %
Rwork0.1757 --
obs0.1774 167913 55.67 %
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: 25.29 Å2
精密化ステップサイクル: LAST / 解像度: 1.97→57.38 Å
タンパク質核酸リガンド溶媒全体
原子数27648 0 581 2282 30511
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.339
X-RAY DIFFRACTIONf_dihedral_angle_d14.7810797
X-RAY DIFFRACTIONf_chiral_restr0.0874358
X-RAY DIFFRACTIONf_plane_restr0.0054996
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-20.626810.233656X-RAY DIFFRACTION1
2-2.020.3203160.2601263X-RAY DIFFRACTION3
2.02-2.040.3403280.2466503X-RAY DIFFRACTION5
2.04-2.070.2769390.2347700X-RAY DIFFRACTION7
2.07-2.10.2692590.24311115X-RAY DIFFRACTION12
2.1-2.130.2627810.24651502X-RAY DIFFRACTION16
2.13-2.160.3082970.2361777X-RAY DIFFRACTION19
2.16-2.190.21891190.23412125X-RAY DIFFRACTION22
2.19-2.220.27891290.23732488X-RAY DIFFRACTION26
2.22-2.260.29151370.23732861X-RAY DIFFRACTION30
2.26-2.30.24741530.23613346X-RAY DIFFRACTION35
2.3-2.340.26141990.24353835X-RAY DIFFRACTION40
2.34-2.380.25572360.22914142X-RAY DIFFRACTION44
2.38-2.430.25722210.2234629X-RAY DIFFRACTION48
2.43-2.490.27162810.2284984X-RAY DIFFRACTION53
2.49-2.540.27163050.22965488X-RAY DIFFRACTION58
2.54-2.610.25673240.21745891X-RAY DIFFRACTION62
2.61-2.680.25673720.21746309X-RAY DIFFRACTION67
2.68-2.760.23273240.21316942X-RAY DIFFRACTION72
2.76-2.850.27184060.20417284X-RAY DIFFRACTION77
2.85-2.950.23863740.19577927X-RAY DIFFRACTION83
2.95-3.060.23974680.19078719X-RAY DIFFRACTION91
3.07-3.20.22274940.1889435X-RAY DIFFRACTION99
3.2-3.370.22524620.1689578X-RAY DIFFRACTION100
3.37-3.580.1975190.15189527X-RAY DIFFRACTION100
3.58-3.860.18244490.14149616X-RAY DIFFRACTION100
3.86-4.250.16975160.12619568X-RAY DIFFRACTION100
4.25-4.860.13775460.11799553X-RAY DIFFRACTION100
4.86-6.130.16964900.1549642X-RAY DIFFRACTION100
6.13-57.380.20235040.19559759X-RAY DIFFRACTION100
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)
10.43810.11120.14080.54460.08450.5253-0.0493-0.081-0.0062-0.01670.0163-0.10150.01380.12860.01010.05230.03190.00250.11550.01250.135677.074711.787934.6896
20.61910.0225-0.0630.49490.15480.48930.1084-0.21460.17130.1715-0.12340.12620.0258-0.01030.0060.1198-0.03680.05720.1886-0.06310.145161.710210.368359.5093
30.6630.1648-0.13390.42880.05970.4524-0.0018-0.10.16920.0506-0.03930.0356-0.08410.02460.02010.04180.0003-0.00480.0892-0.02850.198468.161424.914642.5836
41.19660.651-0.52071.3806-0.58640.9886-0.0119-0.2912-0.12020.1756-0.1009-0.13540.14060.17050.10920.11510.0317-0.00190.1530.00440.152471.7762-3.475350.7402
53.5706-1.55390.88082.2976-0.06141.6012-0.0934-0.1423-0.38080.124-0.05480.03350.31240.13860.150.13580.01940.06440.13130.02720.204559.8968-25.320644.0366
61.32790.1179-0.99820.9852-0.18411.4953-0.13240.1765-0.4023-0.1559-0.0254-0.06370.2983-0.04020.14460.17610.02590.00650.1331-0.03930.211964.366-26.311818.8425
70.56590.03660.01240.30270.07950.3395-0.0155-0.0777-0.06890.0196-0.07730.18670.0741-0.04010.05950.0624-0.00120.02720.0701-0.03610.177745.0067-7.642236.8656
