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- PDB-4x6z: Yeast 20S proteasome in complex with PR-VI modulator -

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基本情報

登録情報
データベース: PDB / ID: 4x6z
タイトルYeast 20S proteasome in complex with PR-VI modulator
要素
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
  • synthetic peptide (polymer)
キーワードHYDROLASE / 20S proteasome / low-molecular mass activators / allosteric regulation
機能・相同性
機能・相同性情報


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Ub-specific processing proteases / Neutrophil degranulation / proteasome complex / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol
類似検索 - 分子機能
Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. ...Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 ...Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.7 Å
データ登録者Rostankowski, R. / Witkowska, J. / Borek, D. / Otwinowski, Z. / Jankowska, E.
資金援助 ポーランド, 1件
組織認可番号国
National Science CentreNCN 2011/01/B/ST5/06616 ポーランド
引用ジャーナル: To Be Published
タイトル: Crystal structures revealed the common place of binding of low-molecular mass activators with the 20S proteasome
著者: Witkowska, J. / Rostankowski, R. / Dubin, G. / Grudnik, P. / Golik, P. / Gaczynska, M. / Osmulski, P. / Borek, D. / Otwinowski, Z. / Jankowska, E.
履歴
登録2014年12月9日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02015年12月23日Provider: repository / タイプ: Initial release
改定 1.12024年1月10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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
1: Proteasome subunit beta type-6
2: Proteasome subunit beta type-7
A: Proteasome subunit alpha type-1
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-3
D: Proteasome subunit alpha type-4
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-6
G: Probable proteasome subunit alpha type-7
H: Proteasome subunit beta type-1
I: Proteasome subunit beta type-2
J: Proteasome subunit beta type-3
K: Proteasome subunit beta type-4
L: Proteasome subunit beta type-5
M: Proteasome subunit beta type-6
N: Proteasome subunit beta type-7
O: Proteasome subunit alpha type-1
P: Proteasome subunit alpha type-2
Q: Proteasome subunit alpha type-3
R: Proteasome subunit alpha type-4
S: Proteasome subunit alpha type-5
T: Proteasome subunit alpha type-6
U: Probable proteasome subunit alpha type-7
V: Proteasome subunit beta type-1
W: Proteasome subunit beta type-2
X: Proteasome subunit beta type-3
Y: Proteasome subunit beta type-4
Z: Proteasome subunit beta type-5
a: synthetic peptide (polymer)
e: synthetic peptide (polymer)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)776,078133
ポリマ－770,15430
非ポリマー5,924103
水6,467359
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 area136650 Å2
ΔGint-821 kcal/mol
Surface area211550 Å2
手法PISA
単位格子
Length a, b, c (Å)133.350, 300.790, 144.580
Angle α, β, γ (deg.)90.00, 112.11, 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
111
21M
122
22N
13A
23O
14B
24P
15C
25Q
16D
26R
17E
27S
18F
28T
19G
29U
110H
210V
111I
211W
112J
212X
113K
213Y
114L
214Z

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
11GLNGLNASPASP1A-8 - 21320 - 241
21GLNGLNASPASPMO-8 - 21320 - 241
12THRTHRILEILE2B-7 - 22534 - 266
22THRTHRILEILENP-7 - 22534 - 266
13GLYGLYGLUGLUAC11 - 25011 - 250
23GLYGLYGLUGLUOQ11 - 25011 - 250
14THRTHRGLUGLUBD2 - 2482 - 248
24THRTHRGLUGLUPR2 - 2482 - 248
15GLYGLYTHRTHRCE2 - 2452 - 245
25GLYGLYTHRTHRQS2 - 2452 - 245
16GLYGLYGLNGLNDF3 - 2433 - 243
26GLYGLYGLNGLNRT3 - 2433 - 243
17ASPASPGLUGLUEG9 - 2509 - 250
27ASPASPGLUGLUSU9 - 2509 - 250
18ARGARGILEILEFH3 - 2343 - 234
28ARGARGILEILETV3 - 2343 - 234
19GLYGLYASNASNGI4 - 2475 - 248
29GLYGLYASNASNUW4 - 2475 - 248
110THRTHRLEULEUHJ1 - 19620 - 215
210THRTHRLEULEUVX1 - 19620 - 215
111THRTHRASNASNIK1 - 21930 - 248
211THRTHRASNASNWY1 - 21930 - 248
112SERSERASPASPJL-7 - 1962 - 205
212SERSERASPASPXZ-7 - 1962 - 205
113METMETGLNGLNKM0 - 1951 - 196
213METMETGLNGLNYAA0 - 1951 - 196
114THRTHRGLYGLYLN1 - 21276 - 287
214THRTHRGLYGLYZBA1 - 21276 - 287

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

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要素

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Proteasome subunit beta type- ... , 7種, 14分子 1M2NHVIWJXKYLZ

#1: タンパク質 Proteasome subunit beta type-6 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


分子量: 26905.076 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: P23724, proteasome endopeptidase complex
#2: タンパク質 Proteasome subunit beta type-7 / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component ...Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


分子量: 29471.289 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: P30657, proteasome endopeptidase complex
#10: タンパク質 Proteasome subunit beta type-1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


