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- PDB-6ql9: Structure of Fatty acid synthase complex from Saccharomyces cerev... -

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基本情報

登録情報
データベース: PDB / ID: 6ql9
タイトルStructure of Fatty acid synthase complex from Saccharomyces cerevisiae at 2.9 Angstrom
要素(Fatty acid synthase subunit ...) x 3
キーワードTRANSFERASE / Fatty acid synthase / Acyl carrier protein / Ketosynthase / Ketoreductase / Enoyl reductase / Dehydratase / Malonyl/palmitoyl transferase / Acetyl transferase / Phosphopantetheine transferase
機能・相同性
機能・相同性情報


fatty-acyl-CoA synthase system / fatty acid synthase complex / fatty-acyl-CoA synthase activity / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / holo-[acyl-carrier-protein] synthase activity / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / [acyl-carrier-protein] S-malonyltransferase ...fatty-acyl-CoA synthase system / fatty acid synthase complex / fatty-acyl-CoA synthase activity / palmitoyltransferase activity / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / holo-[acyl-carrier-protein] synthase activity / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / [acyl-carrier-protein] S-malonyltransferase / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / [acyl-carrier-protein] S-malonyltransferase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / long-chain fatty acid biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid synthase activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / mitochondrion / cytosol / cytoplasm
類似検索 - 分子機能
Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase subunit beta, insertion domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase subunit alpha, acyl carrier domain ...Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase, meander beta sheet domain / Fatty acid synthase subunit beta, N-terminal domain / N-terminal domain in fatty acid synthase subunit beta / Fatty acid synthase meander beta sheet domain / Fatty acid synthase subunit beta, insertion domain / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase subunit alpha, acyl carrier domain / Fatty acid synthase subunit alpha Acyl carrier domain / Fatty acid synthase type I, helical / : / Fatty acid synthase type I helical domain / : / Fatty acid synthase / N-terminal of MaoC-like dehydratase / FAS1-like, dehydratase domain region / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / MaoC-like dehydratase domain / MaoC like domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / HotDog domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site. / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
類似検索 - ドメイン・相同性
ADENOSINE-2'-5'-DIPHOSPHATE / ACETATE ION / FLAVIN MONONUCLEOTIDE / MALONATE ION / TRIETHYLENE GLYCOL / 4'-PHOSPHOPANTETHEINE / Fatty acid synthase subunit beta / Fatty acid synthase subunit alpha
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.82 Å
データ登録者Singh, K. / Graf, B. / Linden, A. / Sautner, V. / Urlaub, H. / Tittmann, K. / Stark, H. / Chari, A.
資金援助 ドイツ, 1件
組織認可番号国
German Research FoundationSFB860-TP A5 ドイツ
引用ジャーナル: Cell / 年: 2020
タイトル: Discovery of a Regulatory Subunit of the Yeast Fatty Acid Synthase.
著者: Kashish Singh / Benjamin Graf / Andreas Linden / Viktor Sautner / Henning Urlaub / Kai Tittmann / Holger Stark / Ashwin Chari /
要旨: Fatty acid synthases (FASs) are central to metabolism but are also of biotechnological interest for the production of fine chemicals and biofuels from renewable resources. During fatty acid ...Fatty acid synthases (FASs) are central to metabolism but are also of biotechnological interest for the production of fine chemicals and biofuels from renewable resources. During fatty acid synthesis, the growing fatty acid chain is thought to be shuttled by the dynamic acyl carrier protein domain to several enzyme active sites. Here, we report the discovery of a γ subunit of the 2.6 megadalton α-βS. cerevisiae FAS, which is shown by high-resolution structures to stabilize a rotated FAS conformation and rearrange ACP domains from equatorial to axial positions. The γ subunit spans the length of the FAS inner cavity, impeding reductase activities of FAS, regulating NADPH turnover by kinetic hysteresis at the ketoreductase, and suppressing off-pathway reactions at the enoylreductase. The γ subunit delineates the functional compartment within FAS. As a scaffold, it may be exploited to incorporate natural and designed enzymatic activities that are not present in natural FAS.
履歴
登録2019年1月31日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年3月18日Provider: repository / タイプ: Initial release
改定 1.12020年3月25日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
改定 1.22020年4月8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 ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Fatty acid synthase subunit alpha
B: Fatty acid synthase subunit alpha
C: Fatty acid synthase subunit alpha
D: Fatty acid synthase subunit alpha
E: Fatty acid synthase subunit alpha
F: Fatty acid synthase subunit alpha
G: Fatty acid synthase subunit beta
H: Fatty acid synthase subunit beta
I: Fatty acid synthase subunit beta
J: Fatty acid synthase subunit beta
K: Fatty acid synthase subunit beta
L: Fatty acid synthase subunit beta
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)2,630,308145
ポリマ－2,617,09312
非ポリマー13,215133
水5,909328
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area204330 Å2
ΔGint-1113 kcal/mol
Surface area859010 Å2
手法PISA
単位格子
Length a, b, c (Å)217.616, 347.596, 265.266
Angle α, β, γ (deg.)90.00, 107.88, 90.00
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F
116G
216H
117G
217I
118G
218J
119G
219K
120G
220L
121H
221I
122H
222J
123H
223K
124H
224L
125I
225J
126I
226K
127I
227L
128J
228K
129J
229L
130K
230L