82.61530.01271.6360.07550.0231.0257-0.0568-0.10240.08010.0745-0.04330.27380.018-0.30140.09490.1312-0.01160.07820.21-0.10830.442824.41023.292440.375
90.55720.0082-0.08740.52380.07040.3892-0.00480.0286-0.0411-0.124-0.05520.11710.05770.00070.06540.0590.01160.010.0666-0.01860.149451.9402-8.073825.2472
100.5841-0.194-0.7350.20750.34811.75220.0261-0.0429-0.0045-0.067-0.0365-0.13220.08980.27660.01830.12110.04370.01430.14020.00890.166269.1211-14.678128.7706
111.1844-0.02090.68180.3031-0.85862.7650.10750.39310.1405-0.61650.01230.14250.113-0.0974-0.07880.43090.045-0.07420.33920.10520.228255.82847.7093-3.5863
121.2874-0.90860.65982.3005-1.33821.03370.16050.62260.4368-0.6867-0.2964-0.1658-0.22280.17130.0960.47360.02060.02750.3130.09910.272261.734511.7878-4.5368
130.6640.2813-0.77952.4659-1.67391.6861-0.00590.4380.2835-0.4595-0.02860.2171-0.0506-0.0741-0.05920.38460.021-0.11480.21520.05390.25351.137111.8114-2.5214
141.6218-0.04930.15690.1376-0.59472.57540.07650.29880.0699-0.4182-0.02150.1424-0.12840.2074-0.04750.32660.0546-0.08530.18630.03540.188548.909514.10653.1893
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224.306-2.94840.76745.27440.26067.3014-0.1668-0.16630.45080.17380.0624-0.0725-0.4761-0.04630.10240.34940.03730.07630.147-0.10020.35857.250183.194345.6078
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260.9866-1.18940.80493.6231-0.39291.0003-0.1416-0.00650.193-0.00350.0282-0.2424-0.2880.21330.05550.365-0.0546-0.11210.2923-0.1310.522521.316977.052246.5561
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282.1435-0.152-0.97681.00840.16812.70210.13480.2040.095-0.2827-0.07450.0964-0.0061-0.2336-0.06270.17090.12180.01020.206-0.01860.2464-34.647976.083537.5882
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302.3758-1.1188-0.72990.7070.14942.07310.08880.20210.4524-0.0313-0.04630.0668-0.437-0.2985-0.06190.26760.1410.05690.27610.03240.2387-48.618487.075361.8926
311.059-0.4602-0.52181.8566-0.04331.32960.0904-0.07210.3037-0.0874-0.0761-0.0891-0.14650.058-0.03230.20180.10740.00540.2238-0.01450.2301-32.240284.707554.2257
321.07750.0507-0.59581.57890.1521.5781-0.1565-0.0954-0.03210.27360.09920.01260.0817-0.11410.06440.3150.1630.02470.30810.01980.177-46.993475.489169.5245
332.4951-0.13360.13113.06132.22771.9787-0.0229-0.1333-0.53230.29530.12010.03961.15580.0481-0.09410.57940.08070.07290.27780.08640.4564-40.78860.445567.5385
340.5698-1.10830.09383.8962-1.47880.9807-0.0304-0.05480.6798-0.245-0.12750.2687-0.4531-0.41160.16490.42150.20780.0820.3094-0.05060.5481-25.40794.917138.6989
350.67770.04720.52660.0464-0.10510.8786-0.0741-0.06450.27560.040.0669-0.1501-0.1302-0.02670.02310.21220.13260.06730.12730.01130.2439-14.643881.117135.0894
361.19050.2951.21770.23620.27961.62550.18150.1107-0.2139-0.0603-0.0002-0.10920.1270.0769-0.11680.2090.14160.0390.24660.09370.2682-25.790879.075723.7991
373.9495-0.55940.55323.45511.68721.00090.28470.54910.2711-0.5123-0.1084-0.0724-0.2284-0.0405-0.09380.32150.16080.07620.26090.06390.2084-19.76883.681918.5709