分子量: 23573.604 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: P38624, proteasome endopeptidase complex
#11: タンパク質 Proteasome subunit beta type-2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component ...Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


分子量: 28299.889 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: P25043, proteasome endopeptidase complex
#12: タンパク質 Proteasome subunit beta type-3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


分子量: 22627.842 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: P25451, proteasome endopeptidase complex
#13: タンパク質 Proteasome subunit beta type-4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


分子量: 22545.676 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: P22141, proteasome endopeptidase complex
#14: タンパク質 Proteasome subunit beta type-5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component ...Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


分子量: 31670.539 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: P30656, proteasome endopeptidase complex

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Proteasome subunit alpha type- ... , 6種, 12分子 AOBPCQDRESFT

#3: タンパク質 Proteasome subunit alpha type-1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


分子量: 28033.830 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: P21243, proteasome endopeptidase complex
#4: タンパク質 Proteasome subunit alpha type-2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


分子量: 27191.828 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: P23639, proteasome endopeptidase complex
#5: タンパク質 Proteasome subunit alpha type-3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


分子量: 28748.230 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: P23638, proteasome endopeptidase complex
#6: タンパク質 Proteasome subunit alpha type-4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


分子量: 28478.111 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: P40303, proteasome endopeptidase complex
#7: タンパク質 Proteasome subunit alpha type-5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


分子量: 28649.086 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: P32379, proteasome endopeptidase complex
#8: タンパク質 Proteasome subunit alpha type-6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


分子量: 25634.000 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: P40302, proteasome endopeptidase complex

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タンパク質 / タンパク質・ペプチド , 2種, 4分子 GUae

#15: タンパク質・ペプチド synthetic peptide (polymer)


分子量: 1673.000 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#9: タンパク質 Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


分子量: 31575.068 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: P21242, proteasome endopeptidase complex

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非ポリマー , 4種, 462分子

#16: 化合物
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / (S)-2-メチル-2,4-ペンタンジオ-ル


分子量: 118.174 Da / 分子数: 9 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#17: 化合物...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 38 / 由来タイプ: 合成 / 式: C3H8O3
#18: 化合物...
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 56 / 由来タイプ: 合成 / 式: Mg
#19: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 359 / 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

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試料調製

結晶マシュー密度: 3.49 Å3/Da / 溶媒含有率: 64.74 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.2 / 詳細: 30mM magnesium acetate, 12% MPD, 0.1M MES pH 7.2

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 19-ID / 波長: 0.979 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2011年8月10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: 0.979 Å / 相対比: 1
反射解像度: 2.7→49.46 Å / Num. obs: 207816 / % possible obs: 68.4 % / 冗長度: 1 % / Rsym value: 0.192 / Net I/σ(I): 6.5
反射 シェル解像度: 2.7→2.72 Å / 冗長度: 1 % / Mean I/σ(I) obs: 2.9 / % possible all: 20.2

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解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0049精密化
HKL-3000データ削減
Cootモデル構築
MOLREP位相決定
HKL-3000データスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 1RYP