NCSドメイン領域:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYSAA1 - 18861 - 1886
21METMETLYSLYSBB1 - 18861 - 1886
12METMETLYSLYSAA1 - 18861 - 1886
22METMETLYSLYSCC1 - 18861 - 1886
13METMETLYSLYSAA1 - 18861 - 1886
23METMETLYSLYSDD1 - 18861 - 1886
14METMETLYSLYSAA1 - 18861 - 1886
24METMETLYSLYSEE1 - 18861 - 1886
15METMETLYSLYSAA1 - 18861 - 1886
25METMETLYSLYSFF1 - 18861 - 1886
16METMETLYSLYSBB1 - 18861 - 1886
26METMETLYSLYSCC1 - 18861 - 1886
17METMETLYSLYSBB1 - 18861 - 1886
27METMETLYSLYSDD1 - 18861 - 1886
18METMETLYSLYSBB1 - 18861 - 1886
28METMETLYSLYSEE1 - 18861 - 1886
19METMETLYSLYSBB1 - 18861 - 1886
29METMETLYSLYSFF1 - 18861 - 1886
110METMETLYSLYSCC1 - 18861 - 1886
210METMETLYSLYSDD1 - 18861 - 1886
111METMETLYSLYSCC1 - 18861 - 1886
211METMETLYSLYSEE1 - 18861 - 1886
112METMETLYSLYSCC1 - 18861 - 1886
212METMETLYSLYSFF1 - 18861 - 1886
113METMETLYSLYSDD1 - 18861 - 1886
213METMETLYSLYSEE1 - 18861 - 1886
114METMETLYSLYSDD1 - 18861 - 1886
214METMETLYSLYSFF1 - 18861 - 1886
115METMETLYSLYSEE1 - 18861 - 1886
215METMETLYSLYSFF1 - 18861 - 1886
116SERSERGLNGLNGG5 - 20505 - 2050
216SERSERGLNGLNHH5 - 20505 - 2050
117SERSERGLNGLNGG5 - 20505 - 2050
217SERSERGLNGLNII5 - 20505 - 2050
118SERSERGLNGLNGG5 - 20505 - 2050
218SERSERGLNGLNJJ5 - 20505 - 2050
119SERSERGLNGLNGG5 - 20505 - 2050
219SERSERGLNGLNKK5 - 20505 - 2050
120SERSERGLNGLNGG5 - 20505 - 2050
220SERSERGLNGLNLL5 - 20505 - 2050
121SERSERGLUGLUHH5 - 20495 - 2049
221SERSERGLUGLUII5 - 20495 - 2049
122TYRTYRGLNGLNHH4 - 20504 - 2050
222TYRTYRGLNGLNJJ4 - 20504 - 2050
123TYRTYRGLNGLNHH4 - 20504 - 2050
223TYRTYRGLNGLNKK4 - 20504 - 2050
124TYRTYRGLNGLNHH4 - 20504 - 2050
224TYRTYRGLNGLNLL4 - 20504 - 2050
125SERSERGLUGLUII5 - 20495 - 2049
225SERSERGLUGLUJJ5 - 20495 - 2049
126SERSERGLUGLUII5 - 20495 - 2049
226SERSERGLUGLUKK5 - 20495 - 2049
127SERSERGLNGLNII5 - 20505 - 2050
227SERSERGLNGLNLL5 - 20505 - 2050
128TYRTYRGLNGLNJJ4 - 20504 - 2050
228TYRTYRGLNGLNKK4 - 20504 - 2050
129TYRTYRGLNGLNJJ4 - 20504 - 2050
229TYRTYRGLNGLNLL4 - 20504 - 2050
130TYRTYRGLNGLNKK4 - 20504 - 2050
230TYRTYRGLNGLNLL4 - 20504 - 2050

