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- PDB-6q8x: Respiratory complex I from Thermus thermophilus with bound Pyridaben. -

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基本情報

登録情報
データベース: PDB / ID: 6q8x
タイトルRespiratory complex I from Thermus thermophilus with bound Pyridaben.
要素
  • (NADH-quinone oxidoreductase subunit ...) x 15
  • Uncharacterized protein
キーワードMEMBRANE PROTEIN / Respiratory chain / complex I / NADH:ubiquinone oxidoreductase / electron transfer / proton translocation
機能・相同性
機能・相同性情報


トランスロカーゼ; ヒドロンの輸送の触媒; 酸化還元酵素反応を伴う / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase activity / iron-sulfur cluster assembly / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I ...トランスロカーゼ; ヒドロンの輸送の触媒; 酸化還元酵素反応を伴う / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase activity / iron-sulfur cluster assembly / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / ferric iron binding / aerobic respiration / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / iron ion binding / metal ion binding / plasma membrane
類似検索 - 分子機能
Domain of unknown function DUF3197 / TTHA1528-like superfamily / Protein of unknown function (DUF3197) / NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Frataxin/CyaY superfamily / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Soluble ligand binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit ...Domain of unknown function DUF3197 / TTHA1528-like superfamily / Protein of unknown function (DUF3197) / NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Frataxin/CyaY superfamily / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Soluble ligand binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Ubiquitin-like (UB roll) - #600 / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / SLBB domain / Molybdopterin oxidoreductase Fe4S4 domain / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / Molybdopterin oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / de novo design (two linked rop proteins) / Cro/C1-type helix-turn-helix domain / 2Fe-2S iron-sulfur cluster binding domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / : / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Aspartate decarboxylase-like domain superfamily / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
類似検索 - ドメイン・相同性
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Pyridaben / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit 7 / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Pyridaben / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit 7 / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 / NADH-quinone oxidoreductase subunit 9 / NADH-quinone oxidoreductase subunit 10 / NADH-quinone oxidoreductase subunit 11 / NADH-quinone oxidoreductase subunit 12 / NADH-quinone oxidoreductase subunit 13 / NADH-quinone oxidoreductase subunit 14 / Uncharacterized protein / NADH-quinone oxidoreductase subunit 15 / NADH-quinone oxidoreductase subunit 8
類似検索 - 構成要素
生物種Thermus thermophilus (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: 3.508 Å
データ登録者Gutierrez-Fernandez, J. / Minhas, G.S. / Sazanov, L.A.
資金援助 英国, 1件
組織認可番号国
Medical Research Council (United Kingdom)MC_U105674180 英国
引用ジャーナル: Nat Commun / 年: 2020
タイトル: Key role of quinone in the mechanism of respiratory complex I.
著者: Javier Gutiérrez-Fernández / Karol Kaszuba / Gurdeep S Minhas / Rozbeh Baradaran / Margherita Tambalo / David T Gallagher / Leonid A Sazanov /
要旨: Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in ...Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.
履歴
登録2018年12月16日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年9月2日Provider: repository / タイプ: Initial release
改定 1.12024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
改定 1.22024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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
1: NADH-quinone oxidoreductase subunit 1
2: NADH-quinone oxidoreductase subunit 2
3: NADH-quinone oxidoreductase subunit 3
4: NADH-quinone oxidoreductase subunit 4
5: NADH-quinone oxidoreductase subunit 5
6: NADH-quinone oxidoreductase subunit 6
9: NADH-quinone oxidoreductase subunit 9
7: NADH-quinone oxidoreductase subunit 15
W: Uncharacterized protein
A: NADH-quinone oxidoreductase subunit 7
J: NADH-quinone oxidoreductase subunit 10
K: NADH-quinone oxidoreductase subunit 11
L: NADH-quinone oxidoreductase subunit 12
M: NADH-quinone oxidoreductase subunit 13
N: NADH-quinone oxidoreductase subunit 14
H: NADH-quinone oxidoreductase subunit 8
B: NADH-quinone oxidoreductase subunit 1
C: NADH-quinone oxidoreductase subunit 2
D: NADH-quinone oxidoreductase subunit 3
E: NADH-quinone oxidoreductase subunit 4
F: NADH-quinone oxidoreductase subunit 5
G: NADH-quinone oxidoreductase subunit 6
O: NADH-quinone oxidoreductase subunit 9
I: NADH-quinone oxidoreductase subunit 15
X: Uncharacterized protein
P: NADH-quinone oxidoreductase subunit 7
R: NADH-quinone oxidoreductase subunit 10
S: NADH-quinone oxidoreductase subunit 11
T: NADH-quinone oxidoreductase subunit 12
U: NADH-quinone oxidoreductase subunit 13
V: NADH-quinone oxidoreductase subunit 14
Q: NADH-quinone oxidoreductase subunit 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,081,30754
ポリマ－1,074,03832
非ポリマー7,26922
水00
1
1: NADH-quinone oxidoreductase subunit 1
2: NADH-quinone oxidoreductase subunit 2
3: NADH-quinone oxidoreductase subunit 3
4: NADH-quinone oxidoreductase subunit 4
5: NADH-quinone oxidoreductase subunit 5
6: NADH-quinone oxidoreductase subunit 6
9: NADH-quinone oxidoreductase subunit 9
7: NADH-quinone oxidoreductase subunit 15
W: Uncharacterized protein
A: NADH-quinone oxidoreductase subunit 7
J: NADH-quinone oxidoreductase subunit 10
K: NADH-quinone oxidoreductase subunit 11
L: NADH-quinone oxidoreductase subunit 12
M: NADH-quinone oxidoreductase subunit 13
N: NADH-quinone oxidoreductase subunit 14
H: NADH-quinone oxidoreductase subunit 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)540,65427
ポリマ－537,01916
非ポリマー3,63411
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: NADH-quinone oxidoreductase subunit 1
C: NADH-quinone oxidoreductase subunit 2
D: NADH-quinone oxidoreductase subunit 3
E: NADH-quinone oxidoreductase subunit 4
F: NADH-quinone oxidoreductase subunit 5
G: NADH-quinone oxidoreductase subunit 6
O: NADH-quinone oxidoreductase subunit 9
I: NADH-quinone oxidoreductase subunit 15
X: Uncharacterized protein
P: NADH-quinone oxidoreductase subunit 7
R: NADH-quinone oxidoreductase subunit 10
S: NADH-quinone oxidoreductase subunit 11
T: NADH-quinone oxidoreductase subunit 12
U: NADH-quinone oxidoreductase subunit 13
V: NADH-quinone oxidoreductase subunit 14
Q: NADH-quinone oxidoreductase subunit 8
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)540,65427
ポリマ－537,01916
非ポリマー3,63411
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)95.190, 338.640, 263.230
Angle α, β, γ (deg.)90.00, 100.41, 90.00
Int Tables number4
Space group name H-MP1211

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要素

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NADH-quinone oxidoreductase subunit ... , 15種, 30分子 1B2C3D4E5F6G9O7IAPJRKSLTMUNVHQ

