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- PDB-4l3c: Structure of HLA-A2 in complex with D76N b2m mutant and NY-ESO1 d... -

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基本情報

登録情報
データベース: PDB / ID: 4l3c
タイトルStructure of HLA-A2 in complex with D76N b2m mutant and NY-ESO1 double mutant
要素
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • NY-ESO1 double mutant (1Y, 9V)
キーワードIMMUNE SYSTEM / MHC / beta-2 microglobulin / HLA_A0201 / NY-ESO1 / D76N variant / immunglobulin / beta sandwitch / amyloid aggregation
機能・相同性
機能・相同性情報


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / Interferon alpha/beta signaling / positive regulation of protein binding / antibacterial humoral response / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus
類似検索 - 分子機能
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.64 Å
データ登録者Halabelian, L. / Giorgetti, S. / Bellotti, V. / Bolognesi, M. / Ricagno, S.
引用ジャーナル: J.Biol.Chem. / 年: 2014
タイトル: Class I Major Histocompatibility Complex, the Trojan Horse for Secretion of Amyloidogenic beta 2-Microglobulin.
著者: Halabelian, L. / Ricagno, S. / Giorgetti, S. / Santambrogio, C. / Barbiroli, A. / Pellegrino, S. / Achour, A. / Grandori, R. / Marchese, L. / Raimondi, S. / Mangione, P.P. / Esposito, G. / Al- ...著者: Halabelian, L. / Ricagno, S. / Giorgetti, S. / Santambrogio, C. / Barbiroli, A. / Pellegrino, S. / Achour, A. / Grandori, R. / Marchese, L. / Raimondi, S. / Mangione, P.P. / Esposito, G. / Al-Shawi, R. / Simons, J.P. / Speck, I. / Stoppini, M. / Bolognesi, M. / Bellotti, V.
履歴
登録2013年6月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02013年12月25日Provider: repository / タイプ: Initial release
改定 1.12014年1月8日Group: Database references
改定 1.22014年2月26日Group: Database references
改定 1.32023年9月20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_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
改定 1.42024年10月30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

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集合体

登録構造単位
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
m: NY-ESO1 double mutant (1Y, 9V)
C: HLA class I histocompatibility antigen, A-2 alpha chain
D: Beta-2-microglobulin
i: NY-ESO1 double mutant (1Y, 9V)
E: HLA class I histocompatibility antigen, A-2 alpha chain
F: Beta-2-microglobulin
k: NY-ESO1 double mutant (1Y, 9V)
G: HLA class I histocompatibility antigen, A-2 alpha chain
H: Beta-2-microglobulin
f: NY-ESO1 double mutant (1Y, 9V)
I: HLA class I histocompatibility antigen, A-2 alpha chain
J: Beta-2-microglobulin
l: NY-ESO1 double mutant (1Y, 9V)
K: HLA class I histocompatibility antigen, A-2 alpha chain
L: Beta-2-microglobulin
h: NY-ESO1 double mutant (1Y, 9V)
M: HLA class I histocompatibility antigen, A-2 alpha chain
N: Beta-2-microglobulin
e: NY-ESO1 double mutant (1Y, 9V)
O: HLA class I histocompatibility antigen, A-2 alpha chain
P: Beta-2-microglobulin
n: NY-ESO1 double mutant (1Y, 9V)
Q: HLA class I histocompatibility antigen, A-2 alpha chain
R: Beta-2-microglobulin
p: NY-ESO1 double mutant (1Y, 9V)
S: HLA class I histocompatibility antigen, A-2 alpha chain
T: Beta-2-microglobulin
o: NY-ESO1 double mutant (1Y, 9V)
U: HLA class I histocompatibility antigen, A-2 alpha chain
V: Beta-2-microglobulin
c: NY-ESO1 double mutant (1Y, 9V)
W: HLA class I histocompatibility antigen, A-2 alpha chain
X: Beta-2-microglobulin
g: NY-ESO1 double mutant (1Y, 9V)
Y: HLA class I histocompatibility antigen, A-2 alpha chain
Z: Beta-2-microglobulin
q: NY-ESO1 double mutant (1Y, 9V)
a: HLA class I histocompatibility antigen, A-2 alpha chain
b: Beta-2-microglobulin
j: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)633,135100
ポリマ－629,94642
非ポリマー3,18958
水2,414134
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
m: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1957
ポリマ－44,9963
非ポリマー1984
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-45 kcal/mol
Surface area19370 Å2
手法PISA
2
C: HLA class I histocompatibility antigen, A-2 alpha chain
D: Beta-2-microglobulin
i: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,3799
ポリマ－44,9963
非ポリマー3836
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-47 kcal/mol
Surface area19320 Å2
手法PISA
3
E: HLA class I histocompatibility antigen, A-2 alpha chain
F: Beta-2-microglobulin
k: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1596
ポリマ－44,9963
非ポリマー1633
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-37 kcal/mol
Surface area19310 Å2
手法PISA
4
G: HLA class I histocompatibility antigen, A-2 alpha chain
H: Beta-2-microglobulin
f: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1596
ポリマ－44,9963
非ポリマー1633
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-32 kcal/mol
Surface area19530 Å2
手法PISA
5
I: HLA class I histocompatibility antigen, A-2 alpha chain
J: Beta-2-microglobulin
l: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2659
ポリマ－44,9963
非ポリマー2696
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-60 kcal/mol
Surface area19280 Å2
手法PISA
6
K: HLA class I histocompatibility antigen, A-2 alpha chain
L: Beta-2-microglobulin
h: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2517
ポリマ－44,9963
非ポリマー2554
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-35 kcal/mol
Surface area19510 Å2
手法PISA
7
M: HLA class I histocompatibility antigen, A-2 alpha chain
N: Beta-2-microglobulin
e: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1957
ポリマ－44,9963
非ポリマー1984
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-45 kcal/mol
Surface area19330 Å2
手法PISA
8
O: HLA class I histocompatibility antigen, A-2 alpha chain
P: Beta-2-microglobulin
n: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2517
ポリマ－44,9963
非ポリマー2554
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-35 kcal/mol
Surface area19510 Å2
手法PISA
9
Q: HLA class I histocompatibility antigen, A-2 alpha chain
R: Beta-2-microglobulin
p: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2659
ポリマ－44,9963
非ポリマー2696
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-57 kcal/mol
Surface area19330 Å2
手法PISA
10
S: HLA class I histocompatibility antigen, A-2 alpha chain
T: Beta-2-microglobulin
o: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2517
ポリマ－44,9963
非ポリマー2554
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-34 kcal/mol
Surface area19340 Å2
手法PISA
11
U: HLA class I histocompatibility antigen, A-2 alpha chain
V: Beta-2-microglobulin
c: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1596
ポリマ－44,9963
非ポリマー1633
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-41 kcal/mol
Surface area19500 Å2
手法PISA
12
W: HLA class I histocompatibility antigen, A-2 alpha chain
X: Beta-2-microglobulin
g: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1957
ポリマ－44,9963
非ポリマー1984
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-46 kcal/mol
Surface area19410 Å2
手法PISA
13
Y: HLA class I histocompatibility antigen, A-2 alpha chain
Z: Beta-2-microglobulin
q: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,2517
ポリマ－44,9963
非ポリマー2554
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-36 kcal/mol
Surface area19460 Å2
手法PISA
14
a: HLA class I histocompatibility antigen, A-2 alpha chain
b: Beta-2-microglobulin
j: NY-ESO1 double mutant (1Y, 9V)
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)45,1596
ポリマ－44,9963
非ポリマー1633
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-36 kcal/mol
Surface area19390 Å2
手法PISA
単位格子
Length a, b, c (Å)102.110, 314.500, 316.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21C
31E
41G
51I
61K
71M
81O
91Q
101S
111U
121W
131Y
141a
12B
22D
32F
42H
52J
62L
72N
82P
92R
102T
112V
122X
132Z
142b

