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- PDB-4l29: Structure of wtMHC class I with NY-ESO1 double mutant -

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基本情報

登録情報
データベース: PDB / ID: 4l29
タイトルStructure of wtMHC class I with 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
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 / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / 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 / Golgi membrane / external side of plasma 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 / フーリエ合成 / 解像度: 3.09 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4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 1.32024年11月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
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)632,86592
ポリマ－629,95942
非ポリマー2,90550
水99155
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)45,1606
ポリマ－44,9973
非ポリマー1633
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-35 kcal/mol
Surface area19190 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)45,3448
ポリマ－44,9973
非ポリマー3475
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-40 kcal/mol
Surface area19210 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)45,1606
ポリマ－44,9973
非ポリマー1633
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-35 kcal/mol
Surface area19040 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)45,1606
ポリマ－44,9973
非ポリマー1633
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-33 kcal/mol
Surface area19330 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)45,2318
ポリマ－44,9973
非ポリマー2345
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-49 kcal/mol
Surface area19180 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)45,2527
ポリマ－44,9973
非ポリマー2554
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-35 kcal/mol
Surface area19200 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)45,1606
ポリマ－44,9973
非ポリマー1633
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-36 kcal/mol
Surface area19320 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)45,2527
ポリマ－44,9973
非ポリマー2554
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-37 kcal/mol
Surface area19170 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)45,1967
ポリマ－44,9973
非ポリマー1984
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-42 kcal/mol
Surface area19120 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)45,2527
ポリマ－44,9973
非ポリマー2554
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-36 kcal/mol
Surface area19090 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)45,1606
ポリマ－44,9973
非ポリマー1633
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-38 kcal/mol
Surface area19350 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)45,1255
ポリマ－44,9973
非ポリマー1282
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-29 kcal/mol
Surface area19320 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)45,2527
ポリマ－44,9973
非ポリマー2554
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-33 kcal/mol
Surface area19180 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)45,1606
ポリマ－44,9973
非ポリマー1633
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-35 kcal/mol
Surface area19080 Å2
手法PISA
単位格子
Length a, b, c (Å)101.570, 313.360, 314.460
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 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPROCD1 - 2761 - 276