#1: タンパク質 NADH-quinone oxidoreductase subunit 1 / NADH dehydrogenase I chain 1 / NDH-1 subunit 1


分子量: 48693.715 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56222, NADH dehydrogenase (quinone)
#2: タンパク質 NADH-quinone oxidoreductase subunit 2 / NADH dehydrogenase I chain 2 / NDH-1 subunit 2


分子量: 20309.162 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56221, NADH dehydrogenase (quinone)
#3: タンパク質 NADH-quinone oxidoreductase subunit 3 / NADH dehydrogenase I chain 3 / NDH-1 subunit 3


分子量: 86656.203 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56223, NADH dehydrogenase (quinone)
#4: タンパク質 NADH-quinone oxidoreductase subunit 4 / NADH dehydrogenase I chain 4 / NDH-1 subunit 4


分子量: 46428.027 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56220, NADH dehydrogenase (quinone)
#5: タンパク質 NADH-quinone oxidoreductase subunit 5 / NADH dehydrogenase I chain 5 / NDH-1 subunit 5


分子量: 23893.254 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56219, NADH dehydrogenase (quinone)
#6: タンパク質 NADH-quinone oxidoreductase subunit 6 / NADH dehydrogenase I subunit 6 / NDH-1 subunit 6


分子量: 20262.564 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56218, NADH dehydrogenase (quinone)
#7: タンパク質 NADH-quinone oxidoreductase subunit 9 / NADH dehydrogenase I subunit 9 / NDH-1 subunit 9


分子量: 20106.309 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56224, NADH dehydrogenase (quinone)
#8: タンパク質 NADH-quinone oxidoreductase subunit 15 / NADH dehydrogenase I chain 15 / NDH-1 subunit 15


分子量: 14812.074 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SKZ7, NADH dehydrogenase (quinone)
#10: タンパク質 NADH-quinone oxidoreductase subunit 7 / NADH dehydrogenase I chain 7 / NDH-1 subunit 7


分子量: 13154.656 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56217, NADH dehydrogenase (quinone)
#11: タンパク質 NADH-quinone oxidoreductase subunit 10 / NADH dehydrogenase I chain 10 / NDH-1 subunit 10


分子量: 18563.330 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56225, NADH dehydrogenase (quinone)
#12: タンパク質 NADH-quinone oxidoreductase subunit 11 / NADH dehydrogenase I chain 11 / NDH-1 subunit 11


分子量: 10002.788 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56226, NADH dehydrogenase (quinone)
#13: タンパク質 NADH-quinone oxidoreductase subunit 12 / NADH dehydrogenase I chain 12 / NDH-1 subunit 12


分子量: 65189.930 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56227, NADH dehydrogenase (quinone)
#14: タンパク質 NADH-quinone oxidoreductase subunit 13 / NADH dehydrogenase I chain 13 / NDH-1 subunit 13


分子量: 49247.117 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56228, NADH dehydrogenase (quinone)
#15: タンパク質 NADH-quinone oxidoreductase subunit 14 / NADH dehydrogenase I chain 14 / NDH-1 subunit 14


分子量: 44463.895 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q56229, NADH dehydrogenase (quinone)
#16: タンパク質 NADH-quinone oxidoreductase subunit 8 / NADH dehydrogenase I subunit 8 / NDH-1 subunit 8


分子量: 41034.523 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q60019, NADH dehydrogenase (quinone)

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タンパク質 , 1種, 2分子 WX

#9: タンパク質 Uncharacterized protein


分子量: 14201.612 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (バクテリア)
株: HB8 / ATCC 27634 / DSM 579 / 参照: UniProt: Q5SI52

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非ポリマー , 4種, 22分子

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


分子量: 351.640 Da / 分子数: 14 / 由来タイプ: 合成 / 式: Fe4S4
#18: 化合物 ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / FMN


分子量: 456.344 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C17H21N4O9P
#19: 化合物
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


分子量: 175.820 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Fe2S2
#20: 化合物 ChemComp-HQK / Pyridaben / ピリダベン


分子量: 364.933 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C19H25ClN2OS / タイプ: SUBJECT OF INVESTIGATION

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詳細

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: 3.89 Å3/Da / 溶媒含有率: 68.34 %
結晶化温度: 296 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6
詳細: 100 mM Bis-Tris pH 6.0, 21% (w/v) PEG 4000, 100 mM KCl, 100 mM glutaric acid and 1.02 mM octyl-maltoside fluorinated

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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: Diamond / ビームライン: I03 / 波長: 0.9 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2013年9月29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: 0.9 Å / 相対比: 1
Reflection twinOperator: -H,-K,H+L / Fraction: 0.49
反射解像度: 3.5→58.41 Å / Num. obs: 195828 / % possible obs: 95.5 % / 冗長度: 2.3 % / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.121 / Net I/σ(I): 5
反射 シェル解像度: 3.5→3.69 Å / 冗長度: 2.1 % / Rmerge(I) obs: 2.364 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 27050 / Rpim(I) all: 1.823 / % possible all: 90.6

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.13rc1_2961: ???)精密化
XDSデータ削減
XSCALE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: 4HEA