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPRO5AA1 - 2761 - 276
21GLYGLYPROPRO5CD1 - 2761 - 276
31GLYGLYPROPRO5EG1 - 2761 - 276
41GLYGLYPROPRO5GJ1 - 2761 - 276
51GLYGLYPROPRO5IM1 - 2761 - 276
61GLYGLYPROPRO5KP1 - 2761 - 276
71GLYGLYPROPRO5MS1 - 2761 - 276
81GLYGLYPROPRO5OV1 - 2761 - 276
91GLYGLYPROPRO5QY1 - 2761 - 276
101GLYGLYPROPRO5SBA1 - 2761 - 276
111GLYGLYPROPRO5UEA1 - 2761 - 276
121GLYGLYPROPRO5WHA1 - 2761 - 276
131GLYGLYPROPRO5YKA1 - 2761 - 276
141GLYGLYPROPRO5aNA1 - 2761 - 276
12ILEILEMETMET4BB1 - 992 - 100
22ILEILEMETMET4DE1 - 992 - 100
32ILEILEMETMET4FH1 - 992 - 100
42ILEILEMETMET4HK1 - 992 - 100
52ILEILEMETMET4JN1 - 992 - 100
62ILEILEMETMET4LQ1 - 992 - 100
72ILEILEMETMET4NT1 - 992 - 100
82ILEILEMETMET4PW1 - 992 - 100
92ILEILEMETMET4RZ1 - 992 - 100
102ILEILEMETMET4TCA1 - 992 - 100
112ILEILEMETMET4VFA1 - 992 - 100
122ILEILEMETMET4XIA1 - 992 - 100
132ILEILEMETMET4ZLA1 - 992 - 100
142ILEILEMETMET4bOA1 - 992 - 100

NCSアンサンブル:
ID
1
2

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要素

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タンパク質 , 2種, 28分子 ACEGIKMOQSUWYaBDFHJLNPRTVXZb

#1: タンパク質
HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


分子量: 31951.316 Da / 分子数: 14 / 断片: UNP RESIDUES 25-300 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-A, HLAA, HLA_A0201 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P01892, UniProt: P04439*PLUS
#2: タンパク質
Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


分子量: 11878.372 Da / 分子数: 14 / 断片: UNP RESIDUES 21-119 / Mutation: D76N / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, CDABP0092, HDCMA22P, NM_004048 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P61769

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タンパク質・ペプチド , 1種, 14分子 mikflhenpocgqj

#3: タンパク質・ペプチド
NY-ESO1 double mutant (1Y, 9V)


分子量: 1166.431 Da / 分子数: 14 / 由来タイプ: 合成

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非ポリマー , 3種, 192分子

#4: 化合物...
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 38 / 由来タイプ: 合成 / 式: Cl
#5: 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: 20 / 由来タイプ: 合成 / 式: C3H8O3
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 134 / 由来タイプ: 天然 / 式: H2O

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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: 4.03 Å3/Da / 溶媒含有率: 69.48 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 1.9 M ammonium sulphate, 2% PEG 6K, 100 mM Tris-HCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
PH範囲: 8.0-8.2

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データ収集

回折平均測定温度: 110 K
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID14-4 / 波長: 0.9393 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2012年9月16日
放射モノクロメーター: channel cut ESRF monochromator / 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: 0.9393 Å / 相対比: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.801
11-H, L, K20.199
反射解像度: 2.64→70.63 Å / Num. all: 294283 / Num. obs: 293400 / % possible obs: 99.7 % / 冗長度: 5.3 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 6.8
反射 シェル解像度: 2.64→2.79 Å / 冗長度: 5.4 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 1.9 / % possible all: 99.7

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解析

ソフトウェア
名称バージョン分類
MxCuBEデータ収集
PHASER位相決定
REFMAC5.5.0109精密化
MOSFLMデータ削減
SCALA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: PDB entry 1S9W

1s9w


解像度: 2.64→66.48 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.666 / SU ML: 0.136 / 交差検証法: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.05 / 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
Rfree0.21834 14628 5 %RANDOM
Rwork0.19914 ---
obs0.2001 278467 97.72 %-
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: 1.4 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 38.669 Å2
Baniso -1Baniso -2Baniso -3
1--19.43 Å20 Å2-0 Å2
2--12.51 Å20 Å2
3---6.92 Å2
精密化ステップサイクル: LAST / 解像度: 2.64→66.48 Å
タンパク質核酸リガンド溶媒全体
原子数44422 0 158 134 44714
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.010.02145838
X-RAY DIFFRACTIONr_bond_other_d0.0010.0231410
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.92362204
X-RAY DIFFRACTIONr_angle_other_deg0.796375516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25755348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.84423.1432450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.637157448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.59815392
X-RAY DIFFRACTIONr_chiral_restr0.0750.26314
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02151324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210150
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_it0.6511.526866
X-RAY DIFFRACTIONr_mcbond_other0.0921.510822
X-RAY DIFFRACTIONr_mcangle_it1.253243344
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.445318972
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5014.518860
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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