31GLYGLYPROPROEG1 - 2761 - 276
41GLYGLYPROPROGJ1 - 2761 - 276
51GLYGLYPROPROIM1 - 2761 - 276
61GLYGLYPROPROKP1 - 2761 - 276
71GLYGLYPROPROMS1 - 2761 - 276
81GLYGLYPROPROOV1 - 2761 - 276
91GLYGLYPROPROQY1 - 2761 - 276
101GLYGLYPROPROSBA1 - 2761 - 276
111GLYGLYPROPROUEA1 - 2761 - 276
121GLYGLYPROPROWHA1 - 2761 - 276
131GLYGLYPROPROYKA1 - 2761 - 276
141GLYGLYPROPROaNA1 - 2761 - 276
12ILEILEMETMETBB1 - 992 - 100
22ILEILEMETMETDE1 - 992 - 100
32ILEILEMETMETFH1 - 992 - 100
42ILEILEMETMETHK1 - 992 - 100
52ILEILEMETMETJN1 - 992 - 100
62ILEILEMETMETLQ1 - 992 - 100
72ILEILEMETMETNT1 - 992 - 100
82ILEILEMETMETPW1 - 992 - 100
92ILEILEMETMETRZ1 - 992 - 100
102ILEILEMETMETTCA1 - 992 - 100
112ILEILEMETMETVFA1 - 992 - 100
122ILEILEMETMETXIA1 - 992 - 100
132ILEILEMETMETZLA1 - 992 - 100
142ILEILEMETMETbOA1 - 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: 11879.356 Da / 分子数: 14 / 断片: UNP RESIDUES 21-119 / 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, 105分子

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


分子量: 35.453 Da / 分子数: 30 / 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: 55 / 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: 3.97 Å3/Da / 溶媒含有率: 69.03 %
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: BM14 / 波長: 1.0716 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2013年4月5日 / 詳細: bent collimating mirror and toroid
放射モノクロメーター: Si(111) 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: 1.0716 Å / 相対比: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.671
11-H, L, K20.329
反射解像度: 3.09→53.88 Å / Num. all: 182537 / Num. obs: 182537 / % possible obs: 100 % / 冗長度: 5.8 % / Rmerge(I) obs: 0.192 / Net I/σ(I): 9.3
反射 シェル解像度: 3.09→3.27 Å / 冗長度: 5.5 % / Rmerge(I) obs: 0.01015 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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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
REFMAC5.5.0109精密化
MOSFLMデータ削減
SCALAデータスケーリング
REFMAC5.5.0109位相決定
精密化構造決定の手法: フーリエ合成 / 解像度: 3.09→53.8 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.896 / SU B: 23.54 / SU ML: 0.197 / 交差検証法: THROUGHOUT / ESU R Free: 0.068 / 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
Rfree0.20054 9155 5 %RANDOM
Rwork0.17058 ---
obs0.17208 173264 98.82 %-
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: BABINET MODEL WITH MASK
原子変位パラメータBiso mean: 48.226 Å2
Baniso -1Baniso -2Baniso -3
1--29 Å20 Å20 Å2
2--5.71 Å20 Å2
3---23.3 Å2
精密化ステップサイクル: LAST / 解像度: 3.09→53.8 Å
タンパク質核酸リガンド溶媒全体
原子数44422 0 150 55 44627
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02145838
X-RAY DIFFRACTIONr_bond_other_d0.0010.0231410
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.92462204
X-RAY DIFFRACTIONr_angle_other_deg0.772375516
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09555348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32723.1432450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.895157448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.14415392
X-RAY DIFFRACTIONr_chiral_restr0.0680.26314
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02151324
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_it0.481.526866
X-RAY DIFFRACTIONr_mcbond_other0.0571.510822
X-RAY DIFFRACTIONr_mcangle_it0.91243344
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.952318972