4hea


解像度: 3.508→58.41 Å / 交差検証法: FREE R-VALUE / 位相誤差: 21.1
詳細: TLS refinement. Twin refinement. TWINNING INFORMATION: FRACTION: 0.490 OPERATOR: -h,-k,h+l Data cut anisotropically to limits (Angstrom) along a*, b* and c*: 3.5, 4.0, 3.6
Rfactor反射数%反射
Rfree0.2316 1809 1.09 %
Rwork0.215 --
obs0.2185 166363 81.57 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 97.3 Å2
精密化ステップサイクル: LAST / 解像度: 3.508→58.41 Å
タンパク質核酸リガンド溶媒全体
原子数73896 0 238 0 74134
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00576240
X-RAY DIFFRACTIONf_angle_d0.848103986
X-RAY DIFFRACTIONf_dihedral_angle_d6.77844638
X-RAY DIFFRACTIONf_chiral_restr0.04511644
X-RAY DIFFRACTIONf_plane_restr0.00613104
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5152-3.61860.3028260.31341857X-RAY DIFFRACTION11
3.6186-3.73520.3054950.27017257X-RAY DIFFRACTION43
3.7352-3.86850.26221050.253911226X-RAY DIFFRACTION66
3.8685-4.02320.24531410.241314539X-RAY DIFFRACTION87
4.0232-4.2060.2441730.229215965X-RAY DIFFRACTION95
4.206-4.42730.25741770.219915919X-RAY DIFFRACTION95
4.4273-4.7040.2171580.212916120X-RAY DIFFRACTION95
4.704-5.06610.20181890.209316165X-RAY DIFFRACTION96
5.0661-5.57390.22631730.215316458X-RAY DIFFRACTION97
5.5739-6.37580.23721770.216916448X-RAY DIFFRACTION97
6.3758-8.01520.21971420.198716347X-RAY DIFFRACTION97
8.0152-33.89380.23291820.204616150X-RAY DIFFRACTION95
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)
10.4599-0.1052-0.07460.02310.01710.01310.1459-0.07930.28420.0898-0.02370.02520.03420.17730.01411.6151-0.09450.06030.85320.34510.7998-41.408119.5711407.808
20.00680.00730.00220.00820.0020.00060.10190.035-0.10630.00840.071-0.01540.03130.029601.2319-0.0172-0.12531.2110.00560.9285-24.604527.6982398.5132
30.01760.00550.0060.11350.00850.2208-0.0527-0.1066-0.19610.09810.02360.03020.1736-0.0529-0.28620.91220.0116-0.03010.48230.35920.5892-30.027325.8867385.162
40.06150.0214-0.03960.101-0.05450.0437-0.0270.0894-0.02210.1095-0.02190.11530.2953-0.33590.04940.8428-0.37980.00211.39450.12640.3763-44.971531.1438394.7602
50.38270.07290.2170.26960.01110.2436-0.0343-0.24360.3070.1314-0.23050.17780.0359-0.0435-0.59150.7667-0.2788-0.0430.3865-0.09070.5685-39.366432.6787386.0724
6-0.00340.0037-0.01180.0681-0.03930.0719-0.019-0.076-0.020.0383-0.0951-0.02220.03260.0799-1.18280.5082-0.1845-0.13410.25160.17410.1781-48.87027.876387.8183
70.08160.0327-0.13080.0187-0.04850.22190.0258-0.1396-0.04260.0583-0.01780.1031-0.07170.00210.25930.8669-0.15480.02370.24010.26830.6764-58.5545.0421371.5089
80.09310.0488-0.04350.145-0.17380.2083-0.0125-0.1019-0.01710.0237-0.0960.0106-0.03070.1242-0.26690.6017-0.14190.22810.4935-0.10340.2996-52.136149.6655386.3945
90.0076-0.00510.00030.00340.00010.00030.1193-0.0071-0.07130.01510.14560.04720.00010.03220.00180.98060.1963-0.01951.532-0.3370.844-57.651442.5482383.781
100.0003-0.000100.00220.0040.0058-0.12310.03240.23360.0515-0.23210.0022-0.01260.0112-00.6372-0.01110.10750.9988-0.26890.8431-60.181244.3031375.0144
110.0237-0.0141-0.02210.00650.01130.01720.09460.1655-0.1071-0.0190.1342-0.0953-0.01970.09970.00041.003-0.0827-0.05131.0159-0.45621.1814-66.187434.8524381.0852
120.01450.00440.00250.0181-0.01390.0129-0.11420.13710.0437-0.0686-0.01190.00840.19480.205-0.00031.3399-0.30930.00230.74050.19190.8966-66.43919.2832386.9881
130.0893-0.00060.0150.01950.01330.0118-0.02540.0504-0.0748-0.052-0.0298-0.10780.0881-0.00210.00191.2379-0.37890.18550.54150.06180.579-76.306417.561385.3508
140.0067-0.0061-0.00840.00630.00750.01-0.00420.0229-0.00250.0274-0.01790.1247-0.0247-0.04540.00020.7291-0.0084-0.09510.7203-0.02490.6016-79.454529.8411383.0165
150.13050.0655-0.00850.0863-0.00050.0036-0.0275-0.0429-0.0654-0.048-0.0779-0.0533-0.0202-0.0029-0.00931.0142-0.0435-0.09371.44060.11450.412-64.663621.2686388.1314
160.0366-0.02870.00310.1141-0.10440.1153-0.01010.0153-0.0737-0.00260.03920.0643-0.07490.024-0.01321.0256-0.65160.11341.009-0.01340.7923-65.77324.5293394.3192
170.00680.0006-0.00450.00140.00350.0150.0089-0.02150.0179-0.00050.00350.01750.0350.0207-0.0371.2797-0.27610.44491.33860.42230.8954-77.035322.5712396.8601
180.06180.0080.00420.0031-0.00140.0025-0.0389-0.00830.00930.0015-0.06510.0239-0.02330.00370.0021.2399-0.33960.20541.4233-0.24581.6203-73.053532.903402.5719
190.0005-0.0004-0.0024-0.00020.0010.00960.02630.0547-0.04360.0097-0.0497-0.0342-0.02860.1865-0.00011.1032-0.12360.20021.59340.23130.6451-64.03116.3277404.1263
200.0341-0.0138-0.03210.00630.01590.0346-0.07360.0090.2867-0.35550.07620.13350.0366-0.0332-0.70060.7268-0.08160.16110.053-0.05990.7032-39.714320.6672353.5155
210.0479-0.0047-0.02560.02610.0220.02190.04610.08260.1650.01890.03550.0483-0.0132-0.01610.91380.2436-0.15890.26310.3251-0.00260.4735-57.726924.239354.7062
220.20460.06310.12030.12890.11370.39450.1347-0.21830.01580.08420.11350.0715-0.08410.01652.5870.2759-0.29370.23820.0823-0.3370.4963-54.056942.7125345.8388
230.12890.0261-0.08210.16320.02630.05690.00240.02860.0013-0.06080.050.0818-0.0416-0.0847-0.48540.2766-0.1158-0.05330.0833-0.04210.3321-54.352170.5623318.9627
240.07730.00640.05820.13580.07110.08520.0183-0.38350.18570.19760.05030.1126-0.02560.07430.17790.4622-0.03720.15230.4558-0.15550.1536-36.681954.387349.7464
250.1173-0.00250.03150.0413-0.05820.13250.0882-0.12370.00930.2356-0.08420.0392-0.0592-0.1058-0.46420.6525-0.1857-0.12980.1593-0.21610.7939-39.656669.3308346.5665