Ens-IDDom-IDAuth asym-ID数タイプRms dev position (Å)Weight position
11A1623medium positional0.230.5
11C1623medium positional0.230.5
11E1623medium positional0.250.5
11G1623medium positional0.240.5
11I1623medium positional0.290.5
11K1623medium positional0.20.5
11M1623medium positional0.210.5
11O1623medium positional0.310.5
11Q1623medium positional0.270.5
11S1623medium positional0.270.5
11U1623medium positional0.270.5
11W1623medium positional0.230.5
11Y1623medium positional0.260.5
11a1623medium positional0.280.5
22B1419medium positional0.480.5
22D1419medium positional0.380.5
22F1419medium positional0.380.5
22H1419medium positional0.380.5
22J1419medium positional0.360.5
22L1419medium positional0.380.5
22N1419medium positional0.40.5
22P1419medium positional0.430.5
22R1419medium positional0.430.5
22T1419medium positional0.380.5
22V1419medium positional0.320.5
22X1419medium positional0.420.5
22Z1419medium positional0.380.5
22b1419medium positional0.390.5
11A2221loose positional0.685
11C2221loose positional0.675
11E2221loose positional0.695
11G2221loose positional0.655
11I2221loose positional0.685
11K2221loose positional0.525
11M2221loose positional0.685
11O2221loose positional0.615
11Q2221loose positional0.665
11S2221loose positional0.695
11U2221loose positional0.695
11W2221loose positional0.645
11Y2221loose positional0.675
11a2221loose positional0.725
11B1623medium thermal4.982
11D1623medium thermal6.042
11F1623medium thermal4.342
11H1623medium thermal4.132
11J1623medium thermal4.72
11L1623medium thermal4.872
11N1623medium thermal2.682
11P1623medium thermal3.862
11R1623medium thermal3.572
11T1623medium thermal5.872
11V1623medium thermal1.852
11X1623medium thermal5.112
11Z1623medium thermal8.172
11b1623medium thermal8.492
22A1419medium thermal0.442
22C1419medium thermal0.612
22E1419medium thermal0.432
22G1419medium thermal0.362
22I1419medium thermal0.442
22K1419medium thermal0.412
22M1419medium thermal0.382
22O1419medium thermal0.332
22Q1419medium thermal0.382
22S1419medium thermal0.642
22U1419medium thermal0.362
22W1419medium thermal0.452
22Y1419medium thermal0.492
22a1419medium thermal0.922
11B2221loose thermal4.6410
11D2221loose thermal5.5610
11F2221loose thermal4.1610
11H2221loose thermal3.8910
11J2221loose thermal4.4210
11L2221loose thermal4.6310
11N2221loose thermal2.5310
11P2221loose thermal3.5510
11R2221loose thermal3.4810
11T2221loose thermal5.510
11V2221loose thermal1.9610
11X2221loose thermal4.710
11Z2221loose thermal7.6610
11b2221loose thermal7.6910
LS精密化 シェル解像度: 2.64→2.703 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.308 887 -
Rwork0.287 16688 -
obs--79.87 %
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)
14.2010.70810.16310.18730.14450.2221-0.04720.08410.0504-0.07910.03190.0124-0.0660.01080.01520.35220.00160.02140.360.01650.34646.3644-14.8227-3.4015
20.68170.1790.16410.3466-0.08820.13890.00020.0580.0121-0.044-0.0047-0.0153-0.0612-0.01440.00440.3640.0270.01540.35920.01520.337839.394-6.788-8.4502
34.1881-2.34291.05451.9313-1.51321.66670.08040.10770.0209-0.0429-0.00920.00920.03540.0492-0.07120.34950.0140.02120.3784-0.03230.343353.4373-10.09096.7223
41.5412-0.50340.28440.17-0.06051.33380.07230.00440.02140.00070.0272-0.02350.02850.0397-0.09950.34450.00920.02750.33540.02250.352155.1109-17.64536.2993
50.089-0.347-0.0441.6209-0.08190.54110.0460.0357-0.0163-0.0105-0.09690.14210.0886-0.05290.05090.3337-0.00330.02920.3898-0.00590.323725.0847-20.39040.9429
60.7773-0.2371-0.15070.29750.14440.7294-0.03440.0323-0.01820.06370.0172-0.02710.047-0.03320.01710.35860.00720.01270.33890.01630.338342.7334-20.493712.9675
70.86120.23580.86130.33280.31933.2339-0.035-0.03810.0225-0.0254-0.02480.0202-0.1111-0.23770.05980.33190.02150.01990.3625-0.00040.342526.3644-13.1494-2.5922
80.0709-0.2459-0.11840.99280.56560.55670.0099-0.0423-0.02840.0127-0.0193-0.00040.0667-0.0370.00940.35-0.01090.01620.37780.00860.334136.825-39.0228-21.4029
90.5062-0.6982-0.21852.26160.4780.5139-0.0617-0.0076-0.10220.1469-0.02280.08580.148-0.06640.08450.352-0.03270.03320.35320.0060.337131.3364-44.4853-23.0772
100.21930.12570.49580.31510.13661.2450.0184-0.02490.00120.00580.01270.03570.1349-0.1076-0.03110.3310.01320.00210.3692-0.00760.340947.1423-26.6199-22.2487
110.3024-0.1963-0.46220.22690.54591.32570.04230.02770.0921-0.01890.0006-0.022-0.09310.0447-0.04290.3374-0.00120.02510.37310.01160.334453.998-20.5605-19.6504