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6684.518860
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 positional0.270.5
11C1623medium positional0.240.5
11E1623medium positional0.310.5
11G1623medium positional0.330.5
11I1623medium positional0.330.5
11K1623medium positional0.250.5
11M1623medium positional0.260.5
11O1623medium positional0.340.5
11Q1623medium positional0.310.5
11S1623medium positional0.330.5
11U1623medium positional0.330.5
11W1623medium positional0.260.5
11Y1623medium positional0.280.5
11a1623medium positional0.30.5
22B586medium positional0.560.5
22D586medium positional0.220.5
22F586medium positional0.240.5
22H586medium positional0.310.5
22G586medium positional0.270.5
22L586medium positional0.230.5
22N586medium positional0.230.5
22P586medium positional0.250.5
22R586medium positional0.20.5
22T586medium positional0.280.5
22V586medium positional0.230.5
22X586medium positional0.260.5
22Z586medium positional0.250.5
22b586medium positional0.310.5
11A2221loose positional0.825
11C2221loose positional0.735
11E2221loose positional0.775
11G2221loose positional0.735
11I2221loose positional0.755
11K2221loose positional0.615
11M2221loose positional0.765
11O2221loose positional0.75
11Q2221loose positional0.725
11S2221loose positional0.775
11U2221loose positional0.755
11W2221loose positional0.75
11Y2221loose positional0.735
11a2221loose positional0.845
22B833loose positional0.895
22D833loose positional0.655
22F833loose positional0.685
22H833loose positional0.765
22G833loose positional0.685
22L833loose positional0.695
22N833loose positional0.715
22P833loose positional0.885
22R833loose positional0.725
22T833loose positional0.835
22V833loose positional0.775
22X833loose positional0.835
22Z833loose positional0.725
22b833loose positional0.745
11A1623medium thermal3.982
11C1623medium thermal5.542
11E1623medium thermal3.972
11G1623medium thermal3.832
11I1623medium thermal4.332
11K1623medium thermal4.092
11M1623medium thermal1.972
11O1623medium thermal3.562
11Q1623medium thermal4.542
11S1623medium thermal4.452
11U1623medium thermal2.992
11W1623medium thermal4.332
11Y1623medium thermal5.592
11a1623medium thermal6.522
22B586medium thermal1.612
22D586medium thermal3.892
22F586medium thermal2.822
22H586medium thermal2.212
22G586medium thermal2.82
22L586medium thermal2.062
22N586medium thermal1.672
22P586medium thermal2.42
22R586medium thermal3.152
22T586medium thermal3.682
22V586medium thermal2.182
22X586medium thermal2.582
22Z586medium thermal2.512
22b586medium thermal4.432
11A2221loose thermal3.5910
11C2221loose thermal5.1710
11E2221loose thermal3.7910
11G2221loose thermal3.6310
11I2221loose thermal4.1710
11K2221loose thermal3.9210
11M2221loose thermal2.0510
11O2221loose thermal3.410
11Q2221loose thermal4.4810
11S2221loose thermal4.2410
11U2221loose thermal2.9610
11W2221loose thermal4.1610
11Y2221loose thermal5.2710
11a2221loose thermal5.9110
22B833loose thermal1.8710
22D833loose thermal3.7510
22F833loose thermal2.7410
22H833loose thermal2.1710
22G833loose thermal2.7310
22L833loose thermal2.2610
22N833loose thermal1.7410
22P833loose thermal2.4910
22R833loose thermal3.0210
22T833loose thermal3.5710
22V833loose thermal2.1810
22X833loose thermal2.5510
22Z833loose thermal2.4510
22b833loose thermal4.310
LS精密化 シェル解像度: 3.09→3.167 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.258 576 -
Rwork0.204 11059 -