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

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要素

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Fatty acid synthase subunit ... , 3種, 12分子 ABCDEFGJHIKL

#1: タンパク質
Fatty acid synthase subunit alpha


分子量: 207184.422 Da / 分子数: 6 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c
参照: UniProt: P19097, fatty-acyl-CoA synthase system, 3-oxoacyl-[acyl-carrier-protein] reductase, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: タンパク質 Fatty acid synthase subunit beta


分子量: 228940.375 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c
参照: UniProt: P07149, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S-acetyltransferase, ...参照: UniProt: P07149, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, oleoyl-[acyl-carrier-protein] hydrolase
#3: タンパク質
Fatty acid synthase subunit beta


分子量: 229026.406 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
株: ATCC 204508 / S288c
参照: UniProt: P07149, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S-acetyltransferase, ...参照: UniProt: P07149, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, oleoyl-[acyl-carrier-protein] hydrolase

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非ポリマー , 9種, 461分子

#4: 化合物
ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / パンテテイン4′-りん酸


分子量: 358.348 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C11H23N2O7PS
#5: 化合物...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 67 / 由来タイプ: 天然 / 式: C2H6O2 / 由来: (天然) Saccharomyces cerevisiae (パン酵母)
株: BJ2168 (MATa prc1-407 prb1-1122 pep4-3 leu2 trp1 ura3-52 gal2 tma17::kanMX)
#6: 化合物...
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 39 / 由来タイプ: 天然 / 式: Na / 由来: (天然) Saccharomyces cerevisiae (パン酵母)
株: BJ2168 (MATa prc1-407 prb1-1122 pep4-3 leu2 trp1 ura3-52 gal2 tma17::kanMX)
#7: 化合物
ChemComp-A2P / ADENOSINE-2'-5'-DIPHOSPHATE / 2′,5′-ADP


分子量: 427.201 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C10H15N5O10P2
#8: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 6 / 由来タイプ: 天然 / 式: C2H3O2 / 由来: (天然) Saccharomyces cerevisiae (パン酵母)
株: BJ2168 (MATa prc1-407 prb1-1122 pep4-3 leu2 trp1 ura3-52 gal2 tma17::kanMX)
#9: 化合物 ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 1 / 由来タイプ: 天然 / 式: C6H14O4 / 由来: (天然) Saccharomyces cerevisiae (パン酵母)
株: BJ2168 (MATa prc1-407 prb1-1122 pep4-3 leu2 trp1 ura3-52 gal2 tma17::kanMX)
#10: 化合物
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / FMN


分子量: 456.344 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C17H21N4O9P
#11: 化合物 ChemComp-MLI / MALONATE ION / マロナ-ト


分子量: 102.046 Da / 分子数: 2 / 由来タイプ: 天然 / 式: C3H2O4 / 由来: (天然) Saccharomyces cerevisiae (パン酵母)
株: BJ2168 (MATa prc1-407 prb1-1122 pep4-3 leu2 trp1 ura3-52 gal2 tma17::kanMX)
#12: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 328 / 由来タイプ: 天然 / 式: H2O