120.09040.0660.02280.05210.06654.8048-0.00830.0060.02420.01180.0280.0351-0.0404-0.0599-0.01970.3350.01640.01070.35540.0040.339148.3772-23.7187-20.3815
132.03770.39541.99760.07740.39241.99610.08090.1433-0.04820.01350.0417-0.01440.050.2258-0.12260.33470.01690.0110.3803-0.00970.344260.4038-28.6214-18.2034
149.78896.1246-4.394315.8369-4.23812.1638-0.4291-0.2264-0.554-0.89890.33311.16230.2555-0.00150.09590.32450.05680.01330.3692-0.12570.376747.8065-32.9996-30.9528
157.0911-0.13211.48330.0752-0.04610.32490.0997-0.1144-0.026-0.0124-0.0569-0.00640.0047-0.0459-0.04280.35780.00740.00920.3563-0.00920.34185.4073-49.2411-55.48
160.0086-0.05320.01790.5756-0.21940.10190.0135-0.0315-0.01970.00290.03820.0282-0.06910.0076-0.05170.36990.00060.010.3529-0.00220.341785.3493-40.6484-58.6851
172.33382.194-0.1152.14560.07670.46250.04120.05130.11120.03890.01080.1194-0.0653-0.0135-0.05190.34760.01050.00680.34330.00750.355786.9992-45.6076-66.8935
181.62750.0017-0.40870.36680.49740.78590.02840.0880.0108-0.029-0.0743-0.001-0.0328-0.12920.0460.34610.01140.01090.36050.03070.351272.7675-58.6368-58.9302
193.29241.95141.0941.39291.1271.41020.0694-0.0527-0.07520.0390.0219-0.14220.08440.0343-0.09140.32060.0227-0.00690.3516-0.00720.3696103.4862-54.5821-53.1769
201.1291-0.18350.06730.41630.10190.0404-0.0049-0.056-0.01060.02190.0286-0.02820.0346-0.0079-0.02370.36030.01410.01850.3370.00750.348385.7302-65.6601-58.3316
210.5750.78440.28423.40731.89551.11880.0096-0.0374-0.0787-0.04160.0725-0.1189-0.0480.0791-0.08210.35080.0086-0.00020.3456-0.00120.3513102.1477-48.4009-58.2657
220.022-0.0135-0.16880.238-0.03711.4891-0.01460.0066-0.02130.01820.02770.04230.08190.027-0.01310.35720.0161-0.00090.3527-0.0060.35491.5557-42.6772-26.9537
230.95480.0977-0.83880.04960.01422.1706-0.0843-0.0847-0.10820.04370.04070.0170.19980.19640.04360.37020.0559-0.01020.33220.00380.335697.1099-43.6287-21.2429
240.5405-1.7639-0.73745.92022.16862.15010.04120.00170.0482-0.03050.0096-0.32070.1066-0.2669-0.05080.3564-0.01670.02140.33170.02420.379973.8195-52.0108-41.6349
250.6473-0.7031-0.6010.77140.65320.55840.007-0.02590.07110.03570.0565-0.10760.00450.0154-0.06350.3640.0191-0.00110.3575-0.00730.343484.7525-29.7044-36.4506
260.7517-0.2716-0.18281.90241.27020.8554-0.00170.04180.0186-0.1229-0.07610.1624-0.0505-0.02870.07780.34080.0275-0.00020.34970.00610.331574.4684-37.0321-45.3592
270.13740.24020.20991.34630.52630.3514-0.0236-0.01160.0293-0.0191-0.00960.0645-0.0053-0.00040.03320.33440.01160.01530.35950.00230.342975.6435-37.9076-40.0806
280.11020.26340.02440.64920.1226.56950.09550.0032-0.02670.33650.0015-0.0194-0.00370.2039-0.0970.36350.06340.04480.3372-0.01620.25777.4497-33.0107-29.7745
294.8352-1.51450.04860.7899-0.08820.02080.0354-0.04680.03680.0138-0.0283-0.01850.0232-0.0084-0.00710.3759-0.00620.00950.3550.00030.3358109.5028-21.703132.7174
300.6084-0.2416-0.14110.29840.08630.13520.01250.00290.00220.0733-0.02620.01090.00950.00960.01380.3705-0.0048-0.00290.34670.00460.3435116.0686-16.582140.5292
314.01610.01212.78121.60840.13971.93710.1450.0454-0.05560.0447-0.10420.00070.09880.0123-0.04080.34260.00540.01740.38170.01230.3235103.5815-12.347226.3492
320.65240.21330.44710.4021-0.41781.28170.00340.0756-0.02170.04260.07390.0568-0.0036-0.0248-0.07720.34130.00750.01860.3654-0.01570.359899.8668-18.731922.3203
330.7049-0.26730.87140.8789-0.53631.1494-0.02750.0065-0.0323-0.0705-0.003-0.02710.02290.05380.03050.34610.02650.02650.38120.00090.3635130.3243-25.996426.6729
341.80640.114-0.18580.8823-0.12650.03820.02180.04490.0094-0.0899-0.0456-0.01380.0382-0.00740.02380.35370.01030.00930.37140.00080.3178113.0099-20.019615.5942
350.30880.13610.3240.5758-0.76852.03850.06560.038-0.04760.0522-0.0734-0.1035-0.07950.08580.00780.3250.00880.01660.3620.02470.3618129.2403-20.788932.9649
360.13240.3635-0.0441.2819-0.31580.20230.01830.0150.0092-0.0693-0.0159-0.03170.0414-0.0182-0.00240.35210.02590.0070.34390.00890.3552117.3139-51.628738.8992
371.37470.92990.34332.3650.03560.1253-0.06120.0685-0.1272-0.17830.0267-0.13720.0241-0.0190.03450.3730.02770.03930.33050.0060.3372122.5955-57.5738.2015
380.09870.1716-0.29630.7295-0.74171.0305-0.02450.0018-0.0264-0.0806-0.01270.04040.1815-0.01640.03720.3510.00760.01440.3277-0.00580.3536106.9346-40.512842.9473
390.0670.06260.14230.647-0.55681.16670.00580.01990.00890.0362-0.01090.06990.0062-0.04280.00520.35270.00370.03130.34220.01160.349102.1602-35.751844.1036