1ryp


解像度: 2.7→49.46 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / SU B: 24.718 / SU ML: 0.23 / 交差検証法: THROUGHOUT / ESU R Free: 0.359 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.22192 9928 5 %RANDOM
Rwork0.17733 ---
obs0.17957 186914 68.32 %-
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 / 溶媒モデル: MASK
原子変位パラメータBiso mean: 44.523 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å2-1.55 Å2
2--0.42 Å20 Å2
3----1.02 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→49.46 Å
タンパク質核酸リガンド溶媒全体
原子数49481 0 356 359 50196
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01950699
X-RAY DIFFRACTIONr_bond_other_d0.0040.0248553
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.96768524
X-RAY DIFFRACTIONr_angle_other_deg0.983111781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16756343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98424.3742268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.371158784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.39715292
X-RAY DIFFRACTIONr_chiral_restr0.0840.27729
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0257362
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0211348
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_it1.5232.41925426
X-RAY DIFFRACTIONr_mcbond_other1.5232.41925425
X-RAY DIFFRACTIONr_mcangle_it2.5653.62231736
X-RAY DIFFRACTIONr_mcangle_other2.5653.62231737
X-RAY DIFFRACTIONr_scbond_it2.0132.70125273
X-RAY DIFFRACTIONr_scbond_other2.0122.70125273
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3533.9436784
X-RAY DIFFRACTIONr_long_range_B_refined6.01923.042209795
X-RAY DIFFRACTIONr_long_range_B_other6.01723.041209751
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)
111131820.08
12M131820.08
212146470.05
22N146470.05
31A146960.09
32O146960.09
41B146220.07
42P146220.07
51C144320.1
52Q144320.1
61D143010.11
62R143010.11
71E141040.1
72S141040.1
81F136840.1
82T136840.1
91G144260.09
92U144260.09
101H118010.06
102V118010.06
111I126880.08
112W126880.08
121J125120.06
122X125120.06
131K123610.06
132Y123610.06
141L125880.06
142Z125880.06
LS精密化 シェル解像度: 2.7→2.77 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.341 176 -
Rwork0.292 3070 -
obs--15.25 %
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)
110.56580.0808-4.54232.53640.8353.00270.40570.16470.7975-0.15010.0618-0.2868-0.26050.0831-0.46750.21990.0279-0.02890.10640.03560.156467.8535-11.94728.4371
20.7514-0.08510.060.7530.34831.14830.08140.0428-0.1019-0.1752-0.0178-0.29070.03540.0764-0.06370.09820.04130.07490.054-0.0450.257167.9841-20.162526.0715
32.55371.0121-0.52.145-1.30431.3049-0.10680.2628-0.1367-0.50930.0336-0.57180.53410.32330.07320.29720.1130.09740.3265-0.14010.476479.76741.200912.9803
41.9722-0.8696-1.51815.03241.65053.43880.1509-0.1714-0.05750.0244-0.0257-0.5552-0.09780.5005-0.12520.03390.01090.01190.1784-0.06480.329481.0534-7.36630.9893
51.9371-0.24840.39751.6253-0.31611.0240.0825-0.1954-0.12380.2716-0.0569-0.13760.03870.0017-0.02560.1320.019-0.05530.04630.00980.084155.567-18.50658.0789
60.45770.40190.17691.9725-0.2390.85070.01440.0522-0.08780.09110.0199-0.32330.13750.1108-0.03430.06520.0326-0.03960.0275-0.03870.156862.8654-22.673849.6614
71.7116-0.0635-0.10021.6145-0.10881.1932-0.0581-0.2101-0.08220.23090.0328-0.36860.00360.17380.02530.08940.0089-0.12280.05070.01040.187868.2716-11.256663.4996
82.882-2.63581.63625.6652-0.80281.7846-0.1643-0.1640.3680.47040.1517-0.3458-0.2096-0.04390.01270.2158-0.0713-0.02880.0984-0.05040.171157.686312.031771.1466
90.7660.1119-0.04881.0070.02341.73330.0145-0.00950.11360.2778-0.01970.0481-0.1323-0.11090.00520.1305-0.00270.02390.0324-0.04480.089243.702154.7164.6634
100.9463-0.40920.57292.2968-0.56331.61020.1456-0.1204-0.05520.0746-0.0348-0.0318-0.0125-0.0453-0.11080.1643-0.04140.02960.046-0.05320.150651.095356.810466.7462
114.9725-0.858-0.44273.16021.71762.1544-0.066-0.27340.16740.29920.1379-0.3412-0.02370.3827-0.07190.2899-0.0351-0.09080.136-0.02310.083454.831257.952984.7178