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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: 3.76 Å3/Da / 溶媒含有率: 67.32 %
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: 0.1 M hepes pH 7.0, 0.3 M sodium-malonate pH 7.0 , 11.5-13% (w/v) PEG3350

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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: PETRA III, EMBL c/o DESY / ビームライン: P14 (MX2) / 波長: 0.9794 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2018年5月15日 / 詳細: CRL Transfocator
放射モノクロメーター: Si (111) / 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: 0.9794 Å / 相対比: 1
反射解像度: 2.82→191.5 Å / Num. obs: 894158 / % possible obs: 96.5 % / 冗長度: 7.2 % / CC1/2: 0.996 / Rpim(I) all: 0.07272 / Net I/σ(I): 10.91
反射 シェル解像度: 2.82→2.9 Å / 冗長度: 7.2 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 4914 / CC1/2: 0.241 / Rpim(I) all: 1.096 / % possible all: 76.5

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0238精密化
XDSデータ削減
Aimless0.7.3データスケーリング
MOLREP11.6.04位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2UV8

2uv8


解像度: 2.82→191.5 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.928 / SU B: 35.08 / SU ML: 0.275 / 交差検証法: THROUGHOUT / ESU R Free: 0.339 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.21135 35171 5 %RANDOM
Rwork0.19248 ---
obs0.19342 671162 78.63 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å
原子変位パラメータBiso mean: 67.677 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å2-0 Å2-0.98 Å2
2---0.23 Å20 Å2
3----0.1 Å2
精密化ステップサイクル: LAST / 解像度: 2.82→191.5 Å
タンパク質核酸リガンド溶媒全体
原子数178375 0 703 328 179406
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0080.013182757
X-RAY DIFFRACTIONr_bond_other_d0.0010.017170733
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.645247451
X-RAY DIFFRACTIONr_angle_other_deg1.2241.576397551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.996522746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75523.558870
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.311532054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.38915822
X-RAY DIFFRACTIONr_chiral_restr0.0640.224087
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02202822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0236306
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.253.07791080
X-RAY DIFFRACTIONr_mcbond_other1.2493.07791073
X-RAY DIFFRACTIONr_mcangle_it2.1434.614113787
X-RAY DIFFRACTIONr_mcangle_other2.1434.614113788
X-RAY DIFFRACTIONr_scbond_it1.3113.20391677
X-RAY DIFFRACTIONr_scbond_other1.3113.20391678
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2454.749133664
X-RAY DIFFRACTIONr_long_range_B_refined4.3335.708200133
X-RAY DIFFRACTIONr_long_range_B_other4.3335.708200134
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / タイプ: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-ID数Rms dev position (Å)
11A567410.06
12B567410.06
21A567620.05
22C567620.05
31A567410.05
32D567410.05
41A566910.05
42E566910.05
51A566280.06
52F566280.06
61B567580.05
62C567580.05
71B567580.06
72D567580.06
81B567520.06
82E567520.06