260.01470.05610.07270.2250.17440.156-0.0771-0.032-0.0135-0.0426-0.05840.14860.0179-0.0414-1.01960.2553-0.02920.20490.0257-0.12260.5365-44.926357.9977324.6337
270.66890.04350.03540.0179-0.04220.2013-0.0504-0.08590.2123-0.0326-0.0736-0.110.006-0.2217-0.61190.1851-0.10110.1720.3247-0.1390.4903-46.464663.9251345.0575
280.01830.00040.00660.00230.00390.0111-0.0350.00090.0488-0.04210.01570.1253-0.018-0.01880.18710.2873-0.18750.1130.2921-0.28270.5082-58.77471.7085355.1277
290.08960.08820.0420.12590.09720.0820.04310.1632-0.17040.15840.0858-0.05180.2330.03111.59910.456-0.16930.1621-0.2165-0.05920.6068-53.21257.7979308.9464
300.0651-0.087-0.03870.10960.04360.0224-0.0361-0.07540.04090.1164-0.11980.04450.0874-0.0762-0.15790.7224-0.1992-0.12410.1519-0.08740.8528-68.6674-1.9625312.5693
310.0782-0.1728-0.07830.50950.21450.13760.10040.1598-0.0211-0.2478-0.11190.04310.0377-0.0757-0.06170.72670.37170.06180.5401-0.24580.7579-47.4064-7.9541296.8921
32-0.0127-0.02020.01450.0625-0.10320.17210.09850.2268-0.22840.0512-0.0501-0.01110.3065-0.00730.30380.8274-0.25480.1229-0.1394-0.20630.9063-51.96151.8763317.1897
330.010.0110.00420.01090.00410.0011-0.0311-0.0542-0.0003-0.0033-0.02190.0507-0.03140.01530.00061.22230.0456-0.1781.77590.01021.6779-22.6914-6.0827320.1087
340.1255-0.0524-0.0250.05830.02090.05940.01-0.00650.0203-0.0540.0205-0.0418-0.00540.054-0.00490.90410.24590.0610.327-0.16450.9591-27.6454.5988323.4633
350.04110.03340.01580.0729-0.00380.0124-0.0392-0.0736-0.03170.00280.02140.0396-0.05910.0559-0.20711.05630.30810.26410.8578-0.36660.9279-21.1452.9418310.5744
360.0041-0.00050.00540.0007-0.00150.017-0.0046-0.04550.04020.03330.0001-0.0023-0.0340.0012-0.14980.41760.1437-0.0660.0752-0.12640.4205-32.383912.3229318.8429
370.05050.05090.06210.22380.01820.0849-0.05050.1561-0.0390.0121-0.0607-0.10560.18220.0128-0.22680.6360.34530.15770.6396-0.18650.8936-33.411-2.3463311.9777
380.09540.073-0.05070.13260.10150.31050.1861-0.01030.0713-0.06150.1128-0.00850.03690.04390.20950.5590.1251-0.23160.2272-0.13590.6863-27.79711.2507311.6146
390.03460.0059-0.01480.0105-0.01440.0501-0.1909-0.00110.0128-0.0157-0.0219-0.041-0.1138-0.0182-0.04950.41260.19320.12160.80540.23910.6185-36.68414.5388304.9527
400.44320.1223-0.01280.1439-0.10880.10370.00750.13540.01080.0058-0.00830.04030.0917-0.02150.04490.54680.07160.35431.0423-0.10930.741-35.861919.7853302.6349
410.02590.03830.02930.05990.02010.0491-0.0206-0.01670.0567-0.14140.01060.0946-0.1038-0.0697-0.29770.7232-0.04870.21670.0177-0.04070.6405-51.763730.6061320.4923
420.06510.0024-0.00190.04860.04090.0347-0.0111-0.0174-0.00050.01480.01130.0014-0.0157-0.0056-0.0660.7262-0.0421-0.00640.09270.07540.6977-43.398926.9258339.1397
430.49220.1687-0.29050.1461-0.00880.4106-0.0322-0.16620.1242-0.00950.1235-0.0231-0.09560.00170.27720.57-0.0989-0.22530.529-0.0970.3339-43.34939.8158340.0479
440.09310.06720.02270.09420.08970.1240.01130.0361-0.15660.0350.0504-0.11420.09750.05050.01960.3855-0.1217-0.04270.3068-0.15270.8217-86.692729.7901289.4616
450.0753-0.02720.02410.1345-0.14390.1602-0.07480.02680.0243-0.0999-0.09260.0032-0.03540.0587-0.47570.65580.2106-0.05020.27080.08830.7261-68.824313.618300.1129
460.27380.1737-0.16970.1133-0.1090.1059-0.17450.2173-0.0715-0.0864-0.03240.0380.0510.0456-0.10820.6295-0.42290.09810.8356-0.0640.4898-73.659514.4471293.8343
470.027-0.0746-0.02780.23480.09450.0375-0.01740.0366-0.1126-0.2814-0.01910.162-0.0277-0.0721-0.35060.53970.0773-0.12530.1227-0.3171.0286-68.40627.0448302.3245
480.0467-0.0047-0.0040.0013-0.00120.00570.02420.0103-0.03250.02810.0006-0.03770.04430.0533-0.18780.66450.0323-0.24860.424-0.26960.6386-73.7102-12.3401290.3182
490.0035-0.0178-0.00280.1116-0.02280.0502-0.0256-0.05560.05070.0499-0.0024-0.0875-0.07930.0586-0.43260.3064-0.2276-0.12230.2926-0.12560.4076-80.67746.4174311.3797
500.19440.04830.03580.0908-0.06620.0793-0.0513-0.018-0.0669-0.08650.03080.171-0.0796-0.04250.28140.531-0.10090.01280.1185-0.01510.6243-78.852121.4894332.2126
510.0201-0.00640.04850.0622-0.07550.17610.0222-0.0933-0.0649-0.05950.09720.0442-0.0069-0.09220.58150.4526-0.16470.09810.25230.28030.5481-67.438827.6045332.7174
520.07740.03570.11550.01770.05050.17340.16140.00120.01580.09380.09250.0573-0.11740.03810.94750.372-0.0864-0.07840.0089-0.00450.435-71.166126.3238332.3843
530.0202-0.0054-0.03360.01490.00040.0485-0.0364-0.0070.041-0.0183-0.10880.0299-0.1656-0.0379-0.13990.4418-0.04150.06370.0714-0.0420.5308-75.480425.4896317.8561
540.09070.0301-0.06160.0216-0.02220.0435-0.0394-0.01550.0303-0.00120.02740.15860.0278-0.0527-0.01420.5823-0.32090.02570.3428-0.05150.7344-85.089721.363318.4832
550.04660.02850.03830.01770.02140.03880.10170.1182-0.0342-0.0723-0.20310.1226-0.0326-0.12790.00060.8656-0.1830.11980.6989-0.19430.643-85.325511.4737327.2927
560.1642-0.11610.14940.1104-0.10750.13670.07440.0507-0.2104-0.09810.0960.0272-0.0154-0.10140.00530.9362-0.41590.39631.60350.18111.2555-84.94524.9017361.2078
570.0373-0.0452-0.0750.30040.06230.5650.01710.07610.0562-0.0826-0.0468-0.0150.2386-0.06780.3870.5793-0.01580.32040.6351-0.18590.5162-76.962324.144350.8158
580.2890.16770.20040.1470.07260.1792-0.08770.04610.05670.0509-0.00850.0478-0.13630.0054-0.54860.6777-0.29910.03180.36720.09550.8549-73.151824.7299360.8912