124.9257-0.8392-2.77634.65332.75439.1531-0.1502-0.5980.09970.66580.04030.0976-0.00430.2790.10990.2093-0.0050.01040.15490.03690.142947.276149.753187.1892
133.4086-0.93970.84970.66580.16181.6103-0.0311-0.00080.0154-0.0142-0.0513-0.08-0.095-0.12140.08230.1697-0.05340.03910.0353-0.00660.147855.818464.343541.3436
142.05660.4136-6.0260.1504-1.198717.72570.15270.00230.03240.0446-0.1695-0.0363-0.5543-0.07250.01680.221-0.0034-0.05440.41790.01270.452363.574859.814463.1295
151.2257-0.25970.09341.10390.09350.77060.00230.14370.0957-0.0114-0.0057-0.3477-0.15380.04650.00340.0954-0.03870.03620.0364-0.02280.177863.966154.76941.2882
161.46880.4777-0.30593.2718-1.13891.3184-0.0658-0.21220.11320.05220.169-0.3484-0.17110.1711-0.10320.0774-0.0636-0.02940.142-0.06620.248778.509154.067452.7462
173.24210.3257-0.43381.0119-0.34381.6846-0.0239-0.11650.1089-0.2385-0.06590.1276-0.46680.03310.08980.2690.0159-0.03440.02940.0350.200146.72867.472222.2397
182.97691.39015.95252.81642.188512.0633-0.07310.0160.0907-0.1184-0.07370.1519-0.12160.05560.14680.2577-0.07370.10440.41650.03840.437270.764664.563428.7087
191.66140.2681-0.18650.69330.26880.8411-0.10050.05890.1428-0.20950.0958-0.0654-0.16850.0620.00470.1735-0.02920.0660.03770.04250.148453.583155.496915.6899
204.13180.19291.60974.58551.0663.59690.050.3105-0.03840.03680.037-0.6461-0.04790.5538-0.0870.2292-0.08340.13220.30870.07860.25471.865664.297511.144
210.57180.6016-0.95271.49220.22724.27990.0450.02210.1584-0.1218-0.04290.0623-0.30.1242-0.0020.16490.0641-0.02410.10580.0960.274728.364165.985712.0537
227.17594.13213.09922.38131.78471.3395-0.2808-0.06310.5918-0.1597-0.00130.3468-0.1299-0.02490.28210.8881-0.09590.05760.45960.05740.494648.414563.68082.1902
231.09790.2563-0.01012.2477-0.8472.0723-0.08950.15870.1049-0.46840.1260.026-0.2069-0.0106-0.03650.2375-0.0331-0.02340.04110.05440.140528.784458.74231.373
241.954-0.93861.08830.7011-0.99782.4830.1070.43570.39890.1855-0.1426-0.2868-0.43750.640.03560.499-0.05080.12860.5339-0.08980.463138.369164.8428-14.5097
250.84330.3025-3.33234.7391-1.462613.21550.0915-0.01790.02680.3095-0.1097-0.2998-0.42220.05290.01820.18830.0196-0.07110.171-0.03940.445113.570267.870333.5361
262.3335-0.3158-1.34651.6827-0.77812.81590.04510.00270.2105-0.1938-0.01280.1762-0.1871-0.157-0.03230.25980.07-0.13190.09850.08960.33395.729859.03158.944
273.2313.70440.49166.49331.8261.41890.1018-0.2746-0.07210.40110.0727-0.37540.03730.2741-0.17450.15280.0706-0.0060.15680.02660.181510.938848.056824.0985
281.73950.6250.10961.5288-1.53062.7114-0.04390.01060.1102-0.21210.10060.3821-0.1179-0.3106-0.05680.21920.1136-0.12210.10720.04220.431-4.272360.80118.7443
290.6256-0.13860.46270.2410.10781.509-0.0681-0.08440.0999-0.0654-0.03620.2488-0.258-0.09440.10440.15260.10190.010.0837-0.0170.51131.354959.47443.2808
300.24750.37760.67234.4868-0.41842.4239-0.05110.0062-0.04260.11060.0614-0.1189-0.1687-0.0164-0.01030.09840.05970.04210.087-0.01090.20337.852944.523247.0001
313.07880.60921.08010.36870.61351.376-0.0379-0.17760.17090.0591-0.07110.2112-0.1431-0.22040.1090.21610.10540.13980.1121-0.01170.4502-3.744455.093451.2809
321.0415-0.6436-0.32342.4211-0.2834.68370.0327-0.16560.1885-0.02630.13680.5958-0.1487-0.6087-0.16950.05590.11490.02980.320.04740.5945-17.467554.136845.3338
331.36850.09040.27110.7232-0.01990.7516-0.0141-0.11570.08510.13420.02260.1959-0.117-0.0926-0.00850.19130.05320.10810.0995-0.06240.180919.868652.788864.7569
343.82170.1427-1.209513.75-5.053834.3671-0.1024-0.23550.20320.42490.07630.3081-1.0054-0.56150.02610.1560.01820.0550.1873-0.06720.280714.443263.954276.1428
358.5947-0.42031.88153.20240.21263.2403-0.131-0.21370.61190.4341-0.01260.1374-0.5792-0.25560.14360.33330.0360.14980.2668-0.10870.20519.663957.711583.5201
365.2712-3.06361.61594.6484-0.51081.64430.0788-0.07590.04060.1682-0.11380.509-0.1727-0.36430.0350.2355-0.01530.21240.202-0.05740.2593.18350.340878.1485