91B567560.06
92F567560.06
101C567280.05
102D567280.05
111C567250.05
112E567250.05
121C566840.05
122F566840.05
131D566280.06
132E566280.06
141D566660.06
142F566660.06
151E566050.06
152F566050.06
161G659230.06
162H659230.06
171G658660.06
172I658660.06
181G659190.06
182J659190.06
191G656470.06
192K656470.06
201G657620.06
202L657620.06
211H660450.06
212I660450.06
221H660890.06
222J660890.06
231H659280.06
232K659280.06
241H659010.06
242L659010.06
251I660580.05
252J660580.05
261I660330.05
262K660330.05
271I659520.06
272L659520.06
281J658020.06
282K658020.06
291J658710.06
292L658710.06
301K656670.06
302L656670.06
LS精密化 シェル解像度: 2.819→2.892 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.327 121 -
Rwork0.352 2172 -
obs--3.46 %
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)
11.2416-0.1247-1.03921.7150.03361.85990.23150.32850.1487-0.53040.0691-0.0717-0.4895-0.1502-0.30060.75390.06720.14520.4977-0.01120.5505104.880660.36698.9802
20.37790.1232-0.1871.7503-1.42071.29120.03390.30330.0322-0.5329-0.121-0.35280.24090.13160.08710.69950.03060.06460.6655-0.08640.827556.196136.559536.9624
30.475-0.58550.17931.0189-0.20150.2894-0.0341-0.02780.2305-0.0589-0.0008-0.3073-0.09220.26750.03490.0825-0.02890.02320.4889-0.08660.2947117.348725.837781.3928
40.95880.07510.1480.56120.05510.6466-0.0323-0.0891-0.0674-0.05390.0306-0.04070.08430.18560.00160.03820.07710.04650.32090.05750.1113108.2983-24.379272.7523
51.7824-1.05710.51525.6863-1.850.71170.27460.1456-0.13550.0912-0.3605-0.75070.12440.37310.0860.63480.25860.00841.23640.10560.8573150.3372-51.627776.9156
61.3263-0.6782-0.28211.29250.55181.71450.0230.09640.0998-0.29390.0757-0.0479-0.13190.2373-0.09870.3279-0.00840.03190.5935-0.0030.392286.5518-70.966210.8297
71.7534-0.6586-0.74710.8420.55950.68980.13610.523-0.1628-0.4456-0.0387-0.0918-0.00220.128-0.09740.62860.0501-0.05360.78080.02120.727768.8198-24.084645.6279
81.2447-0.05170.33510.2834-0.0980.4756-0.0110.1224-0.4258-0.05780.01580.06660.27080.0057-0.00480.23480.05150.15170.15690.0440.404316.6976-79.751651.4096
90.7040.02470.0510.78560.05130.6264-0.04420.0766-0.1265-0.0433-0.02140.02150.1052-0.04630.06560.0547-0.01970.08790.0481-0.05330.1961-14.8364-45.355329.0789
107.410.8881.43631.91230.49482.0349-0.17140.3239-0.8175-0.15350.06360.41780.6839-0.27870.10780.6236-0.07680.08070.5518-0.17790.7237-51.5588-67.49853.1525
111.21360.19340.52290.8047-0.25762.8558-0.02820.3162-0.106-0.2128-0.0609-0.05170.25970.24470.08910.6925-0.05010.16640.4243-0.06920.5522-12.02479.8111-30.6258
120.49030.45460.69421.12141.07461.4411-0.16450.43940.1159-0.49120.1071-0.2052-0.19430.31050.05740.5969-0.09590.08160.67690.04590.763112.8155-6.577724.1297
130.55160.5074-0.03411.33070.16230.317-0.04060.21370.1916-0.29640.0250.1535-0.1817-0.12820.01560.18750.0887-0.00410.16390.01860.25-16.923463.509230.0569
140.8449-0.12310.0730.6799-0.0870.56770.01170.08050.2116-0.12230.0069-0.0698-0.12720.0556-0.01860.1577-0.00780.03620.0265-0.00620.245632.104477.995938.1277
151.57351.5361.15314.6331-0.59862.0067-0.39040.01170.5372-0.46660.12820.2034-0.601-0.07290.26220.9055-0.04250.08430.53250.15421.158840.1322125.503324.1017