401.69651.1196-0.68561.1683-0.2822.69370.1681-0.23090.11720.0253-0.030.0562-0.21630.2834-0.13820.2780.0380.01950.31320.01740.3236104.4641-30.789643.4858
410.0883-0.17710.23850.4378-0.79682.11180.0206-0.0307-0.04710.02990.02470.0622-0.0339-0.0717-0.04520.3316-0.00280.01860.32770.0070.3623100.6067-38.695444.8493
420.1018-0.2278-0.14614.4181.36880.4882-0.18640.0710.00170.24450.2061-0.07120.23220.0073-0.01970.4442-0.0102-0.00420.32520.03310.3732106.1068-49.237449.4487
437.15591.1239-1.15490.2182-0.20630.27840.12230.14440.01370.0913-0.0340.00970.0287-0.0308-0.08830.3639-0.00870.00870.3356-0.00710.364358.2553-87.3725-61.4355
440.29950.18610.0320.122-0.00630.46620.0316-0.0034-0.0018-0.022-0.0143-0.01020.05890.0019-0.01730.36490.00740.0060.3239-0.00230.386264.9707-96.6746-62.7046
450.5356-0.1092-0.00810.9468-1.01211.11370.11340.1303-0.0649-0.0680.00640.14430.0554-0.0528-0.11980.3381-0.01550.00530.3635-0.01630.387251.3104-85.6155-49.0826
460.4405-0.5463-0.34360.76980.64740.9406-0.0721-0.08730.0240.02140.00940.01090.0502-0.07940.06270.34750.0102-0.00770.34270.00830.382449.4245-80.8619-54.4127
471.5803-0.9477-0.73021.3574-0.13880.7683-0.06020.16060.0790.1017-0.0177-0.16040.0218-0.09750.07790.3292-0.00250.00480.3491-0.01350.391279.6501-80.6016-61.6264
481.57490.04810.05180.2536-0.17040.31480.0437-0.0413-0.00370.0046-0.03810.0392-0.08640.0323-0.00560.3639-0.01570.01370.3213-0.00440.358362.6463-75.1-49.3098
490.5061-0.2158-0.35880.78850.46330.79620.02580.00940.03620.0370.012-0.13880.04690.0246-0.03780.35020.0056-0.00290.33560.00960.367878.2729-88.5688-61.2848
500.2839-0.26060.40290.4444-0.54070.9553-0.0199-0.0275-0.0045-0.0116-0.0143-0.0041-0.06750.01750.03430.3604-0.01160.01740.3555-0.02560.346165.8401-73.128-88.6416
511.6048-1.04360.6631.6122-1.02181.209-0.09650.01430.11410.0223-0.0373-0.0746-0.1880.06430.13380.3774-0.0509-0.00310.3111-0.02010.335771.0168-68.7452-92.8611
520.5636-0.0696-0.65890.8210.73651.4631-0.0365-0.1183-0.0326-0.1710.11050.0825-0.21520.1597-0.0740.33540.015-0.00380.3690.02320.333354.3943-80.5788-78.3242
530.0270.06760.23820.26440.81962.62690.0153-0.0279-0.0355-0.03270.01460.0356-0.0224-0.0287-0.02990.3586-0.0127-0.00860.34750.00880.358952.4276-87.7499-82.3683
545.1048-0.17772.72310.5575-0.86222.55130.1709-0.0356-0.4536-0.1390.0133-0.06880.3542-0.0709-0.18420.3875-0.03980.00410.3352-0.03440.378849.1006-95.2031-80.5479
550.1085-0.1199-0.28870.65410.73121.0949-0.01110.042-0.01970.0075-0.0002-0.01350.0212-0.06560.01130.3465-0.00090.00810.34870.01550.361751.296-85.215-79.3448
560.88780.8893-1.46392.5122-0.65724.03710.12880.24530.3023-0.16010.1721-0.0686-0.2686-0.285-0.30080.34250.01640.01080.40940.03870.413650.5309-81.5824-90.3051
579.1673-1.92820.40460.4542-0.09980.03710.08230.01470.21720.0001-0.066-0.1110.005-0.0063-0.01630.35390.00880.00140.3648-0.01080.346767.3492-25.570132.9148
580.8313-0.3874-0.08580.4238-0.06610.0560.0087-0.05980.00190.0289-0.0251-0.014-0.01610.01590.01640.37530.00540.0110.35910.01060.330664.8809-29.466642.711
593.12470.135-1.61650.30630.30941.36020.0376-0.25730.0124-0.0204-0.0385-0.0264-0.01580.220.0010.35490.0218-0.00270.39240.00490.344776.8467-36.897728.8234
600.17340.40140.04891.03690.20180.09140.0103-0.0026-0.0567-0.01880.0182-0.1315-0-0.0081-0.02850.3580.0116-0.00540.39020.01710.339977.4496-30.75524.8441
611.2685-0.0982-1.88971.1605-0.26873.01220.09980.06540.1001-0.0725-0.0395-0.038-0.0335-0.1309-0.06030.33260.0007-0.00810.37520.0080.336547.7828-23.019727.4692
620.80890.2541-0.07370.52040.08250.58140.00750.0324-0.0039-0.0242-0.02940.0055-0.00810.00040.02190.35330.01090.00420.35580.00840.332766.0239-32.357117.7201
630.56670.0545-0.34791.31461.42021.98030.0078-0.0431-0.0315-0.0353-0.04870.08780.0015-0.10140.04090.35070.00380.0060.35190.01570.333550.4299-27.203934.9047
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1510.35890.3986-0.46410.4472-0.51810.6037-0.01610.02960.01720.020.02720.0362-0.0143-0.029-0.01110.36040.0046-0.01580.3495-0.00010.358743.4686-36.3086-72.0699
1520.97330.9887-0.16641.4126-0.22740.08920.0227-0.0766-0.01540.1344-0.1291-0.2896-0.10580.08960.10640.3463-0.0612-0.06360.35340.0540.369156.1793-36.4214-66.8398
1530.1322-0.19110.09570.7701-0.6290.8183-0.01560.0376-0.00030.0417-0.04620.0008-0.06260.00560.06180.3367-0.0034-0.00330.354-0.00720.355849.8957-39.7877-66.572