381.4128-0.3409-0.40890.09040.11090.13530.02140.03430.26070.01160.0388-0.078-0.1159-0.07430.00890.31680.12080.08930.15670.03040.3414-19.422587.971931.2263
390.79270.8157-0.12732.06570.40291.8716-0.0936-0.24390.43430.08830.09320.0664-0.3256-0.15860.08660.25470.15970.05490.20570.0030.352-21.105385.099641.3911
402.5362-0.3996-0.43531.0645-0.21251.1987-0.05640.3114-0.0847-0.32380.0429-0.29520.07310.02140.0050.1758-0.02020.07090.1374-0.04290.200916.077942.9158-15.88
410.15110.20360.12590.43130.17151.209-0.03470.01620.0538-0.05120.0299-0.0674-0.02090.02450.0090.0556-0.01330.04620.0299-0.01650.18710.54646.280912.8231
420.7016-0.2828-0.10060.20350.2330.42150.0257-0.02270.0978-0.0720.0036-0.026-0.1088-0.0837-0.03560.11020.02240.04530.090.06230.1863-5.891255.44237.9947
430.7999-0.02190.18340.44530.30210.44010.05110.09260.0668-0.0679-0.02440.0834-0.0953-0.2927-0.01420.05830.04470.00260.17810.03230.1205-19.22452.52018.3393
440.4443-0.45780.28441.0777-0.40931.0579-0.1624-0.0079-0.2113-0.0850.0869-0.07910.129-0.2680.04810.0863-0.02810.03120.15840.02640.1603-17.326740.35794.9309
450.42550.0895-0.08531.4024-0.94361.698-0.00470.0643-0.0804-0.0611-0.00460.07860.0143-0.15040.01370.023-0.02080.0150.12530.01060.1725-14.55536.12814.6597
460.2406-0.1399-0.23380.22450.10740.7641-0.03250.0413-0.0496-0.06120.0595-0.00870.0512-0.1398-0.02540.0515-0.03350.0350.10250.0120.1678-6.794335.847311.8544
470.30860.15930.03920.538-0.14770.2197-0.05180.0007-0.20640.0110.0081-0.07290.1772-0.0599-0.03560.1186-0.05440.09410.0345-0.01170.20652.63623.39347.9695
480.57870.167-0.18320.6043-0.25670.8211-0.03950.1314-0.0479-0.12920.0904-0.09770.0727-0.0626-0.05090.1226-0.03260.07250.0861-0.03090.19347.399635.3933-4.7198
491.0876-0.6263-0.23941.01450.53860.65380.05050.13780.1625-0.1215-0.02250.0161-0.2219-0.1176-0.02550.1850.04950.03580.10320.08030.2194-6.643263.69474.4498
500.17420.0470.30470.9098-0.44920.84860.06420.10520.3307-0.187-0.0039-0.1561-0.3914-0.03920.08010.28230.06590.09980.10180.03190.322-3.655282.187922.0947
510.7555-0.0968-0.25270.5230.04230.29110.0688-0.03880.18250.00620.0592-0.2909-0.25340.1284-0.05110.2961-0.0560.0930.1311-0.05360.451221.077580.471128.1216
520.0665-0.01180.02320.2341-0.00230.21450.0143-0.0150.06680.02490.0616-0.0102-0.1794-0.0960.01630.10.1030.080.02220.0140.2116-3.035162.992931.8641
530.3552-0.80320.23313.102-0.0580.32440.0567-0.01050.14760.11710.0478-0.0018-0.1162-0.1076-0.06730.12780.06340.04670.15140.04680.147-10.372554.063447.6929
541.5-0.20721.15550.79160.2662.5519-0.1276-0.2634-0.01640.22050.16480.2732-0.0695-0.4723-0.0190.12890.04940.08030.22130.05440.2325-16.529447.516549.4301
550.1524-0.0338-0.04940.46470.05490.3866-0.02470.00010.19060.01960.078-0.0884-0.12070.0234-0.03510.08080.02410.01190.048-0.00710.23058.781961.329432.9447
560.33270.22220.15920.3675-0.09420.25810.08020.10990.2566-0.17460.0403-0.2192-0.16630.0456-0.06820.2096-0.01450.0850.11120.01410.306213.298271.319317.5558