160.96120.3686-0.24610.4639-0.31411.7591-0.0535-0.1801-0.09430.29530.02970.0765-0.088-0.28620.02380.52620.15080.15820.81990.05930.651-10.3652-66.1136111.7225
172.43080.9921-0.7030.702-0.33710.35910.1556-0.7129-0.1460.4651-0.12340.0099-0.0003-0.0754-0.03210.65470.0232-0.02670.81630.00660.70427.1659-22.551871.4463
181.11550.0810.36750.3530.10270.54580.0077-0.2764-0.33050.1652-0.0012-0.04740.28520.049-0.00650.25650.12240.12440.24790.10760.39559.4405-78.45372.0709
190.6394-0.02620.09770.7615-0.06750.5337-0.018-0.2076-0.09820.08540.0040.02030.09340.1080.0140.07120.11410.0740.33440.10460.171791.2866-41.627490.1389
206.24520.45871.66142.5982-1.23111.98630.0948-0.256-0.53860.1810.0294-0.39250.37110.191-0.12410.53020.1843-0.03920.73890.12140.5211128.6136-61.0129117.5572
211.3098-0.03490.50260.77590.21122.41960.0683-0.4689-0.08970.2549-0.08640.11970.3510.11940.01810.63150.16950.08581.01980.01490.637888.222120.3312141.8564
220.548-0.36050.87130.5861-0.95992.2775-0.1686-0.50610.16430.43670.12760.1214-0.2973-0.27670.0410.6290.13290.03760.8413-0.07040.839163.6854-2.440290.7426
230.6151-0.36010.10141.1402-0.19490.3549-0.0598-0.23990.2720.23080.0589-0.1807-0.22040.15920.00090.1643-0.09280.00270.3597-0.14370.402593.699366.447475.1412
240.81430.03260.06750.68490.03280.6119-0.0024-0.16930.320.08210.0269-0.05-0.23550.0085-0.02450.1704-0.03470.01910.1453-0.09690.335443.917585.549165.7376
252.2169-1.41180.40182.1915-0.90010.8054-0.1050.28360.7826-0.21570.07110.1807-0.2948-0.30590.03380.8721-0.0068-0.08140.98330.15681.121193.5869-19.6575-46.8538
261.73830.7846-0.45461.8685-0.57652.0004-0.04780.33330.0928-0.31080.07430.1508-0.055-0.1254-0.02650.3538-0.06180.07450.5856-0.05510.383199.3046-50.2468-36.0444
270.3310.30450.44120.35480.45190.70150.03610.055-0.0475-0.0489-0.0480.01190.0976-0.15890.01190.2856-0.02890.13190.5307-0.0450.3746123.101-33.0886-2.237
280.2083-0.1453-0.09750.3148-0.00420.22460.04170.03620.1352-0.18030.0102-0.1379-0.13810.0673-0.05180.3061-0.0790.07280.5172-0.0410.46127.973622.57635.3691
291.22580.47650.6931.336-0.50362.6696-0.04290.06270.5009-0.1828-0.02090.3253-1.0625-0.29040.06380.85790.05290.13070.5393-0.0110.6398104.015971.763519.1727
301.678-0.5726-1.03940.22970.3550.6480.1066-0.2446-0.00440.004-0.0601-0.0501-0.04210.1753-0.04640.7837-0.11710.01250.7597-0.10690.76620.130753.392583.4402
310.73570.4726-0.07790.82180.16220.3614-0.02040.00130.1895-0.0264-0.03890.2212-0.1101-0.21040.05930.090.0690.00060.1507-0.02230.1654-35.465318.316229.5453
320.2748-0.0647-0.02950.7342-0.21420.3113-0.056-0.10550.06720.16380.04280.055-0.1003-0.0680.01320.06430.02150.01370.1542-0.09770.1243-27.9522-0.42346.5449
330.68-0.12990.16550.65240.16290.7581-0.0433-0.0163-0.17780.0121-0.02530.12780.1676-0.170.06860.0582-0.03660.05370.1441-0.09090.1861-39.3028-32.07537.9138
342.1531.77390.39756.45470.58770.24870.1347-0.0640.02-0.0225-0.16780.58010.1709-0.39040.03320.5886-0.18320.14560.9756-0.13840.8652-73.3158-53.542842.3791
351.7192-0.3711-0.27650.69590.16210.8276-0.02770.02480.25830.22770.0053-0.4976-0.3270.42610.02240.8166-0.14490.0650.6927-0.03710.581441.6257-4.9294-64.0022