590.0298-0.0788-0.06160.20190.15120.11250.0359-0.1086-0.0818-0.00770.0808-0.03290.0344-0.09390.1850.4794-0.16840.1780.43840.10990.5084-77.739921.9291371.2568
600.0256-0.01090.0090.0043-0.0030.00460.06330.00650.0929-0.09660.0702-0.0104-0.06570.0506-0.04290.37980.04030.12520.7699-0.01230.479-79.623636.5537371.5696
610.0022-0.0011-0.00610.0020.00160.01240.0446-0.0246-0.00010.0156-0.10380.05380.0138-0.1191-0.03740.90470.1582-0.00960.6759-0.41040.9546-47.465153.622310.097
620.0857-0.02320.07650.2908-0.05230.0779-0.02780.0955-0.0349-0.0508-0.0376-0.06720.06450.0708-0.32620.51270.13370.12560.0743-0.00020.6093-48.170248.6615299.7431
630.1191-0.0168-0.01980.1327-0.01240.00650.0147-0.0135-0.0442-0.0288-0.05210.0028-0.0222-0.02990.06680.4282-0.20050.16910.9156-0.2750.4826-63.296242.4164311.3409
640.01170.0254-0.00740.0507-0.02130.02310.00840.0412-0.0473-0.0327-0.07390.02990.0675-0.0201-0.27990.556-0.03260.07810.1148-0.20750.5976-49.302547.8779305.6329
650.03520.02-0.02190.0185-0.02050.04150.0069-0.01690.04630.0936-0.06430.12940.0495-0.0439-0.21210.4177-0.12490.05160.0314-0.14380.3656-54.161543.898299.308
660.00640.0080.01030.01420.0070.0316-0.00670.0153-0.0305-0.02760.00490.023-0.01170.0041-0.06130.50770.09210.03050.2247-0.2820.5253-47.836645.0884318.0366
670.00870.0399-0.00010.1859-0.00080.0181-0.0092-0.0174-0.03580.0462-0.03240.01440.04120.0008-0.29280.4127-0.0821-0.12370.0712-0.02990.5436-42.839737.5501312.5172
680.0097-0.0388-0.01060.1450.03040.02090.00070.016-0.01890.0479-0.01610.04560.080.0114-0.40780.20280.089-0.12020.0774-0.17570.3694-58.407438.0412301.0254
690.38420.36230.04060.51990.39420.59850.13920.14310.0226-0.26680.02410.0988-0.1116-0.12891.65710.5368-0.0078-0.22160.4153-0.24720.4285-66.586412.0054265.5118
700.03230.00860.01320.0262-0.02440.04630.0063-0.0520.0340.04980.00510.0027-0.05050.0048-0.00480.8780.05750.04720.4649-0.40050.5674-55.6394-13.0285256.8198
710.0226-0.00220.01490.0040.00180.01720.06580.00730.00670.03-0.2644-0.0505-0.17130.1055-0.0021.0755-0.10860.08820.84190.15780.8381-67.041323.3425247.4849
720.0025-0.0066-0.00080.01150.00550.0012-0.00720.0117-0.00450.01480.0133-0.02460.0134-0.0065-0.07770.50210.16970.1640.4145-0.18180.4897-64.631511.0143253.5204
730.5556-0.0496-0.1890.0462-0.0920.35910.2803-0.23020.07390.389-0.07840.0238-0.34880.1225-0.11481.1687-0.1064-0.05940.34850.05630.6254-49.022925.7673245.4056
740.0137-0.07170.0620.382-0.33510.28930.11470.05380.0485-0.1168-0.33750.12510.0304-0.1817-0.21540.7084-0.036-0.05230.7724-0.16250.2528-61.6545-1.7366242.9223
750.08990.04030.03860.0210.02640.03140.1458-0.11590.0102-0.0733-0.0534-0.0433-0.10160.11910.00291.35360.03990.24010.6939-0.10020.4312-57.807620.387242.1996
760.3757-0.14650.37340.2385-0.25790.44440.03850.19990.0418-0.05530.24290.02590.0551-0.05850.10040.3188-0.04740.0211.2908-0.30020.4985-61.052610.7947241.908
770.29860.0067-0.18920.29510.33260.5023-0.30640.1786-0.1379-0.3470.0051-0.10920.2006-0.1217-0.10650.8653-0.14150.020.2316-0.01690.4691-54.58724.0383248.8119
780.0037-0.00860.00640.0223-0.01760.0140.0481-0.0026-0.0048-0.01750.0452-0.0135-0.00830.0124-0.00141.879-0.03210.0721.8971-0.37611.6206-39.317715.4902261.4263
790.0097-0.003-0.00430.00410.0050.00620.0166-0.02980.00430.01650.02990.03850.03190.01970.00031.0208-0.2731-0.05261.0516-0.23840.9622-32.727318.4471250.1749
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1680.0002-0.0027-0.00370.00470.00340.0042-0.0816-0.1153-0.0155-0.1586-0.2003-0.08440.16130.0074-0.00151.9621-0.12410.80751.65550.01071.4635-107.8527124.6487403.4887
1690.0374-0.0159-0.00170.0070.00340.01880.1713-0.0756-0.11-0.1254-0.1238-0.05620.1579-0.0820.00051.4693-0.1378-0.12880.8425-0.47290.9766-106.8845136.7313408.0077
170-0.0002-0.00010.00040.01290.00850.0057-0.01410.03890.05020.04140.0191-0.0279-0.0093-0.00970.00051.2579-0.04170.05890.8797-0.29590.9111-93.1645127.3455392.7115
1710.0275-0.0119-0.00320.0672-0.03150.07480.01920.1186-0.1014-0.21050.0198-0.07810.13670.1311-0.00621.3581-0.2345-0.33550.58830.01730.6101-114.348598.8017413.467
1720.03630.02090.02140.01010.01280.01180.19710.0712-0.17280.04970.2083-0.0692-0.0062-0.07190.00071.3766-0.45270.40281.8381-0.56481.5099-115.2153111.0717409.6974
1730.00350.0013-0.00640.0005-0.00260.0113-0.0043-0.08170.04810.01130.02150.0216-0.02450.00450.00011.316-0.22390.08290.8773-0.25871.1075-102.6134110.6711398.7679
1740.0042-0.0008-0.00650.0005-0.00090.0125-0.03940.0165-0.02890.0329-0.00380.0210.01390.10710.00041.39850.14220.10111.4096-0.42871.2648-92.044796.1259402.7109
1750.1996-0.18310.10350.1746-0.06270.2473-0.00080.01450.06040.0516-0.0445-0.0127-0.03320.0631-0.04690.3669-0.09850.00590.207-0.11160.4507-100.413496.1136424.2466
1760.0061-0.0065-0.00090.0127-0.00980.01660.04910.1491-0.05050.0207-0.0520.01760.0153-0.10910.00141.3213-0.2346-0.20831.7797-0.13171.0966-121.8918113.576429.4936
1770.1362-0.16480.02330.24170.0620.16830.0850.0070.03450.118-0.07360.0714-0.0186-0.0549-0.3290.97990.16380.10630.5695-0.34950.8575-103.8777128.6458413.1951
1780.2814-0.0203-0.09320.02040.11050.57160.15440.1236-0.0955-0.020.05050.03740.14080.2593-0.01091.16960.06760.11470.3907-0.05060.7884-105.0053101.6396418.5471
1790.22580.2605-0.26030.7175-0.38530.31830.05580.16030.16660.4689-0.21920.2703-0.08920.12910.09791.1073-0.0422-0.16951.0259-0.26960.553-106.2917114.607416.0335