376.9153-2.2204-1.91388.81226.15676.4364-0.0811-0.33530.20830.6404-0.09270.25710.1995-0.13210.17380.137-0.0159-0.03230.09190.03690.094238.949612.787177.1595
380.8524-0.8632-0.46112.05910.50770.99510.0280.0208-0.02250.1872-0.0160.0401-0.11210.0359-0.01210.1439-0.02660.00270.0318-0.03990.066441.89221.94665.4289
391.1069-0.39490.25672.6472-0.77941.06990.0178-0.1520.07090.2450.05450.1397-0.11410.0049-0.07230.1016-0.02840.02990.043-0.02890.034532.430813.118570.3079
401.9795-0.7988-0.72423.64172.30072.0068-0.0826-0.319-0.12540.42920.0579-0.24930.17110.25630.02480.19360.0105-0.05820.19130.05320.097846.27846.791177.4068
410.9767-0.7717-0.82844.56931.44260.90180.06490.0076-0.0264-0.4434-0.1348-0.1732-0.18130.01870.06990.1461-0.0336-0.04350.18450.02620.285368.496717.814149.0206
420.48421.67640.60085.89032.110.9493-0.00060.0362-0.1426-0.08870.1724-0.46350.06330.2194-0.17170.1340.0323-0.00690.1674-0.02510.180659.522832.406650.1218
431.4165-0.55850.11221.8580.31571.0301-0.04110.0042-0.04740.06830.1116-0.32540.00540.1853-0.07060.0803-0.0214-0.02930.0432-0.02140.138865.953716.067154.6379
441.99410.38550.66692.001-2.02934.66570.11550.20690.2908-0.0656-0.0202-0.337-0.24360.3991-0.09530.0967-0.06450.16490.2618-0.05070.3382.187916.174513.9796
450.54490.40640.35072.18870.51221.28880.0035-0.017-0.0736-0.18960.0191-0.1738-0.00910.1236-0.02260.1167-0.0090.13210.06720.00310.168463.101423.3618.0297
461.22941.2904-1.50692.8711-0.6492.42470.1343-0.04490.00180.18150.0613-0.3507-0.13060.1121-0.19570.12040.00720.05840.0365-0.06570.207765.424329.600729.0094
470.5082-0.0909-0.68160.01820.12130.9264-0.0596-0.2601-0.07670.04050.03770.01330.06330.34690.02190.51930.10480.01170.9334-0.06870.577666.547720.144332.6402
482.0410.1923-0.05671.42680.20841.19150.09530.20020.0858-0.03850.0062-0.4758-0.01660.2991-0.10150.1282-0.02350.16170.1132-0.0310.333874.915214.355816.9536
4912.28845.0486-1.70593.6757-0.66781.49890.1816-0.2372-0.11020.119-0.1161-0.0187-0.10680.0394-0.06550.22720.0374-0.00810.1007-0.01780.120439.568316.6099-2.9736
500.98090.13980.45143.05660.74380.618-0.03810.04250.1469-0.38210.04660.0356-0.05390.0091-0.00860.1743-0.01530.04980.08160.02250.092541.09831.25284.2851
511.6341-0.1668-0.25461.60810.22653.0095-0.01960.03180.1243-0.25530.0663-0.21820.07020.016-0.04670.1661-0.0120.08760.0192-0.00780.061949.949420.00550.6667
520.670.7466-0.11485.3853-0.20770.1721-0.02550.3028-0.0749-0.7050.0320.13180.1297-0.0639-0.00650.2513-0.00770.00920.2466-0.01170.102141.396115.1435-9.746
531.13070.4179-0.40340.72350.50921.23020.01860.03320.0132-0.17690.00650.1778-0.1016-0.0185-0.02510.13760.0398-0.10020.05270.04650.242412.436923.39228.974
543.6411-2.01192.95328.237-7.627811.9287-0.12640.30170.2026-0.1526-0.0066-0.0163-0.46020.05490.1330.214-0.0167-0.03820.13460.0180.210214.650927.4893-0.8953
551.32140.6040.04382.22660.33451.3814-0.03470.1780.0024-0.45870.13450.19140.0106-0.0343-0.09980.17680.0009-0.10110.07310.06110.17429.718513.4523-1.5067
565.95982.0943-1.558310.4368-4.946513.2787-0.07350.5733-0.2934-0.3477-0.07140.43550.0309-0.27930.14490.1474-0.0328-0.08460.1812-0.04220.17-0.5747-3.5356-5.7815
578.8612-0.56862.83612.1493-0.63262.80370.3438-0.0887-0.6003-0.06070.01190.28940.1886-0.154-0.35570.18760.00650.03060.0703-0.02420.1471-0.502312.108431.9065
580.37050.12130.25971.2649-0.35591.15640.0254-0.02160.0635-0.10890.04910.3107-0.0199-0.0719-0.07440.0410.0099-0.00760.01840.04650.2590.620421.313430.8521
592.10030.4211.6941.37981.20153.73430.0045-0.07520.1714-0.244-0.110.4291-0.4016-0.48620.10560.13860.0391-0.08340.14040.09390.3906-11.16481.938214.8564
601.8271-1.2049-0.3974.72040.02112.00360.2217-0.00140.0055-0.2011-0.14470.64980.0929-0.2262-0.07710.0431-0.0192-0.01060.12710.05880.358-12.82167.4733.1393
612.04560.41810.31192.11820.00081.10930.0739-0.210.08390.2698-0.04080.1784-0.1058-0.0756-0.03310.12990.01760.09380.0429-0.0090.093613.843913.40861.5705