obs--86.27 %
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)
111.06862.32651.00440.6730.43350.73380.00140.02390.0380.04190.0068-0.0281-0.0987-0.0501-0.00830.27540.01480.0520.20240.04320.211945.7865-14.9046-3.6188
20.71620.51410.82930.41360.6911.1798-0.00850.0401-0.0615-0.026-0.0482-0.002-0.016-0.07980.05670.24840.04070.01810.26820.06650.241440.9892-9.7846-10.3463
36.3171-0.23842.6141.3566-1.05771.77-0.106-0.03240.29650.17540.02750.042-0.199-0.05860.07860.28670.07820.03720.20190.03110.215535.938-1.9724-5.6705
40.32670.1175-0.32211.50120.38150.4943-0.0410.0351-0.00040.05150.0905-0.19680.02430.0042-0.04950.28690.0140.00840.26640.02650.236655.5753-12.90198.6587
51.33740.81740.130.77280.11190.10050.0321-0.3062-0.18470.0028-0.0721-0.0034-0.0194-0.09230.040.22530.00310.03460.27860.04420.223435.5853-18.62060.2591
61.8271-0.22020.20190.1446-0.25810.5848-0.0005-0.0359-0.06830.04790.00570.03920.0529-0.0059-0.00520.26690.00930.04310.20660.03040.205740.6679-20.731511.7032
70.9264-0.09950.25240.7613-0.05172.8833-0.13280.0228-0.0105-0.0066-0.06580.0853-0.2013-0.26880.19860.23880.02140.03310.2580.02490.220726.1357-13.2288-2.9207
80.3662-0.1378-0.31020.9390.60460.8283-0.0364-0.0839-0.05610.0783-0.05370.00570.1622-0.06190.090.2758-0.01980.02630.23550.05480.251534.8917-40.6617-21.8963
97.542611.10710.083816.51450.25650.11810.18180.1255-0.06310.2386-0.1545-0.0162-0.1337-0.2261-0.02730.30420.2008-0.00090.478-0.10940.294528.8059-48.014-30.7012
100.378-0.28830.70051.1095-1.70742.8583-0.2103-0.15490.16950.0167-0.0155-0.0769-0.1815-0.16980.22590.21850.0457-0.01630.3005-0.01130.253748.5156-28.3019-16.6912
110.0628-0.0668-0.05450.11150.24863.5467-0.0058-0.02270.01-0.03460.02630.0619-0.1592-0.0064-0.02060.25440.02410.03510.22850.0160.238649.9426-21.6419-19.0915
125.139-2.49081.58772.52670.329811.20870.40580.161-0.0536-0.4119-0.2885-0.17010.0320.085-0.11730.2006-0.05760.03750.18180.0350.228550.3711-24.6905-36.696
130.70810.31692.12560.15711.07077.33030.10550.0738-0.07680.00130.0429-0.0262-0.03040.2143-0.14840.25050.00860.0470.3018-0.02220.255759.4393-28.2619-19.5282
148.23526.161-1.97114.6535-2.141815.1436-0.6042-0.26680.1389-0.5608-0.08340.10430.5602-1.02720.68760.38930.00940.00290.2432-0.04610.29147.3295-32.8902-31.4248
158.8267-0.11121.70360.3533-0.24850.6354-0.1073-0.18330.0708-0.12970.10890.0279-0.0473-0.0767-0.00160.29750.05140.00420.1609-0.02170.240381.9109-48.4028-56.2908
160.82350.53191.02030.37650.57311.63210.01740.0402-0.01440.01390.07080.0239-0.10930.0586-0.08820.27510.00710.02780.20610.00920.237686.7503-40.0732-58.0735
172.98412.70040.15712.8853-0.27380.5191-0.02670.03440.0927-0.17260.00770.0751-0.01750.02370.01890.25490.01930.01880.2187-0.03240.229387.0808-44.9373-66.7254
1811.3273-4.1822-0.21991.5822-0.32724.4299-0.01930.25780.3896-0.0093-0.0719-0.16060.0977-0.2250.09120.2991-0.03250.01350.1488-0.0050.264369.2577-62.4544-60.9403
193.70690.5994-0.06470.13330.07690.37610.0439-0.3312-0.1694-0.0247-0.0153-0.0423-0.0182-0.0301-0.02860.22610.00870.01220.20390.01880.282491.441-53.4043-54.5843
202.24990.48310.07480.4647-0.04420.10460.04-0.1013-0.07060.0296-0.0409-0.00910.0468-0.00540.00080.25170.02890.02610.17930.01620.226586.9915-64.7234-57.3847
210.92530.65530.14715.19712.42761.2885-0.0058-0.03580.0101-0.11460.0738-0.18160.02160.0801-0.0680.22380.01280.00790.2204-0.00190.2267101.5852-48.25-57.8948