570.75440.21720.50940.73650.10750.6033-0.22820.01220.23320.21090.1154-0.3494-0.1060.06180.01840.09870.0064-0.04390.114-0.05420.33136.046942.837136.9671
580.9847-1.50560.5072.8071-0.82260.28860.05080.00630.1393-0.2039-0.0942-0.27550.0310.16560.0340.0987-0.00030.04860.1471-0.03010.345539.024139.752931.1632
592.1983-1.2246-0.57191.5665-0.00081.1028-0.0362-0.0699-0.04340.18670.0608-0.090.04460.0526-0.00990.06260.0249-0.02310.1014-0.02110.206527.276137.239940.4529
601.952-0.0735-0.32061.10530.12481.4919-0.1305-0.1194-0.09730.16810.13040.05860.1099-0.0214-0.00870.08940.03770.01210.09630.01630.14811.538637.76846.1101
612.7935-0.12641.55052.1141-0.08712.3911-0.1086-0.4149-0.29860.38130.09370.14760.1696-0.112-0.03830.17940.08640.06560.23640.08910.233-0.909432.760455.3577
625.09991.62631.97220.97260.44432.0251-0.09390.07560.1364-0.2404-0.02080.28360.0162-0.3940.11290.18150.0142-0.10480.1788-0.07310.260628.1612-18.333620.8929
631.4009-1.6049-0.27982.28161.3842.6078-0.056-0.1041-0.07070.0485-0.0851-0.27890.2909-0.00170.12850.1249-0.02660.03750.1002-0.02670.33847.5782-26.575729.2622
643.5494-2.47560.62822.64870.61965.29330.01990.1119-0.6934-0.2571-0.00040.18110.7841-0.4447-0.00670.2234-0.0804-0.00950.1438-0.04780.29343.5534-31.922925.526
650.60660.84190.87725.31410.81385.4264-0.0915-0.2701-0.14360.1973-0.13470.72170.0179-0.50340.20610.2498-0.05770.06830.2397-0.02220.401425.4389-26.083226.1178
662.67711.0497-0.9873.3294-1.01622.00540.1098-0.1731-0.2362-0.0047-0.05540.3107-0.0198-0.3012-0.01770.172-0.0358-0.05010.1834-0.02470.300829.7966-26.431517.8962
671.35810.59520.01091.8658-0.38370.72510.05120.0761-0.1445-0.1467-0.12590.05770.1252-0.12490.04860.1082-0.0154-0.01390.1372-0.06350.21135.0748-20.343620.2888
684.7516-1.23341.92217.0535-1.94035.8633-0.18410.4005-0.1774-0.7772-0.0536-0.28160.19130.08410.22050.3691-0.03670.07220.2501-0.12490.422347.9038-26.654110.1819
693.32390.6035-0.83530.1479-0.33671.11660.2051-0.14880.39170.1092-0.04970.0593-0.24060.1229-0.18180.3779-0.11230.26570.2789-0.09050.458222.8021-15.023767.3776
701.41830.4701-0.39060.3452-0.18640.51550.0688-0.1975-0.13070.1425-0.05950.32670.0268-0.0588-0.04510.2995-0.06820.21520.2437-0.06090.493319.1177-24.901760.8953
710.67480.30330.18840.48550.22780.22420.0912-0.1109-0.10350.11310.02160.1154-0.0059-0.08270.17580.3217-0.08190.24480.26860.0070.69625.3691-36.869164.0896
722.4521-0.0634-0.35380.5744-0.49591.00190.0724-0.1641-0.02790.2473-0.07160.191-0.0044-0.05730.02740.2847-0.06440.1720.2213-0.0220.506514.3584-29.073661.5609
731.87250.2473-0.20620.8209-0.17211.88840.1572-0.0272-0.1780.16630.10680.3268-0.1368-0.4117-0.21630.31880.01150.17710.34370.02540.773-2.9297-25.426159.5599
745.59642.12452.04584.20292.09114.9396-0.14730.10930.9986-0.0813-0.10780.2933-0.8144-0.16690.25770.57970.10670.0940.32670.04420.85490.372-9.991655.323
753.37751.34140.2652.5457-2.11922.5937-0.1739-0.6751-0.66650.4963-0.14570.31140.711-0.07640.28820.4527-0.09830.16990.35310.01060.526737.8923-36.70159.7595