620.43980.124-0.2031.34440.13341.00650.0428-0.03370.07020.1511-0.00620.3724-0.0455-0.0911-0.03660.04980.020.07360.02610.01830.20226.785621.021954.0332
632.4012-0.76570.40011.84520.26981.936-0.0039-0.3242-0.06380.27150.05910.41010.0919-0.2764-0.05520.1215-0.02870.16880.12910.01980.27171.15164.963165.0263
645.3479-3.8506-2.04835.8533-1.14683.0197-0.3213-0.2358-0.55890.23540.18910.52310.15640.0680.13220.3541-0.0820.07590.19280.07380.293512.2689-19.463668.7967
651.35670.05580.58011.0895-0.8991.10780.13210.0257-0.13020.0115-0.08060.0050.20510.108-0.05140.34450.0234-0.03810.07050.08420.172427.2621-65.989256.3358
660.3939-0.9863-0.09262.54370.26050.3378-0.0093-0.0336-0.012-0.08050.0638-0.021-0.0359-0.0315-0.05450.1899-0.0186-0.00860.04080.07060.134524.3408-52.332151.5389
670.2329-0.0550.37021.56421.09992.91640.1366-0.1233-0.1190.1829-0.11860.49150.2107-0.2842-0.01810.1897-0.08570.02610.11040.06340.295613.4893-63.283162.7795
683.4006-0.57020.73942.8205-1.37682.71670.0064-0.4029-0.1480.3130.0429-0.11810.0090.1777-0.04930.26010.01880.00010.1070.05370.097122.2584-62.782176.8849
690.3274-0.4353-0.55452.6137-0.19611.6103-0.05160.03-0.21030.0534-0.1490.20470.13740.00190.20060.2456-0.1022-0.07990.09570.00950.303213.0125-65.029730.4576
704.0814-0.92638.72340.23-1.984918.64810.12-0.0577-0.0282-0.0416-0.05990.02840.2848-0.108-0.06010.22170.00220.02370.278-0.00810.34055.3453-64.451152.5969
711.91410.2505-0.211.1102-0.22680.9782-0.03320.0847-0.1649-0.0711-0.00420.3750.1807-0.17020.03740.1347-0.0776-0.07390.05670.00760.23742.1875-56.521233.186
721.21430.95040.19496.46940.13980.9726-0.0084-0.2236-0.17150.1929-0.01170.67580.2023-0.12150.020.1625-0.07540.04690.1980.07160.2989-8.044-55.416346.6569
732.72880.6503-0.49361.10120.23540.61140.1005-0.1225-0.3033-0.22350.0025-0.12290.32880.0606-0.1030.5716-0.0009-0.11270.0441-0.07860.2722.666-65.326411.6115
744.30283.0041-6.66112.6873-3.65112.01060.15670.15960.13130.2155-0.08880.1871-0.0273-0.5931-0.06790.2593-0.0765-0.09730.3305-0.02610.376-1.5652-62.059316.0648
751.40820.03940.05230.5679-0.11140.069-0.01080.0316-0.0839-0.17060.04840.00340.0753-0.0146-0.03760.2084-0.0377-0.09050.0241-0.02880.161314.0644-52.16436.539
761.98890.2382-0.66323.5379-1.43164.49290.05780.20640.09560.06310.07260.6733-0.1592-0.6616-0.13030.237-0.0456-0.16640.2254-0.030.3338-4.8199-59.45341.8185
770.8283-0.33961.53540.90710.1074.06850.16040.0501-0.2207-0.1516-0.01290.01880.35930.0165-0.14740.25860.00060.03090.0872-0.07910.282240.7518-63.28924.6679
786.08260.63090.52960.11760.08690.0688-0.14280.6785-0.11350.06750.10440.04140.06090.04740.03840.658-0.0738-0.01820.4268-0.14770.264222.9467-57.2608-10.6438
791.18410.0095-0.11241.91310.82261.9405-0.01090.1133-0.1617-0.50850.10480.00170.15030.1793-0.09390.3375-0.00260.01430.0623-0.08860.157439.7665-51.0604-6.2401
801.2874-0.10630.34441.71810.50231.34110.14370.5199-0.3421-0.20650.18550.27150.2654-0.2562-0.32920.6043-0.078-0.12890.4593-0.01240.314529.1409-58.4066-23.2481
810.4859-0.09192.00071.7353-0.915711.91960.0019-0.04020.0136-0.0991-0.129-0.02980.39210.34650.1270.25860.06540.04530.1069-0.03640.303155.3866-66.823418.3885
823.3337-0.39991.41681.4096-0.0912.22170.04630.2055-0.1914-0.3116-0.012-0.2977-0.0273-0.0198-0.03430.28860.05430.160.1126-0.09110.237961.6925-53.0989-2.0771
831.85992.413-0.11654.1248-0.27010.81430.03-0.13750.03810.03490.02020.12310.259-0.0845-0.05030.22410.04890.0280.1543-0.06690.206957.9456-44.057415.5831
842.6295-0.1143-0.30450.39910.3631.76660.02320.2259-0.0991-0.26010.0041-0.29640.13240.2061-0.02730.35070.12920.17360.1284-0.06040.347770.5344-56.0197-1.5704
858.45361.9131-7.35570.4335-1.6676.482-0.24280.2792-0.2997-0.0530.0545-0.07460.3218-0.10690.18830.36520.1329-0.07280.261-0.07280.30351.362-70.825436.5598
860.6468-0.4006-0.3691.33791.22182.12250.1528-0.0128-0.2193-0.182-0.1004-0.2650.25170.2015-0.05240.22140.14230.02780.1488-0.00810.473371.1378-50.944932.3178