220.5919-0.1914-0.45680.2440.01231.4094-0.0315-0.0305-0.0680.05250.07330.05420.04480.0662-0.04180.27370.0224-0.00110.2262-0.00540.23191.4013-42.9472-24.7531
232.3801-1.3146-4.46591.34472.13228.6476-0.1491-0.2912-0.04870.15780.1372-0.06540.23450.64740.01190.23220.0467-0.02030.2782-0.0350.2575102.3756-41.0245-23.4373
243.7392-0.02226.46785.6977-0.44311.22350.5276-0.2055-0.22910.2546-0.1746-0.40930.8651-0.3845-0.3530.17940.00830.07480.2682-0.03370.267471.9639-54.1456-43.1612
251.94781.64-0.00563.39410.47151.4444-0.1947-0.00080.02320.09240.2723-0.08790.05190.0062-0.07750.26120.0414-0.01120.2153-0.01070.208383.4261-35.051-35.9323
260.35150.0413-0.0862.86621.11110.4646-0.08280.02230.0158-0.10810.07350.0596-0.0223-0.00770.00930.26360.00870.0020.23870.00640.194977.8132-37.2423-43.7071
271.43952.04950.99074.60961.22790.72070.046-0.12550.06370.109-0.10530.1289-0.0098-0.15460.05930.21760.03760.0530.2561-0.05380.221371.6518-33.1545-36.5364
280.51520.03791.61961.0631-1.146111.8804-0.411-0.16250.05060.30670.0432-0.1632-0.4275-0.00460.36780.64260.2487-0.03960.2362-0.05850.189576.876-32.9742-29.7706
295.9248-1.40080.4640.6628-0.37980.2569-0.0044-0.19070.13130.0275-0.0131-0.0335-0.02230.02170.01760.2431-0.01570.02910.25460.00460.2264108.6638-21.541132.2219
301.2818-0.65320.33070.842-0.23640.10210.07640.013-0.08830.1623-0.08780.05810.01970.01760.01130.27290.0050.02780.23290.01930.2477113.3763-19.898840.5179
311.23290.45821.93260.21620.61423.3794-0.0283-0.06270.06830.0047-0.0374-0.0051-0.1861-0.12480.06570.2269-0.01220.00790.22710.0070.2499111.9121-11.861233.3393
320.24290.3239-0.13260.65520.16810.68670.00030.00780.02810.04870.02650.11380.040.0304-0.02680.22920.02490.04190.23470.0280.236102.0007-20.005323.6896
333.19180.24181.77570.4784-0.88993.2874-0.024-0.2181-0.1609-0.14910.0249-0.06690.2954-0.1505-0.0010.20310.05310.05330.25050.00610.262128.8705-26.3125.4742
342.02060.5183-0.21991.3278-0.78520.52680.06080.1816-0.0349-0.1614-0.04720.06610.11060.0301-0.01360.24330.01970.04740.2646-0.00280.1894111.7446-19.690614.6228
351.1392-0.3621.06691.7958-2.35483.49640.02540.04280.00720.059-0.1419-0.0293-0.14130.16030.11640.19120.00790.03210.25620.03730.2456128.3112-20.736932.3937
360.59310.2784-0.26211.7864-0.38650.3163-0.00250.06210.0096-0.1259-0.0358-0.03340.0811-0.03080.03830.24310.0330.0090.23230.01880.2284118.2563-53.142938.1284
371.392-3.188-2.385619.4584-6.352315.6135-0.04420.0983-0.1486-0.0252-0.8259-0.401-0.02150.34610.87010.33140.04740.07260.15740.07010.2744123.8652-63.815143.3824
381.4293-0.44571.33270.722-0.52562.79540.01540.23140.0062-0.0336-0.11320.09610.18490.30030.09790.22230.00190.03270.16340.02090.2423105.2303-38.972638.383
390.0596-0.15310.08191.1127-1.34172.0389-0.0685-0.0125-0.01170.05770.0233-0.0606-0.0344-0.04680.04530.24070.00470.02370.22320.01530.2414103.8306-33.968843.5005
404.2201-1.84282.40361.84-3.09375.41960.36650.3273-0.03310.03610.00960.1977-0.1189-0.128-0.37610.3104-0.01910.04910.17540.01720.249102.8323-44.092458.0583
410.1310.1442-0.48551.3999-4.069311.87280.1931-0.0232-0.0412-0.04320.04540.10730.0327-0.0377-0.23850.3007-0.0197-0.00530.17590.02510.316593.6739-38.764540.2311
425.61910.41574.950510.3537-3.42426.8327-0.0436-0.1376-0.490.07350.19470.15620.5316-0.2946-0.15120.3867-0.03810.13850.07210.00230.2519103.3791-48.379447.9814