764.3073-1.6859-2.0513.5777-1.4772.7809-0.08410.1348-0.09980.0443-0.26680.1990.1390.00250.26730.1176-0.05160.06080.12010.00420.12243.3073-26.219848.8515
775.8760.73354.07971.18272.08115.3947-0.10710.23270.4183-0.0296-0.1087-0.0487-0.4260.27480.12660.3489-0.02710.1460.25580.08540.281648.5673-21.314863.1804
781.8236-1.243-0.28891.96782.17123.52370.0644-0.2749-0.18840.294-0.0931-0.13020.30240.22030.00980.2266-0.03030.07540.23260.07910.322756.3579-25.221660.3777
796.02191.157-3.61182.0542-2.54058.5455-0.0858-0.0467-0.38280.1909-0.17830.01170.5480.0770.24010.22740.02150.04750.090.03360.233848.91-30.777649.7899
803.1426-1.15791.26110.6669-1.39534.5018-0.2166-0.32-0.6797-0.04650.04890.07680.47560.24860.24340.2784-0.03070.12070.24210.07310.23942.7408-32.990662.0145
811.45440.3684-0.60210.5507-0.46991.30960.0208-0.0686-0.07020.0349-0.106-0.00480.105-0.0590.09580.1649-0.04380.11180.1342-0.01870.29736.3878-24.970951.1004
823.55083.42852.22744.9541.09152.0792-0.1889-0.2774-1.08630.0740.1116-0.12210.9989-0.35080.160.35-0.05420.12210.22390.05450.427133.599-39.541355.5026
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 253 )
3X-RAY DIFFRACTION3chain 'A' and (resid 254 through 502 )
4X-RAY DIFFRACTION4chain 'A' and (resid 503 through 567 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 35 )
6X-RAY DIFFRACTION6chain 'B' and (resid 36 through 77 )
7X-RAY DIFFRACTION7chain 'B' and (resid 78 through 216 )
8X-RAY DIFFRACTION8chain 'B' and (resid 217 through 244 )
9X-RAY DIFFRACTION9chain 'B' and (resid 245 through 389 )
10X-RAY DIFFRACTION10chain 'B' and (resid 390 through 430 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 22 )
12X-RAY DIFFRACTION12chain 'C' and (resid 23 through 61 )
13X-RAY DIFFRACTION13chain 'C' and (resid 62 through 79 )
14X-RAY DIFFRACTION14chain 'C' and (resid 80 through 105 )
15X-RAY DIFFRACTION15chain 'C' and (resid 106 through 143 )
16X-RAY DIFFRACTION16chain 'C' and (resid 144 through 206 )
17X-RAY DIFFRACTION17chain 'C' and (resid 207 through 225 )
18X-RAY DIFFRACTION18chain 'C' and (resid 226 through 239 )
19X-RAY DIFFRACTION19chain 'C' and (resid 240 through 253 )
20X-RAY DIFFRACTION20chain 'D' and (resid 2 through 10 )
21X-RAY DIFFRACTION21chain 'D' and (resid 11 through 24 )
22X-RAY DIFFRACTION22chain 'D' and (resid 25 through 31 )
23X-RAY DIFFRACTION23chain 'D' and (resid 32 through 44 )
24X-RAY DIFFRACTION24chain 'D' and (resid 45 through 86 )
25X-RAY DIFFRACTION25chain 'D' and (resid 87 through 116 )
26X-RAY DIFFRACTION26chain 'D' and (resid 117 through 125 )
27X-RAY DIFFRACTION27chain 'E' and (resid 1 through 43 )
28X-RAY DIFFRACTION28chain 'E' and (resid 44 through 75 )
29X-RAY DIFFRACTION29chain 'E' and (resid 76 through 132 )
30X-RAY DIFFRACTION30chain 'E' and (resid 133 through 163 )
31X-RAY DIFFRACTION31chain 'E' and (resid 164 through 217 )
32X-RAY DIFFRACTION32chain 'E' and (resid 218 through 326 )
33X-RAY DIFFRACTION33chain 'E' and (resid 327 through 351 )