1540.6514-0.67670.88110.8003-0.32225.0637-0.02310.1308-0.09880.0165-0.110.1421-0.0854-0.00150.13310.3153-0.0364-0.00460.39320.02940.377149.2377-38.5516-79.8465
1554.26240.5121-0.76780.4892-0.14990.1763-0.12380.0669-0.11290.0690.0857-0.00680.0067-0.00020.0380.3840.0283-0.00280.34180.02420.33945.138578.8938-41.0019
1560.72320.4432-0.15820.5675-0.21380.9231-0.00370.0154-0.02160.01790.06460.00780.0269-0.031-0.06090.37190.0047-0.00240.33990.03130.350138.220671.9232-47.3553
1570.6968-0.27930.66791.43411.27372.44450.12310.02340.022-0.02870.0418-0.17740.09350.0443-0.16490.3710.00560.01780.350.02520.372251.92589.4692-47.6972
1581.48010.730.73580.9614-0.10590.7316-0.12210.0590.0205-0.04710.055-0.0559-0.06760.00220.0670.38740.00640.02880.31660.00350.371952.018187.934-40.7564
1595.87432.05220.78651.5587-0.17070.3616-0.064-0.16090.12740.2480.02350.145-0.1523-0.10570.04060.36380.05150.03360.39540.00280.354122.712683.6525-34.3255
1601.2858-0.03910.20760.99940.09910.67060.0127-0.040.07450.0267-0.03680.0124-0.0777-0.04870.02410.39150.0190.01910.30870.00420.361540.211595.8272-39.4162
1610.97920.43550.21850.58-0.37970.6436-0.0770.02190.019-0.07330.16940.12180.0476-0.1932-0.09240.35050.02140.04330.37840.0290.339224.630876.8911-41.1681
1620.3424-0.09630.17350.3348-0.53840.9372-0.0290.05520.08870.10850.0368-0.0052-0.03450.0121-0.00780.39750.02520.03470.32340.01350.352638.260766.6878-12.8257
1630.99050.08150.99420.36-0.18592.0163-0.0929-0.11390.17040.1270.0332-0.0029-0.156-0.14950.05970.40170.05040.02720.3132-0.00070.343133.193166.2173-6.6541
1642.9978-1.46611.01195.0776-1.47372.83780.021-0.07530.43610.30210.06410.2117-0.35130.1167-0.08510.3650.0054-0.01720.34150.03670.423655.564483.7711-28.0533
1650.0608-0.0608-0.01951.4117-0.43360.1639-0.05220.01090.01050.04770.0216-0.02880.0167-0.04710.03060.4014-0.00240.00420.36790.01810.322549.651262.5131-27.1876
1665.7419-3.86281.29013.883-2.1091.54610.00130.6021-0.1819-0.0501-0.2844-0.08350.10720.08020.28310.33490.01780.04080.32940.03090.367254.286759.0729-35.6177
1670.04070.082-0.10471.20860.02770.3310.0034-0.00160.0012-0.0065-0.0347-0.04310.0065-0.01810.03130.3705-0.0070.01140.36260.0270.351652.904265.9592-27.6483
1684.8341-2.4383-4.55881.70430.8968.6768-0.2411-0.0599-0.01290.0940.22110.10430.3199-0.54590.020.36950.05050.02370.3530.02460.410549.334956.8718-17.3432
1695.56230.8234-1.60460.1288-0.25511.1175-0.05420.0714-0.14770.0374-0.0002-0.0046-0.096-0.0270.05440.3827-0.0323-0.03180.32310.01460.367384.429477.2059-36.9652
1700.20420.1261-0.36540.3324-0.07590.81770.01240.01980.01140.0109-0.04540.0182-0.0040.08810.03290.3628-0.0292-0.02560.37250.02030.355491.278767.7065-36.4324
1714.7447-2.20810.95291.3048-0.58940.2705-0.03120.03060.01980.09110.0750.0665-0.0354-0.0673-0.04380.4364-0.015-0.02790.3265-0.00230.327777.935579.8965-25.4593
1720.02150.00260.12460.00770.02880.7496-0.0376-0.01850.00620.01820.0326-0.0064-0.1315-0.05150.0050.3852-0.0337-0.02860.35220.00920.404377.589285-30.7348
1732.5956-0.1055-2.48250.10210.42573.52430.0767-0.01320.0251-0.0427-0.0212-0.0241-0.22760.1414-0.05560.3624-0.0802-0.02850.38150.0480.4101105.725684.7384-39.1446
1741.0523-0.38330.18650.7158-0.65710.63780.07290.1570.17410.1462-0.0847-0.024-0.16120.06970.01180.4317-0.0682-0.04210.2984-0.01290.383288.290392.0013-27.7611
1750.38090.67790.30741.56411.2943.5329-0.0426-0.0130.05680.0736-0.14890.00840.03770.43240.19150.3107-0.0563-0.05480.4120.07060.3549104.319976.2677-36.9402
1760.2432-0.07330.10040.501-0.44521.03160.044-0.0806-0.01960.0306-0.03730.028-0.05860.0081-0.00660.345-0.03410.02250.3453-0.00260.349891.210585.0691-66.5908
1770.7785-0.52570.25850.88-0.68171.0364-0.0368-0.0490.0549-0.0125-0.02750.0063-0.05810.04960.06430.3529-0.03550.00630.3215-0.00690.349596.318488.5654-71.6961
1780.0872-0.2879-0.23931.43960.90530.99-0.0014-0.05030.0924-0.09070.0885-0.0933-0.11760.0066-0.08710.3592-0.0336-0.02110.35460.00420.337880.189179.9232-54.7523
1790.13130.24350.40990.68560.89991.3764-0.0236-0.02160.01040.0156-0.0366-0.0138-0.0453-0.0140.06010.3697-0.048-0.00550.34290.02790.358478.298571.9265-57.0675
1800.69870.63550.65512.07910.49781.59040.0647-0.0651-0.06110.1424-0.1194-0.18540.1129-0.03590.05470.2974-0.04630.01290.35410.01910.36179.190673.0052-49.1148
1810.1983-0.2347-0.48140.52090.64641.20150.00830.0638-0.03060.0163-0.07250.0341-0.0049-0.10120.06420.3434-0.0267-0.00440.36110.01140.364774.681873.3247-57.8237