434.54351.2237-0.01910.3627-0.09830.31010.0531-0.0804-0.1060.0307-0.029-0.02960.0556-0.0114-0.0240.2597-0.00640.02690.1790.01010.333757.9931-87.0342-61.1123
441.17710.5223-0.53110.5047-0.04220.6287-0.030.0677-0.0380.05270.06190.0220.0730.0405-0.03190.25430.0135-0.01620.1977-0.03010.273464.5192-96.4801-62.2931
450.763-0.912-0.68071.9719-0.89154.3176-0.0244-0.03280.02980.14470.02380.00420.0796-0.06620.00060.2369-0.0180.02060.1764-0.02150.295149.0517-83.1667-48.7439
464.1966-0.4002-0.03930.18230.03680.01710.006-0.10540.07490.01280.03460.01850.01790.0234-0.04050.2216-0.00150.01420.2054-0.02860.290667.5888-82.1901-59.8481
471.3599-0.32870.41680.108-0.10190.16220.02460.06110.00420.0293-0.05080.0723-0.0795-0.00430.02620.25620.00550.01460.1951-0.02390.273564.7019-75.6178-55.6087
483.6997-0.9282-0.45240.4457-0.56582.2699-0.1225-0.39230.20740.07450.0987-0.0519-0.1271-0.0180.02380.2852-0.0207-0.01450.1501-0.04410.244663.2819-74.4836-44.6605
492.1203-0.8336-1.59450.78790.45981.47480.00980.00610.07730.10020.1373-0.10890.16290.0315-0.14710.31470.0301-0.04990.2241-0.0370.273477.755-88.458-61.034
500.8844-0.40690.29690.7298-0.58621.0028-0.0704-0.01820.01050.01280.0007-0.0095-0.16210.09150.06970.2885-0.03080.02360.2228-0.0390.225767.2305-71.5582-89.0867
511.46232.8755-2.48836.8345-2.47749.2091-0.1220.0088-0.0147-0.28170.0959-0.05360.30850.15850.02610.35440.01710.05750.25810.00210.260872.5248-68.2718-100.9009
521.23870.1553-0.19690.8002-0.15290.1173-0.0786-0.1468-0.1275-0.08040.0650.1588-0.01540.14560.01370.192-0.0293-0.00670.33220.03690.222254.3332-80.5266-78.2611
530.3017-0.20080.11540.28560.5332.52780.04920.02440.0088-0.0091-0.0155-0.02590.1178-0.0727-0.03370.2416-0.01340.00490.23740.02010.262952.9514-87.6451-77.7129
546.2608-1.6042-0.10281.19372.90910.73820.56570.145-0.1963-0.147-0.1175-0.03530.0663-0.2641-0.44820.1964-0.02280.00070.2271-0.01380.293751.0889-92.4114-94.9274
550.0704-0.2801-0.52192.39674.23287.50670.11350.09540.032-0.0586-0.14150.0242-0.1354-0.39730.0280.25030.05020.01930.38120.12050.259643.3221-81.7268-80.2724
565.96450.938-6.97239.29119.995521.65470.0373-1.06630.8084-0.9671-0.54841.1929-0.9570.6750.51110.47460.0332-0.0030.369-0.06130.416254.0108-81.6758-92.8083
576.9791-2.8499-0.44171.86620.33170.0820.05630.1273-0.02180.0913-0.0857-0.01120.07580.02260.02940.25930.0229-0.00490.27350.02750.163269.6243-26.434734.5952
581.6173-0.36020.30741.5089-0.1370.7427-0.0339-0.0564-0.00170.1238-0.0354-0.01160.03810.00650.06930.2391-0.02180.02710.23090.00610.213362.1121-29.824143.715
590.0526-0.3315-0.03492.31060.37350.2196-0.03840.0240.02890.12640.0031-0.15160.14680.16110.03530.28890.02340.03830.30540.02030.213678.8121-35.890725.0854
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1496.14036.8232-1.53917.6059-1.42594.1256-0.89481.0521-0.1669-0.94881.0907-0.21271.3469-1.3392-0.1960.5983-0.3347-0.0660.65350.0530.214226.9194-45.9135-93.5416
1500.7688-0.56410.70662.619-1.95161.74810.04630.1334-0.3214-0.01370.24140.3493-0.01860.0403-0.28770.16040.0245-0.03740.2077-0.010.276246.3929-45.0454-68.5793
1510.02260.1314-0.14330.9245-1.28582.2073-0.0033-0.00760.03210.0314-0.03090.0815-0.09440.01780.03420.2328-0.0013-0.01960.2334-0.0360.27848.0681-38.9597-64.9786
1522.9243-1.14843.7512.4277-3.73467.41040.06280.3023-0.05860.06810.11780.0728-0.0210.0569-0.18060.28730.02040.00570.22370.03040.306949.491-27.335-78.695