1800.0137-0.00790.00040.0075-0.00360.0035-0.0064-0.0508-0.02410.010.0712-0.0167-0.00710.0302-0.00031.39340.14890.00810.9913-0.04221.1847-86.5891107.5185399.5704
1810.01390.00810.00260.01250.00180.00060.0112-0.0511-0.02170.03840.00540.0214-0.01840.03340.00031.20590.1818-0.01770.74250.08010.7666-80.2966103.1236410.3401
1820.0353-0.0405-0.00040.0323-0.00250.0982-0.02990.4604-0.0306-0.0132-0.00110.0476-0.09960.0057-0.00141.0575-0.0749-0.05310.738-0.1050.9448-25.2411120.9563478.2414
1830.39530.0507-0.1330.1969-0.05220.05430.253-0.05860.1187-0.0565-0.2872-0.0380.2610.3621-0.02970.7469-0.14280.10141.7247-0.09190.446-29.9486102.3094476.5668
1840.0480.0292-0.01490.02140.00140.0080.1703-0.0244-0.03970.34630.1387-0.0110.159-0.0902-0.00011.20620.1021-0.06121.46530.21370.8453-14.164391.7431482.0775
1850.0069-0.00620.00250.0037-0.00490.0121-0.0332-0.12110.06540.0084-0.0753-0.06150.0525-0.02270.00031.0549-0.08960.14741.4237-0.08110.9849-0.5637100.3664474.6062
1860.02080.0238-0.00780.0398-0.02870.0273-0.1070.07470.1446-0.0564-0.1658-0.0057-0.1454-0.0928-0.00371.4765-0.14810.2651.48570.00591.09-24.716598.2846501.5119
1870.0063-0.00330.0179-0.0033-0.00460.05970.17410.2910.0757-0.0941-0.0045-0.2158-0.0207-0.154-0.00021.4773-0.05040.29441.40020.06771.3616-15.174179.6701477.2414
1880.4493-0.20930.0730.53710.19240.58510.15310.02010.0566-0.249-0.35670.1070.05060.149-0.86471.00920.0590.54170.6942-0.08590.9938-70.174698.1179434.5261
1890.0636-0.00610.01970.1433-0.20320.2924-0.32020.17770.11060.0616-0.46470.07240.13880.0734-0.03360.779-0.01830.02110.9001-0.07461.1064-53.476132.6408452.7609
1900.5695-0.5784-0.20871.3679-0.24050.36910.1015-0.61540.40260.1101-0.2817-0.32490.17090.2316-0.25660.5338-0.22240.08011.3158-0.08540.4252-60.2157113.4971452.6274
1910.0661-0.0150.03820.0008-0.00640.04040.1171-0.040.0361-0.10080.13270.23170.064-0.01190.00151.17670.02540.52871.1483-0.04691.2861-40.1515110.2016458.3721
1920.04280.02870.03970.01490.02650.0403-0.0379-0.02820.15150.0195-0.05750.0576-0.0405-0.2068-0.00011.00340.35140.10331.49150.03981.5329-42.0002120.5312462.4192
1930.0486-0.0199-0.01860.02830.0390.05410.0777-0.0015-0.07890.0027-0.0509-0.0189-0.05780.00320.08980.6987-0.093-0.05030.1852-0.19780.7538-87.7702140.3127413.8898
1940.14160.06780.01740.1090.10980.19430.04780.0231-0.04910.1536-0.0638-0.01270.0279-0.06560.05890.5871-0.25830.0740.4846-0.23980.6846-89.9036135.5519428.2834
1951.0911-0.19640.18870.055-0.10110.2615-0.1468-0.1768-0.10750.04430.2006-0.02270.08050.06780.27811.00130.1391-0.04380.4721-0.28340.67-89.0742126.2268415.2989
1960.6657-0.23010.04320.23280.02040.21980.0513-0.00520.1985-0.2307-0.1725-0.06-0.0104-0.1576-0.16180.73770.10290.32110.5712-0.22420.7214-92.5294115.5391425.1777
1970.1248-0.00960.0807-0.003-0.00450.04750.36330.0108-0.1187-0.2925-0.1929-0.14230.2280.33910.00621.0207-0.01140.33760.8541-0.16790.823-74.7305119.4661431.6032
1980.0617-0.05330.05070.1597-0.10640.08450.04220.0750.19240.0818-0.1282-0.0749-0.0184-0.059-0.71780.99330.11650.02030.3161-0.22221.0009-68.8092124.6778431.0903
1990.0759-0.1930.05970.3633-0.12950.0519-0.1411-0.00660.10090.04270.075-0.3382-0.0196-0.1896-0.1510.42440.15920.18720.5837-0.13220.5019-129.3448109.9969385.8193
2000.61860.3848-0.45671.0182-0.52180.40620.0097-0.43220.06920.0764-0.0784-0.4005-0.1217-0.0656-0.96380.79890.1533-0.11540.5573-0.28820.6268-123.5966121.8665391.5504
2010.14660.07770.12480.25540.04690.1063-0.1090.0211-0.12460.0424-0.1598-0.10380.1653-0.0744-0.39160.7530.2442-0.02870.2424-0.19110.7784-115.0551138.984393.1312
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain '1' and (resid 2 through 38 )
2X-RAY DIFFRACTION2chain '1' and (resid 39 through 60 )
3X-RAY DIFFRACTION3chain '1' and (resid 61 through 86 )
4X-RAY DIFFRACTION4chain '1' and (resid 87 through 155 )
5X-RAY DIFFRACTION5chain '1' and (resid 156 through 232 )
6X-RAY DIFFRACTION6chain '1' and (resid 233 through 366 )
7X-RAY DIFFRACTION7chain '1' and (resid 367 through 438 )
8X-RAY DIFFRACTION8chain '2' and (resid 3 through 22 )
9X-RAY DIFFRACTION9chain '2' and (resid 23 through 38 )
10X-RAY DIFFRACTION10chain '2' and (resid 39 through 66 )
11X-RAY DIFFRACTION11chain '2' and (resid 67 through 77 )
12X-RAY DIFFRACTION12chain '2' and (resid 78 through 92 )
13X-RAY DIFFRACTION13chain '2' and (resid 93 through 104 )
14X-RAY DIFFRACTION14chain '2' and (resid 105 through 116 )
15X-RAY DIFFRACTION15chain '2' and (resid 117 through 132 )
16X-RAY DIFFRACTION16chain '2' and (resid 133 through 146 )
17X-RAY DIFFRACTION17chain '2' and (resid 147 through 158 )
18X-RAY DIFFRACTION18chain '2' and (resid 159 through 165 )
19X-RAY DIFFRACTION19chain '2' and (resid 166 through 180 )
20X-RAY DIFFRACTION20chain '3' and (resid 1 through 137 )
21X-RAY DIFFRACTION21chain '3' and (resid 138 through 193 )
22X-RAY DIFFRACTION22chain '3' and (resid 194 through 309 )
23X-RAY DIFFRACTION23chain '3' and (resid 310 through 350 )
24X-RAY DIFFRACTION24chain '3' and (resid 351 through 460 )
25X-RAY DIFFRACTION25chain '3' and (resid 461 through 595 )
26X-RAY DIFFRACTION26chain '3' and (resid 596 through 667 )
27X-RAY DIFFRACTION27chain '3' and (resid 668 through 719 )
28X-RAY DIFFRACTION28chain '3' and (resid 720 through 777 )