8713.66484.97721.57799.39870.75853.6053-0.3580.10940.2969-0.24990.10240.33910.0336-0.22780.25560.23640.08890.04870.11290.01760.18356.2959-53.270339.8501
881.27020.0522-0.04680.6783-0.04492.31570.0427-0.0042-0.241-0.03410.0324-0.49860.29310.5339-0.07510.16570.1602-0.01950.1986-0.08310.554680.1767-56.41436.6669
8911.98540.3353-1.87650.4937-0.56470.8537-0.26410.322-0.6732-0.35850.086-0.04160.4041-0.10050.1780.3043-0.0394-0.03220.09320.01090.194338.3704-72.090343.6171
901.83731.1146-0.00621.3309-1.12642.09720.1773-0.1847-0.66410.0392-0.1248-0.38890.34440.1496-0.05260.33670.1394-0.14840.12670.08630.386861.2016-62.386858.7965
911.2660.2706-0.01550.86720.58521.50480.0432-0.1375-0.15430.1180.0278-0.18340.16860.0417-0.0710.20410.0416-0.06090.05020.04710.161348.8163-54.127556.1507
923.9731-1.4959-1.41134.02560.60991.59580.0338-0.4104-0.33060.20670.0732-0.44940.32530.2548-0.1070.25620.0208-0.18580.19190.1130.263763.1992-61.526569.5812
930.7988-0.0309-0.15281.2163-0.18550.53220.062-0.0776-0.08540.1514-0.00290.16840.05120.0011-0.05910.1377-0.02630.01380.03120.03130.065229.5414-25.619762.4411
942.1719-0.5356-0.19163.54760.90231.97220.0586-0.2471-0.16840.36390.0187-0.14570.22530.0474-0.07730.11-0.0346-0.0160.12490.03930.084637.8646-17.67670.5155
951.4251-1.90271.60124.6774-2.41722.5486-0.0594-0.26930.01340.510.01720.0919-0.0887-0.09590.04220.1452-0.0190.06750.16910.01780.045127.1124-15.864276.2466
967.24972.01822.047713.5568-3.69082.14750.0201-0.52290.59130.2123-0.00010.5032-0.2718-0.1351-0.01990.2927-0.01410.09590.2889-0.00150.129518.1201-12.424277.1921
970.5148-0.3328-0.10291.49830.45350.58670.0311-0.0603-0.02590.0891-0.01640.27360.0789-0.0624-0.01460.0953-0.03420.00170.03810.05130.19756.7175-24.154850.4525
980.01740.04650.10675.0945-0.6821.54950.00630.01160.03490.2271-0.02190.50730.0183-0.23310.01560.0421-0.04080.04270.1780.05470.2695-5.6639-17.963451.0573
9912.5231-12.780616.602813.5361-19.11932.26790.14750.32510.0368-0.265-0.16550.01250.8167-0.0290.0180.1977-0.06090.01120.2669-0.01120.3176-16.973-4.309734.1288
1001.9170.4685-0.8811.83441.71434.45120.02090.3948-0.2172-0.0117-0.04450.45350.1656-0.06280.02360.139-0.0486-0.16780.3156-0.03410.5165-13.7197-14.151810.2436
1010.5780.3042-0.02262.8751-0.92251.1021-0.03-0.0836-0.0083-0.2403-0.00830.24120.0147-0.12670.03830.1063-0.0173-0.11670.04360.00650.15954.8065-20.72715.0899
1022.55031.78210.80713.43840.99462.52230.14590.0211-0.08680.0902-0.0470.29670.1094-0.1036-0.09890.11370.0107-0.03360.04450.04510.14912.8106-28.743424.9026
1039.33650.8411.51850.08530.13560.24960.0019-1.47840.0641-0.009-0.0510.0026-0.0245-0.24770.04910.45220.034-0.01750.87430.13770.7161.9251-20.180130.1452
1040.9905-0.26740.03581.44370.00952.07060.1211-0.008-0.0013-0.0345-0.04860.37520.0064-0.3238-0.07250.0726-0.0207-0.11920.07880.02490.3569-7.0045-11.696815.957
10510.93794.32360.98932.83950.77791.00720.31540.02670.23380.1214-0.10720.01810.19370.0924-0.20830.29920.03380.0050.08130.02750.147627.6455-10.4109-5.1581
1060.5586-0.3418-0.07961.9718-0.23941.2264-0.0662-0.0122-0.0868-0.23150.09330.0736-0.0137-0.0359-0.02710.1864-0.0131-0.05650.00530.00360.053721.382-19.7106-1.1697
1071.14380.9231-0.02955.4050.66920.66770.02450.11130.0366-0.4774-0.0550.0319-0.0342-0.110.03050.20410.0102-0.00830.12420.02150.071924.9395-7.5928-10.3159
10821.178414.7161-5.221610.7344-4.33472.2765-0.2260.40490.7162-0.0961-0.21350.01410.00850.63040.43950.8886-0.20140.17450.8775-0.0381.18728.5472-8.6347-17.5899
1091.86281.12343.59062.23283.036510.4946-0.01230.02570.1247-0.06840.0022-0.1468-0.2571-0.07730.01010.1553-0.03130.08090.10290.00040.230360.1403-7.49763.1727
1100.96960.21550.13711.0637-0.03761.23080.09730.0406-0.0919-0.43870.0277-0.2359-0.06070.0089-0.1250.23350.00720.09310.0467-0.05370.124352.6189-24.61595.3813
1110.60960.48690.5972.72630.0891.066-0.05130.196-0.0043-0.4690.1445-0.07220.13650.1408-0.09320.2996-0.02590.11280.1325-0.04180.161153.5709-8.6954-4.5986