34X-RAY DIFFRACTION34chain 'F' and (resid 5 through 12 )
35X-RAY DIFFRACTION35chain 'F' and (resid 13 through 26 )
36X-RAY DIFFRACTION36chain 'F' and (resid 27 through 34 )
37X-RAY DIFFRACTION37chain 'F' and (resid 35 through 46 )
38X-RAY DIFFRACTION38chain 'F' and (resid 47 through 65 )
39X-RAY DIFFRACTION39chain 'F' and (resid 66 through 81 )
40X-RAY DIFFRACTION40chain 'G' and (resid 2 through 48 )
41X-RAY DIFFRACTION41chain 'G' and (resid 49 through 109 )
42X-RAY DIFFRACTION42chain 'G' and (resid 110 through 159 )
43X-RAY DIFFRACTION43chain 'G' and (resid 160 through 223 )
44X-RAY DIFFRACTION44chain 'G' and (resid 224 through 253 )
45X-RAY DIFFRACTION45chain 'G' and (resid 254 through 286 )
46X-RAY DIFFRACTION46chain 'G' and (resid 287 through 389 )
47X-RAY DIFFRACTION47chain 'G' and (resid 390 through 419 )
48X-RAY DIFFRACTION48chain 'G' and (resid 420 through 502 )
49X-RAY DIFFRACTION49chain 'G' and (resid 503 through 567 )
50X-RAY DIFFRACTION50chain 'H' and (resid 2 through 35 )
51X-RAY DIFFRACTION51chain 'H' and (resid 36 through 77 )
52X-RAY DIFFRACTION52chain 'H' and (resid 78 through 192 )
53X-RAY DIFFRACTION53chain 'H' and (resid 193 through 216 )
54X-RAY DIFFRACTION54chain 'H' and (resid 217 through 244 )
55X-RAY DIFFRACTION55chain 'H' and (resid 245 through 389 )
56X-RAY DIFFRACTION56chain 'H' and (resid 390 through 430 )
57X-RAY DIFFRACTION57chain 'I' and (resid 1 through 22 )
58X-RAY DIFFRACTION58chain 'I' and (resid 23 through 61 )
59X-RAY DIFFRACTION59chain 'I' and (resid 62 through 124 )
60X-RAY DIFFRACTION60chain 'I' and (resid 125 through 206 )
61X-RAY DIFFRACTION61chain 'I' and (resid 207 through 253 )
62X-RAY DIFFRACTION62chain 'J' and (resid 2 through 10 )
63X-RAY DIFFRACTION63chain 'J' and (resid 11 through 24 )
64X-RAY DIFFRACTION64chain 'J' and (resid 25 through 31 )
65X-RAY DIFFRACTION65chain 'J' and (resid 32 through 44 )
66X-RAY DIFFRACTION66chain 'J' and (resid 45 through 58 )
67X-RAY DIFFRACTION67chain 'J' and (resid 59 through 116 )
68X-RAY DIFFRACTION68chain 'J' and (resid 117 through 126 )
69X-RAY DIFFRACTION69chain 'K' and (resid 1 through 22 )
70X-RAY DIFFRACTION70chain 'K' and (resid 23 through 109 )
71X-RAY DIFFRACTION71chain 'K' and (resid 110 through 163 )
72X-RAY DIFFRACTION72chain 'K' and (resid 164 through 234 )
73X-RAY DIFFRACTION73chain 'K' and (resid 235 through 326 )
74X-RAY DIFFRACTION74chain 'K' and (resid 327 through 351 )
75X-RAY DIFFRACTION75chain 'L' and (resid 5 through 12 )
76X-RAY DIFFRACTION76chain 'L' and (resid 13 through 26 )
77X-RAY DIFFRACTION77chain 'L' and (resid 27 through 34 )
78X-RAY DIFFRACTION78chain 'L' and (resid 35 through 46 )
79X-RAY DIFFRACTION79chain 'L' and (resid 47 through 56 )
80X-RAY DIFFRACTION80chain 'L' and (resid 57 through 65 )
81X-RAY DIFFRACTION81chain 'L' and (resid 66 through 75 )
82X-RAY DIFFRACTION82chain 'L' and (resid 76 through 82 )

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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