29X-RAY DIFFRACTION29chain '4' and (resid 26 through 139 )
30X-RAY DIFFRACTION30chain '4' and (resid 140 through 208 )
31X-RAY DIFFRACTION31chain '4' and (resid 209 through 247 )
32X-RAY DIFFRACTION32chain '4' and (resid 248 through 409 )
33X-RAY DIFFRACTION33chain '5' and (resid 1 through 13 )
34X-RAY DIFFRACTION34chain '5' and (resid 14 through 31 )
35X-RAY DIFFRACTION35chain '5' and (resid 32 through 43 )
36X-RAY DIFFRACTION36chain '5' and (resid 44 through 67 )
37X-RAY DIFFRACTION37chain '5' and (resid 68 through 86 )
38X-RAY DIFFRACTION38chain '5' and (resid 87 through 109 )
39X-RAY DIFFRACTION39chain '5' and (resid 110 through 121 )
40X-RAY DIFFRACTION40chain '5' and (resid 122 through 141 )
41X-RAY DIFFRACTION41chain '5' and (resid 142 through 175 )
42X-RAY DIFFRACTION42chain '5' and (resid 176 through 185 )
43X-RAY DIFFRACTION43chain '5' and (resid 186 through 196 )
44X-RAY DIFFRACTION44chain '6' and (resid 20 through 34 )
45X-RAY DIFFRACTION45chain '6' and (resid 35 through 56 )
46X-RAY DIFFRACTION46chain '6' and (resid 57 through 77 )
47X-RAY DIFFRACTION47chain '6' and (resid 78 through 181 )
48X-RAY DIFFRACTION48chain '9' and (resid 2 through 18 )
49X-RAY DIFFRACTION49chain '9' and (resid 19 through 38 )
50X-RAY DIFFRACTION50chain '9' and (resid 39 through 48 )
51X-RAY DIFFRACTION51chain '9' and (resid 49 through 74 )
52X-RAY DIFFRACTION52chain '9' and (resid 75 through 112 )
53X-RAY DIFFRACTION53chain '9' and (resid 113 through 135 )
54X-RAY DIFFRACTION54chain '9' and (resid 136 through 167 )
55X-RAY DIFFRACTION55chain '9' and (resid 168 through 181 )
56X-RAY DIFFRACTION56chain '7' and (resid 3 through 27 )
57X-RAY DIFFRACTION57chain '7' and (resid 28 through 60 )
58X-RAY DIFFRACTION58chain '7' and (resid 61 through 81 )
59X-RAY DIFFRACTION59chain '7' and (resid 82 through 111 )
60X-RAY DIFFRACTION60chain '7' and (resid 112 through 129 )
61X-RAY DIFFRACTION61chain 'W' and (resid 1 through 9 )
62X-RAY DIFFRACTION62chain 'W' and (resid 10 through 35 )
63X-RAY DIFFRACTION63chain 'W' and (resid 36 through 46 )
64X-RAY DIFFRACTION64chain 'W' and (resid 47 through 69 )
65X-RAY DIFFRACTION65chain 'W' and (resid 70 through 95 )
66X-RAY DIFFRACTION66chain 'W' and (resid 96 through 106 )
67X-RAY DIFFRACTION67chain 'W' and (resid 107 through 117 )
68X-RAY DIFFRACTION68chain 'W' and (resid 118 through 127 )
69X-RAY DIFFRACTION69chain 'A' and (resid 2 through 88 )
70X-RAY DIFFRACTION70chain 'A' and (resid 89 through 117 )
71X-RAY DIFFRACTION71chain 'J' and (resid 1 through 24 )
72X-RAY DIFFRACTION72chain 'J' and (resid 25 through 73 )
73X-RAY DIFFRACTION73chain 'J' and (resid 74 through 108 )
74X-RAY DIFFRACTION74chain 'J' and (resid 109 through 160 )
75X-RAY DIFFRACTION75chain 'K' and (resid 1 through 23 )
76X-RAY DIFFRACTION76chain 'K' and (resid 24 through 51 )
77X-RAY DIFFRACTION77chain 'K' and (resid 52 through 78 )
78X-RAY DIFFRACTION78chain 'K' and (resid 79 through 86 )
79X-RAY DIFFRACTION79chain 'K' and (resid 87 through 95 )
80X-RAY DIFFRACTION80chain 'L' and (resid 1 through 70 )
81X-RAY DIFFRACTION81chain 'L' and (resid 71 through 425 )
82X-RAY DIFFRACTION82chain 'L' and (resid 426 through 458 )
83X-RAY DIFFRACTION83chain 'L' and (resid 459 through 510 )
84X-RAY DIFFRACTION84chain 'L' and (resid 511 through 542 )
85X-RAY DIFFRACTION85chain 'L' and (resid 543 through 605 )
86X-RAY DIFFRACTION86chain 'M' and (resid 1 through 114 )
87X-RAY DIFFRACTION87chain 'M' and (resid 115 through 414 )
88X-RAY DIFFRACTION88chain 'M' and (resid 415 through 467 )
89X-RAY DIFFRACTION89chain 'N' and (resid 1 through 127 )
90X-RAY DIFFRACTION90chain 'N' and (resid 128 through 187 )
91X-RAY DIFFRACTION91chain 'N' and (resid 188 through 357 )
92X-RAY DIFFRACTION92chain 'N' and (resid 358 through 395 )
93X-RAY DIFFRACTION93chain 'N' and (resid 396 through 427 )
94X-RAY DIFFRACTION94chain 'H' and (resid 2 through 42 )
95X-RAY DIFFRACTION95chain 'H' and (resid 43 through 104 )
96X-RAY DIFFRACTION96chain 'H' and (resid 105 through 147 )
97X-RAY DIFFRACTION97chain 'H' and (resid 148 through 262 )
98X-RAY DIFFRACTION98chain 'H' and (resid 263 through 296 )
99X-RAY DIFFRACTION99chain 'H' and (resid 297 through 334 )
100X-RAY DIFFRACTION100chain 'H' and (resid 335 through 354 )
101X-RAY DIFFRACTION101chain 'B' and (resid 2 through 38 )
102X-RAY DIFFRACTION102chain 'B' and (resid 39 through 60 )
103X-RAY DIFFRACTION103chain 'B' and (resid 61 through 124 )
104X-RAY DIFFRACTION104chain 'B' and (resid 125 through 267 )
105X-RAY DIFFRACTION105chain 'B' and (resid 268 through 366 )
106X-RAY DIFFRACTION106chain 'B' and (resid 367 through 395 )
107X-RAY DIFFRACTION107chain 'B' and (resid 396 through 438 )
108X-RAY DIFFRACTION108chain 'C' and (resid 3 through 22 )
109X-RAY DIFFRACTION109chain 'C' and (resid 23 through 38 )
110X-RAY DIFFRACTION110chain 'C' and (resid 39 through 53 )
111X-RAY DIFFRACTION111chain 'C' and (resid 54 through 66 )
112X-RAY DIFFRACTION112chain 'C' and (resid 67 through 77 )
113X-RAY DIFFRACTION113chain 'C' and (resid 78 through 92 )
114X-RAY DIFFRACTION114chain 'C' and (resid 93 through 104 )
115X-RAY DIFFRACTION115chain 'C' and (resid 105 through 116 )
116X-RAY DIFFRACTION116chain 'C' and (resid 117 through 146 )
117X-RAY DIFFRACTION117chain 'C' and (resid 147 through 158 )