1120.7771.3990.07386.97290.07980.8954-0.01450.2418-0.0539-0.30330.1154-0.5008-0.08590.1206-0.10090.14850.02220.110.179-0.05310.156966.8837-2.8673-4.2331
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION11-8 - 13
2X-RAY DIFFRACTION2114 - 128
3X-RAY DIFFRACTION31129 - 165
4X-RAY DIFFRACTION41166 - 213
5X-RAY DIFFRACTION52-7 - 62
6X-RAY DIFFRACTION6263 - 148
7X-RAY DIFFRACTION72149 - 205
8X-RAY DIFFRACTION82206 - 225
9X-RAY DIFFRACTION9A11 - 130
10X-RAY DIFFRACTION10A131 - 182
11X-RAY DIFFRACTION11A183 - 223
12X-RAY DIFFRACTION12A224 - 252
13X-RAY DIFFRACTION13B2 - 47
14X-RAY DIFFRACTION14B48 - 63
15X-RAY DIFFRACTION15B64 - 179
16X-RAY DIFFRACTION16B180 - 249
17X-RAY DIFFRACTION17C2 - 48
18X-RAY DIFFRACTION18C49 - 64
19X-RAY DIFFRACTION19C65 - 175
20X-RAY DIFFRACTION20C176 - 245
21X-RAY DIFFRACTION21D3 - 48
22X-RAY DIFFRACTION22D49 - 65
23X-RAY DIFFRACTION23D66 - 210
24X-RAY DIFFRACTION24D211 - 243
25X-RAY DIFFRACTION25E9 - 30
26X-RAY DIFFRACTION26E31 - 83
27X-RAY DIFFRACTION27E84 - 140
28X-RAY DIFFRACTION28E141 - 250
29X-RAY DIFFRACTION29F3 - 81
30X-RAY DIFFRACTION30F82 - 126
31X-RAY DIFFRACTION31F127 - 172
32X-RAY DIFFRACTION32F173 - 234
33X-RAY DIFFRACTION33G4 - 162
34X-RAY DIFFRACTION34G163 - 175
35X-RAY DIFFRACTION35G176 - 207
36X-RAY DIFFRACTION36G208 - 247
37X-RAY DIFFRACTION37H1 - 17
38X-RAY DIFFRACTION38H18 - 84
39X-RAY DIFFRACTION39H85 - 147
40X-RAY DIFFRACTION40H148 - 196
41X-RAY DIFFRACTION41I1 - 45
42X-RAY DIFFRACTION42I46 - 75
43X-RAY DIFFRACTION43I76 - 198
44X-RAY DIFFRACTION44I199 - 221
45X-RAY DIFFRACTION45J-7 - 67
46X-RAY DIFFRACTION46J68 - 114
47X-RAY DIFFRACTION47J115 - 126
48X-RAY DIFFRACTION48J127 - 196
49X-RAY DIFFRACTION49K0 - 28
50X-RAY DIFFRACTION50K29 - 88
51X-RAY DIFFRACTION51K89 - 160
52X-RAY DIFFRACTION52K161 - 195
53X-RAY DIFFRACTION53L1 - 96
54X-RAY DIFFRACTION54L97 - 109
55X-RAY DIFFRACTION55L110 - 197
56X-RAY DIFFRACTION56L198 - 212
57X-RAY DIFFRACTION57M-8 - 17
58X-RAY DIFFRACTION58M18 - 126
59X-RAY DIFFRACTION59M127 - 164
60X-RAY DIFFRACTION60M165 - 213
61X-RAY DIFFRACTION61N-7 - 61
62X-RAY DIFFRACTION62N62 - 141
63X-RAY DIFFRACTION63N142 - 205
64X-RAY DIFFRACTION64N206 - 225
65X-RAY DIFFRACTION65O11 - 77
66X-RAY DIFFRACTION66O78 - 136
67X-RAY DIFFRACTION67O137 - 197
68X-RAY DIFFRACTION68O198 - 251
69X-RAY DIFFRACTION69P2 - 46
70X-RAY DIFFRACTION70P47 - 63
71X-RAY DIFFRACTION71P64 - 195
72X-RAY DIFFRACTION72P196 - 250
73X-RAY DIFFRACTION73Q2 - 44
74X-RAY DIFFRACTION74Q45 - 65
75X-RAY DIFFRACTION75Q66 - 177
76X-RAY DIFFRACTION76Q178 - 245
77X-RAY DIFFRACTION77R3 - 39
78X-RAY DIFFRACTION78R40 - 63
79X-RAY DIFFRACTION79R64 - 187
80X-RAY DIFFRACTION80R188 - 243
81X-RAY DIFFRACTION81S9 - 35
82X-RAY DIFFRACTION82S36 - 85
83X-RAY DIFFRACTION83S86 - 133
84X-RAY DIFFRACTION84S134 - 250
85X-RAY DIFFRACTION85T3 - 24
86X-RAY DIFFRACTION86T25 - 105
87X-RAY DIFFRACTION87T106 - 125
88X-RAY DIFFRACTION88T126 - 234
89X-RAY DIFFRACTION89U4 - 26
90X-RAY DIFFRACTION90U27 - 60
91X-RAY DIFFRACTION91U61 - 171
92X-RAY DIFFRACTION92U172 - 247
93X-RAY DIFFRACTION93V1 - 102
94X-RAY DIFFRACTION94V103 - 143
95X-RAY DIFFRACTION95V144 - 184
96X-RAY DIFFRACTION96V185 - 196
97X-RAY DIFFRACTION97W1 - 150
98X-RAY DIFFRACTION98W151 - 193
99X-RAY DIFFRACTION99W194 - 201
100X-RAY DIFFRACTION100W202 - 220
101X-RAY DIFFRACTION101X-7 - 67
102X-RAY DIFFRACTION102X68 - 114
103X-RAY DIFFRACTION103X115 - 126
104X-RAY DIFFRACTION104X127 - 196
105X-RAY DIFFRACTION105Y0 - 28
106X-RAY DIFFRACTION106Y29 - 159
107X-RAY DIFFRACTION107Y160 - 190
108X-RAY DIFFRACTION108Y191 - 195
109X-RAY DIFFRACTION109Z1 - 32
110X-RAY DIFFRACTION110Z33 - 96
111X-RAY DIFFRACTION111Z97 - 171
112X-RAY DIFFRACTION112Z172 - 212

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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://pdbjlvh1.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