360.2387-0.0628-0.00821.755-0.8690.7840.05650.10780.060.05660.00120.1056-0.32770.0077-0.05770.4234-0.04610.09380.445-0.13430.272218.2599-29.7617-51.4034
370.6415-0.0525-0.21620.2293-0.11480.70470.02240.2046-0.0026-0.0547-0.0203-0.0127-0.04540.0171-0.0020.2776-0.05250.06330.2368-0.16050.314919.6126-59.3236-30.8962
380.3383-0.00890.24280.0825-0.00051.9707-0.03090.0159-0.18970.01760.0279-0.01180.09340.13690.0030.25620.04340.10380.3476-0.01820.472464.6629-75.6721-2.2023
392.14010.0914-0.04881.6639-0.64111.18040.1538-0.2352-0.20590.3979-0.0316-0.4447-0.02170.6426-0.12220.46420.05690.08080.7476-0.01170.553996.0703-80.862223.232
400.80140.14520.53221.17910.48851.73950.13690.1499-0.52170.06390.04190.05380.2374-0.1061-0.17880.55330.01240.12520.68510.04140.738495.197729.3827-47.1364
411.6427-0.57310.06050.34470.04530.0472-0.0368-0.05790.04220.07360.057-0.0948-0.03280.0839-0.02030.79290.03380.19050.56120.12190.397175.848858.8865-36.3394
420.2298-0.0473-0.13850.15850.07930.7120.05270.11710.0435-0.13530.0176-0.0897-0.06160.1148-0.07030.68120.03330.15580.42240.11510.405641.608868.482-31.3897
431.0170.4001-1.0850.495-0.48581.5005-0.00730.14750.0131-0.2419-0.05460.0539-0.0074-0.10890.06190.57850.05940.0130.3953-0.01390.3287-1.511333.1644-33.5107
442.1267-0.0712-0.00781.39270.74091.4828-0.24660.16-0.6551-0.1510.03830.62430.5895-0.39190.20830.8382-0.05120.12840.6425-0.0940.7268-29.664.1335-28.5192
450.7352-0.11570.02131.5460.30320.96620.0035-0.21560.28790.2546-0.0866-0.5206-0.2710.4930.08310.57490.0220.06541.10410.08680.5984-19.1887-22.7589159.0767
460.7938-0.57450.60780.7875-0.68321.24630.0183-0.1074-0.12120.0542-0.096-0.03680.1910.30940.07770.28570.0430.1480.65070.02340.2982-42.6061-27.5385131.705
470.1840.0831-0.03720.430.03930.8592-0.014-0.1459-0.01090.1808-0.03480.02360.10330.09970.04890.10730.02160.07260.4443-0.04630.2843-58.4857-7.0294106.7066
480.44940.3134-0.73510.4702-0.55451.60490.0358-0.05920.09680.0783-0.04390.056-0.2462-0.08460.00810.2769-0.0104-0.02540.4051-0.10720.3675-45.279546.733396.8673
490.7601-0.32070.67631.9367-0.17982.2529-0.0804-0.0530.66770.1268-0.1335-0.1763-1.09290.48970.21381.0183-0.16760.030.6102-0.16390.767-28.646482.671987.031
501.42060.107-0.69671.0829-0.40891.4533-0.0573-0.01180.1974-0.2782-0.04180.46910.0775-0.10660.09910.7440.0544-0.04730.8326-0.12340.601734.594310.9495176.9877
510.13890.12850.0021.77390.59770.2619-0.0277-0.11790.0964-0.07860.0221-0.1339-0.06670.18650.00560.70280.21050.11230.99550.11870.377457.8776-16.2173167.6769
520.3917-0.0145-0.21840.13860.07120.6345-0.0095-0.23570.02920.17730.07440.0212-0.03970.067-0.06490.54910.23920.13020.80530.19640.382556.8383-48.3122151.4946
530.3048-0.04490.37070.1620.23542.327-0.0865-0.1698-0.21490.09430.04670.07450.0869-0.13550.03980.44560.13770.22850.63020.2050.535911.6646-68.807125.0237
542.2132-0.10190.05661.64190.69591.19630.10040.1232-0.5022-0.3466-0.17490.71680.0886-0.72270.07450.64960.10.21160.96420.09490.8953-19.8802-77.6304100.7185