118X-RAY DIFFRACTION118chain 'C' and (resid 159 through 180 )
119X-RAY DIFFRACTION119chain 'D' and (resid 1 through 128 )
120X-RAY DIFFRACTION120chain 'D' and (resid 129 through 193 )
121X-RAY DIFFRACTION121chain 'D' and (resid 194 through 309 )
122X-RAY DIFFRACTION122chain 'D' and (resid 310 through 350 )
123X-RAY DIFFRACTION123chain 'D' and (resid 351 through 546 )
124X-RAY DIFFRACTION124chain 'D' and (resid 547 through 594 )
125X-RAY DIFFRACTION125chain 'D' and (resid 595 through 667 )
126X-RAY DIFFRACTION126chain 'D' and (resid 668 through 719 )
127X-RAY DIFFRACTION127chain 'D' and (resid 720 through 777 )
128X-RAY DIFFRACTION128chain 'E' and (resid 26 through 53 )
129X-RAY DIFFRACTION129chain 'E' and (resid 54 through 139 )
130X-RAY DIFFRACTION130chain 'E' and (resid 140 through 208 )
131X-RAY DIFFRACTION131chain 'E' and (resid 209 through 232 )
132X-RAY DIFFRACTION132chain 'E' and (resid 233 through 409 )
133X-RAY DIFFRACTION133chain 'F' and (resid 1 through 13 )
134X-RAY DIFFRACTION134chain 'F' and (resid 14 through 31 )
135X-RAY DIFFRACTION135chain 'F' and (resid 32 through 86 )
136X-RAY DIFFRACTION136chain 'F' and (resid 87 through 121 )
137X-RAY DIFFRACTION137chain 'F' and (resid 122 through 175 )
138X-RAY DIFFRACTION138chain 'F' and (resid 176 through 196 )
139X-RAY DIFFRACTION139chain 'G' and (resid 20 through 34 )
140X-RAY DIFFRACTION140chain 'G' and (resid 35 through 56 )
141X-RAY DIFFRACTION141chain 'G' and (resid 57 through 88 )
142X-RAY DIFFRACTION142chain 'G' and (resid 89 through 158 )
143X-RAY DIFFRACTION143chain 'G' and (resid 159 through 168 )
144X-RAY DIFFRACTION144chain 'G' and (resid 169 through 181 )
145X-RAY DIFFRACTION145chain 'O' and (resid 2 through 18 )
146X-RAY DIFFRACTION146chain 'O' and (resid 19 through 30 )
147X-RAY DIFFRACTION147chain 'O' and (resid 31 through 48 )
148X-RAY DIFFRACTION148chain 'O' and (resid 49 through 74 )
149X-RAY DIFFRACTION149chain 'O' and (resid 75 through 112 )
150X-RAY DIFFRACTION150chain 'O' and (resid 113 through 125 )
151X-RAY DIFFRACTION151chain 'O' and (resid 126 through 168 )
152X-RAY DIFFRACTION152chain 'O' and (resid 169 through 181 )
153X-RAY DIFFRACTION153chain 'I' and (resid 3 through 27 )
154X-RAY DIFFRACTION154chain 'I' and (resid 28 through 60 )
155X-RAY DIFFRACTION155chain 'I' and (resid 61 through 81 )
156X-RAY DIFFRACTION156chain 'I' and (resid 82 through 111 )
157X-RAY DIFFRACTION157chain 'I' and (resid 112 through 129 )
158X-RAY DIFFRACTION158chain 'X' and (resid 1 through 9 )
159X-RAY DIFFRACTION159chain 'X' and (resid 10 through 21 )
160X-RAY DIFFRACTION160chain 'X' and (resid 22 through 29 )
161X-RAY DIFFRACTION161chain 'X' and (resid 30 through 46 )
162X-RAY DIFFRACTION162chain 'X' and (resid 47 through 59 )
163X-RAY DIFFRACTION163chain 'X' and (resid 60 through 83 )
164X-RAY DIFFRACTION164chain 'X' and (resid 84 through 93 )
165X-RAY DIFFRACTION165chain 'X' and (resid 94 through 106 )
166X-RAY DIFFRACTION166chain 'X' and (resid 107 through 127 )
167X-RAY DIFFRACTION167chain 'P' and (resid 2 through 58 )
168X-RAY DIFFRACTION168chain 'P' and (resid 59 through 83 )
169X-RAY DIFFRACTION169chain 'P' and (resid 84 through 112 )
170X-RAY DIFFRACTION170chain 'P' and (resid 113 through 117 )
171X-RAY DIFFRACTION171chain 'R' and (resid 1 through 24 )
172X-RAY DIFFRACTION172chain 'R' and (resid 25 through 62 )
173X-RAY DIFFRACTION173chain 'R' and (resid 63 through 73 )
174X-RAY DIFFRACTION174chain 'R' and (resid 74 through 87 )
175X-RAY DIFFRACTION175chain 'R' and (resid 88 through 108 )
176X-RAY DIFFRACTION176chain 'R' and (resid 109 through 123 )
177X-RAY DIFFRACTION177chain 'R' and (resid 124 through 160 )
178X-RAY DIFFRACTION178chain 'S' and (resid 1 through 23 )
179X-RAY DIFFRACTION179chain 'S' and (resid 24 through 76 )
180X-RAY DIFFRACTION180chain 'S' and (resid 77 through 86 )
181X-RAY DIFFRACTION181chain 'S' and (resid 87 through 95 )
182X-RAY DIFFRACTION182chain 'T' and (resid 1 through 70 )
183X-RAY DIFFRACTION183chain 'T' and (resid 71 through 290 )
184X-RAY DIFFRACTION184chain 'T' and (resid 291 through 425 )
185X-RAY DIFFRACTION185chain 'T' and (resid 426 through 455 )
186X-RAY DIFFRACTION186chain 'T' and (resid 456 through 488 )
187X-RAY DIFFRACTION187chain 'T' and (resid 489 through 542 )
188X-RAY DIFFRACTION188chain 'T' and (resid 543 through 605 )
189X-RAY DIFFRACTION189chain 'U' and (resid 1 through 95 )
190X-RAY DIFFRACTION190chain 'U' and (resid 96 through 304 )
191X-RAY DIFFRACTION191chain 'U' and (resid 305 through 414 )
192X-RAY DIFFRACTION192chain 'U' and (resid 415 through 467 )
193X-RAY DIFFRACTION193chain 'V' and (resid 1 through 42 )
194X-RAY DIFFRACTION194chain 'V' and (resid 43 through 75 )
195X-RAY DIFFRACTION195chain 'V' and (resid 76 through 127 )
196X-RAY DIFFRACTION196chain 'V' and (resid 128 through 225 )
197X-RAY DIFFRACTION197chain 'V' and (resid 226 through 357 )
198X-RAY DIFFRACTION198chain 'V' and (resid 358 through 427 )
199X-RAY DIFFRACTION199chain 'Q' and (resid 2 through 104 )
200X-RAY DIFFRACTION200chain 'Q' and (resid 105 through 296 )
201X-RAY DIFFRACTION201chain 'Q' and (resid 297 through 354 )

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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