1820.1052-0.54870.91432.9093-4.82818.02380.02020.04320.0482-0.0591-0.295-0.13370.06240.47190.27480.3545-0.02620.00550.37-0.02560.408978.674974.6813-68.6324
1835.69560.9715-0.29640.4387-0.32020.28850.01280.1096-0.05850.05380.0084-0.0096-0.01020.0254-0.02120.4060.0178-0.01850.3586-0.03510.300485.956935.56050.9975
1840.44990.0632-0.06820.53230.08440.2355-0.0768-0.03320.0266-0.00590.0345-0.0644-0.0239-0.02990.04230.3650.01930.00070.3688-0.00730.34292.107428.7813-5.8323
1851.1625-1.6658-0.47883.12340.0590.7428-0.16520.108-0.01140.17790.0902-0.12870.1198-0.27220.0750.34170.0872-0.02590.4748-0.00690.231678.321629.736112.4527
1862.4808-0.5197-0.58020.6593-0.04460.24560.07550.04750.0514-0.05430.08720.09930.079-0.0343-0.16270.37610.0302-0.05070.3991-0.05980.3277.837736.309110.6055
1870.5101-0.21580.38580.5284-1.14292.4886-0.2107-0.12290.20410.1214-0.013-0.1088-0.23680.05870.22370.3957-0.0329-0.04640.3592-0.05960.4221107.162140.72254.6551
1881.3178-0.0024-0.27920.5006-0.18990.1342-0.1174-0.15970.09730.13920.0924-0.0866-0.0549-0.00260.0250.4010.0779-0.05290.4429-0.06210.283491.328136.830617.7478
1890.9669-0.50670.21950.5078-0.29720.1909-0.0853-0.07250.1113-0.07-0.0458-0.2330.08280.07010.13120.375-0.0165-0.03440.3567-0.00520.3843106.277634.726-1.6795
1900.3626-0.09180.16420.7268-0.11920.2696-0.0305-0.0265-0.02790.0972-0.00020.0083-0.0830.03470.03070.3898-0.032-0.01780.3496-0.00230.358393.46563.5003-11.6312
1911.201-1.4597-0.15243.7263-0.15050.1431-0.1175-0.06650.18930.12570.0314-0.249-0.10070.02830.08620.3964-0.0516-0.06390.3431-0.01260.326898.740669.4853-12.2977
1921.8135-2.3882-0.43084.8486-2.8327.02510.0951-0.2666-0.14860.31520.23740.4492-0.60580.3387-0.33240.47920.0206-0.00330.3176-0.09550.427976.347848.79825.9651
1930.21670.0451-0.01091.0017-0.98871.0002-0.0167-0.02120.10150.1217-0.0463-0.0938-0.15830.10370.06310.3742-0.0297-0.02710.3534-0.02040.389885.456953.1313-19.3046
1940.61360.1324-0.02270.2043-0.32910.637-0.11450.0453-0.03790.00920.056-0.06370.0488-0.1170.05840.3916-0.0101-0.02630.3455-0.01160.373577.17945.6666-14.9126
1950.23980.1107-0.3250.1948-0.18090.4556-0.04630.01060.06280.03150.0992-0.06350.0101-0.0585-0.05290.3910.0094-0.02750.3658-0.00120.366278.56348.5752-11.7138
1964.4113-3.4217-3.55613.20080.679645.32310.59-1.06971.3119-0.8951-0.1485-1.5959-0.5521-0.873-0.44150.41820.16960.42221.70720.5761.113581.896959.3639-20.9424
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION2A20 - 70
3X-RAY DIFFRACTION3A71 - 83
4X-RAY DIFFRACTION4A84 - 98
5X-RAY DIFFRACTION5A99 - 112
6X-RAY DIFFRACTION6A113 - 153
7X-RAY DIFFRACTION7A154 - 181
8X-RAY DIFFRACTION8A182 - 242
9X-RAY DIFFRACTION9A243 - 275
10X-RAY DIFFRACTION10B0 - 23
11X-RAY DIFFRACTION11B24 - 54
12X-RAY DIFFRACTION12B55 - 78
13X-RAY DIFFRACTION13B79 - 94
14X-RAY DIFFRACTION14B95 - 99
15X-RAY DIFFRACTION15C1 - 16
16X-RAY DIFFRACTION16C17 - 52
17X-RAY DIFFRACTION17C53 - 81
18X-RAY DIFFRACTION18C82 - 98
19X-RAY DIFFRACTION19C99 - 112
20X-RAY DIFFRACTION20C113 - 153
21X-RAY DIFFRACTION21C154 - 181
22X-RAY DIFFRACTION22C182 - 242
23X-RAY DIFFRACTION23C243 - 275
24X-RAY DIFFRACTION24D0 - 7
25X-RAY DIFFRACTION25D8 - 26
26X-RAY DIFFRACTION26D27 - 56
27X-RAY DIFFRACTION27D57 - 91
28X-RAY DIFFRACTION28D92 - 99
29X-RAY DIFFRACTION29E1 - 19
30X-RAY DIFFRACTION30E20 - 72
31X-RAY DIFFRACTION31E73 - 80
32X-RAY DIFFRACTION32E81 - 98
33X-RAY DIFFRACTION33E99 - 112
34X-RAY DIFFRACTION34E113 - 153
35X-RAY DIFFRACTION35E154 - 181
36X-RAY DIFFRACTION36E182 - 242
37X-RAY DIFFRACTION37E243 - 275
38X-RAY DIFFRACTION38F0 - 19
39X-RAY DIFFRACTION39F20 - 43
40X-RAY DIFFRACTION40F44 - 59
41X-RAY DIFFRACTION41F60 - 94
42X-RAY DIFFRACTION42F95 - 99
43X-RAY DIFFRACTION43G1 - 19
44X-RAY DIFFRACTION44G20 - 71
45X-RAY DIFFRACTION45G72 - 84
46X-RAY DIFFRACTION46G85 - 98
47X-RAY DIFFRACTION47G99 - 112
48X-RAY DIFFRACTION48G113 - 153
49X-RAY DIFFRACTION49G154 - 181
50X-RAY DIFFRACTION50G182 - 242
51X-RAY DIFFRACTION51G243 - 275
52X-RAY DIFFRACTION52H0 - 14
53X-RAY DIFFRACTION53H15 - 42
54X-RAY DIFFRACTION54H43 - 53
55X-RAY DIFFRACTION55H54 - 90
56X-RAY DIFFRACTION56H91 - 99
57X-RAY DIFFRACTION57I1 - 16
58X-RAY DIFFRACTION58I17 - 70
59X-RAY DIFFRACTION59I71 - 83
60X-RAY DIFFRACTION60I84 - 99
61X-RAY DIFFRACTION61I100 - 112
62X-RAY DIFFRACTION62I113 - 153
63X-RAY DIFFRACTION63I154 - 181
64X-RAY DIFFRACTION64I182 - 242
65X-RAY DIFFRACTION65I243 - 275