550.8274-0.21990.33051.4089-0.47770.95720.0134-0.3465-0.49440.34620.0632-0.25820.44860.0191-0.07660.7948-0.0627-0.08730.8498-0.07160.6282-18.845843.66156.0455
562.10050.77210.04360.3716-0.05660.1372-0.093-0.04210.0084-0.04830.10580.02570.09280.0297-0.01280.5459-0.05080.01150.6912-0.28060.42390.527271.0697141.1458
570.218-0.0613-0.14530.2156-0.12110.5552-0.0054-0.18580.01190.0797-0.00360.03190.0406-0.02690.00910.4336-0.1062-0.01210.6953-0.29640.495734.986179.5415135.0957
580.8351-0.3954-0.96080.46390.6241.2260.0055-0.26050.01540.1125-0.0365-0.03870.01020.14890.0310.45430.0177-0.03710.9287-0.07280.474977.858243.9775141.7147
591.37950.1924-0.16481.5057-0.86031.2461-0.1645-0.335-0.54970.218-0.1095-0.6530.61490.2870.2740.84940.16410.02911.26460.04270.8407105.799914.3238140.4092
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 146
2X-RAY DIFFRACTION2A147 - 355
3X-RAY DIFFRACTION3A356 - 969
4X-RAY DIFFRACTION4A970 - 1778
5X-RAY DIFFRACTION5A1779 - 1887
6X-RAY DIFFRACTION6B1 - 146
7X-RAY DIFFRACTION7B147 - 355
8X-RAY DIFFRACTION8B356 - 969
9X-RAY DIFFRACTION9B970 - 1778
10X-RAY DIFFRACTION10B1779 - 1887
11X-RAY DIFFRACTION11C1 - 146
12X-RAY DIFFRACTION12C147 - 355
13X-RAY DIFFRACTION13C356 - 969
14X-RAY DIFFRACTION14C970 - 1778
15X-RAY DIFFRACTION15C1779 - 1887
16X-RAY DIFFRACTION16E1 - 146
17X-RAY DIFFRACTION17E147 - 355
18X-RAY DIFFRACTION18E356 - 969
19X-RAY DIFFRACTION19E970 - 1778
20X-RAY DIFFRACTION20E1779 - 1887
21X-RAY DIFFRACTION21F1 - 146
22X-RAY DIFFRACTION22F147 - 355
23X-RAY DIFFRACTION23F356 - 969
24X-RAY DIFFRACTION24F970 - 1778
25X-RAY DIFFRACTION24F1779 - 1887
26X-RAY DIFFRACTION25G1 - 146
27X-RAY DIFFRACTION26G147 - 355
28X-RAY DIFFRACTION27G356 - 969
29X-RAY DIFFRACTION28G970 - 1778
30X-RAY DIFFRACTION29G1779 - 1887
31X-RAY DIFFRACTION30D5 - 324
32X-RAY DIFFRACTION31D325 - 804
33X-RAY DIFFRACTION32D805 - 1292
34X-RAY DIFFRACTION33D1293 - 1772
35X-RAY DIFFRACTION34D1773 - 2048
36X-RAY DIFFRACTION35H5 - 324
37X-RAY DIFFRACTION36H325 - 804
38X-RAY DIFFRACTION37H805 - 1292
39X-RAY DIFFRACTION38H1293 - 1772
40X-RAY DIFFRACTION39H1773 - 2048
41X-RAY DIFFRACTION40I5 - 324
42X-RAY DIFFRACTION41I325 - 804
43X-RAY DIFFRACTION42I805 - 1292
44X-RAY DIFFRACTION43I1293 - 1772
45X-RAY DIFFRACTION44I1773 - 2048
46X-RAY DIFFRACTION45J5 - 324
47X-RAY DIFFRACTION46J325 - 804
48X-RAY DIFFRACTION47J805 - 1292
49X-RAY DIFFRACTION48J1293 - 1772
50X-RAY DIFFRACTION49J1773 - 2048
51X-RAY DIFFRACTION50K5 - 324
52X-RAY DIFFRACTION51K325 - 804
53X-RAY DIFFRACTION52K805 - 1292
54X-RAY DIFFRACTION53K1293 - 1772
55X-RAY DIFFRACTION54K1773 - 2048
56X-RAY DIFFRACTION55L5 - 324
57X-RAY DIFFRACTION56L325 - 804
58X-RAY DIFFRACTION57L805 - 1292
59X-RAY DIFFRACTION58L1293 - 1772
60X-RAY DIFFRACTION59L1773 - 2048

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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

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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

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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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