66X-RAY DIFFRACTION66J0 - 12
67X-RAY DIFFRACTION67J13 - 42
68X-RAY DIFFRACTION68J43 - 53
69X-RAY DIFFRACTION69J54 - 89
70X-RAY DIFFRACTION70J90 - 99
71X-RAY DIFFRACTION71K1 - 19
72X-RAY DIFFRACTION72K20 - 72
73X-RAY DIFFRACTION73K73 - 80
74X-RAY DIFFRACTION74K81 - 98
75X-RAY DIFFRACTION75K99 - 112
76X-RAY DIFFRACTION76K113 - 153
77X-RAY DIFFRACTION77K154 - 181
78X-RAY DIFFRACTION78K182 - 242
79X-RAY DIFFRACTION79K243 - 275
80X-RAY DIFFRACTION80L0 - 6
81X-RAY DIFFRACTION81L7 - 30
82X-RAY DIFFRACTION82L31 - 48
83X-RAY DIFFRACTION83L49 - 93
84X-RAY DIFFRACTION84L94 - 99
85X-RAY DIFFRACTION85M1 - 16
86X-RAY DIFFRACTION86M17 - 51
87X-RAY DIFFRACTION87M52 - 81
88X-RAY DIFFRACTION88M82 - 98
89X-RAY DIFFRACTION89M99 - 112
90X-RAY DIFFRACTION90M113 - 155
91X-RAY DIFFRACTION91M156 - 181
92X-RAY DIFFRACTION92M182 - 242
93X-RAY DIFFRACTION93M243 - 275
94X-RAY DIFFRACTION94N0 - 6
95X-RAY DIFFRACTION95N7 - 42
96X-RAY DIFFRACTION96N43 - 54
97X-RAY DIFFRACTION97N55 - 94
98X-RAY DIFFRACTION98N95 - 99
99X-RAY DIFFRACTION99O1 - 19
100X-RAY DIFFRACTION100O20 - 73
101X-RAY DIFFRACTION101O74 - 83
102X-RAY DIFFRACTION102O84 - 99
103X-RAY DIFFRACTION103O100 - 114
104X-RAY DIFFRACTION104O115 - 181
105X-RAY DIFFRACTION105O182 - 218
106X-RAY DIFFRACTION106O219 - 232
107X-RAY DIFFRACTION107O233 - 275
108X-RAY DIFFRACTION108P0 - 6
109X-RAY DIFFRACTION109P7 - 42
110X-RAY DIFFRACTION110P43 - 57
111X-RAY DIFFRACTION111P58 - 91
112X-RAY DIFFRACTION112P92 - 99
113X-RAY DIFFRACTION113Q1 - 19
114X-RAY DIFFRACTION114Q20 - 70
115X-RAY DIFFRACTION115Q71 - 84
116X-RAY DIFFRACTION116Q85 - 99
117X-RAY DIFFRACTION117Q100 - 113
118X-RAY DIFFRACTION118Q114 - 153
119X-RAY DIFFRACTION119Q154 - 181
120X-RAY DIFFRACTION120Q182 - 242
121X-RAY DIFFRACTION121Q243 - 275
122X-RAY DIFFRACTION122R0 - 7
123X-RAY DIFFRACTION123R8 - 42
124X-RAY DIFFRACTION124R43 - 61
125X-RAY DIFFRACTION125R62 - 94
126X-RAY DIFFRACTION126R95 - 99
127X-RAY DIFFRACTION127S1 - 19
128X-RAY DIFFRACTION128S20 - 73
129X-RAY DIFFRACTION129S74 - 84
130X-RAY DIFFRACTION130S85 - 99
131X-RAY DIFFRACTION131S100 - 112
132X-RAY DIFFRACTION132S113 - 153
133X-RAY DIFFRACTION133S154 - 181
134X-RAY DIFFRACTION134S182 - 242
135X-RAY DIFFRACTION135S243 - 275
136X-RAY DIFFRACTION136T0 - 6
137X-RAY DIFFRACTION137T7 - 42
138X-RAY DIFFRACTION138T43 - 53
139X-RAY DIFFRACTION139T54 - 94
140X-RAY DIFFRACTION140T95 - 99
141X-RAY DIFFRACTION141U1 - 27
142X-RAY DIFFRACTION142U28 - 73
143X-RAY DIFFRACTION143U74 - 84
144X-RAY DIFFRACTION144U85 - 98
145X-RAY DIFFRACTION145U99 - 112
146X-RAY DIFFRACTION146U113 - 155
147X-RAY DIFFRACTION147U156 - 181
148X-RAY DIFFRACTION148U182 - 242
149X-RAY DIFFRACTION149U243 - 275
150X-RAY DIFFRACTION150V0 - 7
151X-RAY DIFFRACTION151V8 - 31
152X-RAY DIFFRACTION152V32 - 46
153X-RAY DIFFRACTION153V47 - 91
154X-RAY DIFFRACTION154V92 - 99
155X-RAY DIFFRACTION155W1 - 19
156X-RAY DIFFRACTION156W20 - 71
157X-RAY DIFFRACTION157W72 - 84
158X-RAY DIFFRACTION158W85 - 99
159X-RAY DIFFRACTION159W100 - 112
160X-RAY DIFFRACTION160W113 - 155
161X-RAY DIFFRACTION161W156 - 181
162X-RAY DIFFRACTION162W182 - 242
163X-RAY DIFFRACTION163W243 - 275
164X-RAY DIFFRACTION164X0 - 4
165X-RAY DIFFRACTION165X5 - 42
166X-RAY DIFFRACTION166X43 - 53
167X-RAY DIFFRACTION167X54 - 94
168X-RAY DIFFRACTION168X95 - 99
169X-RAY DIFFRACTION169Y1 - 19
170X-RAY DIFFRACTION170Y20 - 70
171X-RAY DIFFRACTION171Y71 - 83
172X-RAY DIFFRACTION172Y84 - 99
173X-RAY DIFFRACTION173Y100 - 113
174X-RAY DIFFRACTION174Y114 - 153
175X-RAY DIFFRACTION175Y154 - 181
176X-RAY DIFFRACTION176Y182 - 242
177X-RAY DIFFRACTION177Y243 - 275
178X-RAY DIFFRACTION178Z0 - 14
179X-RAY DIFFRACTION179Z15 - 42
180X-RAY DIFFRACTION180Z43 - 60
181X-RAY DIFFRACTION181Z61 - 93
182X-RAY DIFFRACTION182Z94 - 99
183X-RAY DIFFRACTION183a1 - 19
184X-RAY DIFFRACTION184a20 - 73
185X-RAY DIFFRACTION185a74 - 84
186X-RAY DIFFRACTION186a85 - 98
187X-RAY DIFFRACTION187a99 - 112
188X-RAY DIFFRACTION188a113 - 155
189X-RAY DIFFRACTION189a156 - 181
190X-RAY DIFFRACTION190a182 - 242
191X-RAY DIFFRACTION191a243 - 275
192X-RAY DIFFRACTION192b0 - 4
193X-RAY DIFFRACTION193b5 - 19
194X-RAY DIFFRACTION194b20 - 50
195X-RAY DIFFRACTION195b51 - 94
196X-RAY DIFFRACTION196b95 - 99

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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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