1530.0577-0.21440.20427.1768-6.37295.66450.0810.0981-0.05940.0222-0.08730.007-0.00410.12720.00630.20960.0609-0.01370.2935-0.02710.303357.0029-43.1996-68.1022
1547.9359-4.46352.85593.6703-3.09762.9654-0.09120.40230.10650.1053-0.1438-0.2289-0.09060.10670.2350.2809-0.0377-0.02130.2302-0.05750.251552.1372-40.6604-77.3289
1556.43650.8738-0.94650.8701-0.39890.2701-0.0487-0.3051-0.0103-0.00140.0468-0.0682-0.05530.07310.00190.2682-0.00520.00040.26180.0320.208444.637878.5799-40.8757
1561.07570.29230.53760.4891-0.20720.62490.0556-0.0806-0.1335-0.03830.0042-0.01190.06490.0529-0.05970.2636-0.012-0.00890.25760.05730.256539.889470.6793-44.1124
1574.20044.20330.85544.680.87032.06580.0090.19520.0246-0.1886-0.07670.21120.00130.02540.06770.19990.0523-0.06410.2624-0.0020.264831.820170.5951-52.9063
1580.5259-0.52940.66040.5446-0.67330.86-0.00420.06580.01780.0067-0.0089-0.0314-0.08980.04550.01310.2664-0.03030.04580.2396-0.00010.258950.122287.72-47.3386
1595.29291.2028-0.90920.3324-0.081.0756-0.24880.0314-0.0519-0.03150.10120.00850.0984-0.10730.14760.3050.01980.04620.26230.03550.283835.038483.0503-37.5756
1603.03030.540.24261.04110.32720.87990.1166-0.08670.170.1517-0.07230.087-0.064-0.0156-0.04440.30320.03550.03230.1710.01660.246938.633594.6775-38.2946
1610.8203-0.34720.89180.2019-0.32731.04390.0671-0.0569-0.1234-0.11940.06570.1214-0.0715-0.0746-0.13280.31-0.00020.04030.25890.08140.29924.646777.8566-41.5765
1620.9394-0.17150.4710.32-0.50691.4215-0.07440.00140.17170.12990.0714-0.033-0.0647-0.00850.0030.32510.01530.01520.18770.0180.255636.027466.3437-10.9941
16320.2655-5.857511.66491.6935-3.38267.13220.3205-0.6239-0.5799-0.07580.2090.1743-0.0056-0.4689-0.52950.3130.03670.01560.05530.05350.225930.679559.3345-1.2277
1640.17530.1685-0.16241.80720.4680.43830.03820.10660.20120.21170.08690.2767-0.0421-0.0761-0.12510.30850.01640.00260.24590.08190.270448.43869.2038-25.0851
1650.3408-0.11260.18141.4607-0.99020.7227-0.0330.0845-0.0012-0.12420.0574-0.00230.03940.0331-0.02450.3130.00510.01170.23190.02980.217449.813265.3038-31.0317
1663.66922.4684-0.78598.1886-1.32090.2662-0.1617-0.0668-0.30060.25110.134-0.029-0.0229-0.02280.02770.27310.03820.04870.22210.0850.212151.167848.805-23.7988
1670.99681.08970.17613.5605-1.36651.0580.08410.0569-0.07220.1381-0.1148-0.1188-0.01630.13990.03070.2593-0.00580.05260.2510.04140.249359.596166.8163-24.9632
16818.80971.6298-0.687811.1582-1.67550.2673-0.08720.0186-0.29640.70930.09140.0034-0.0690.0018-0.00420.30510.038-0.0140.23710.04080.192748.570256.8254-17.145
1696.37780.5169-1.11850.10130.1361.4045-0.01570.0025-0.20060.0499-0.0231-0.0269-0.102-0.02080.03880.329-0.03280.02030.16520.03650.329483.87776.9979-36.824
1700.94860.0447-1.55320.025-0.11082.75150.02880.1037-0.00980.0064-0.0240.07010.00550.0439-0.00480.2778-0.03240.00750.25770.00010.279188.301368.7415-39.1718
1711.9409-2.08291.39932.2398-1.47041.2393-0.1776-0.12080.0590.20450.1723-0.0733-0.04050.17530.00530.30560.00520.00210.3589-0.02870.278393.791765.5051-31.0667
1720.26290.5485-0.63111.2213-1.42861.7717-0.0042-0.02470.0460.06090.06480.10360.0635-0.1774-0.06070.372-0.0049-0.00410.2263-0.03830.277274.787283.0895-25.4497
1731.1387-0.2564-0.35680.2951-0.19450.6311-0.1538-0.03180.08960.14870.0295-0.0252-0.16090.12550.12430.3317-0.0867-0.03880.1919-0.02870.299292.377387.768-30.6726
1741.84232.02861.30222.42451.9435.49760.02220.175-0.01020.16640.1-0.1476-0.02910.5516-0.12220.2085-0.0647-0.07170.36960.07480.2757105.186271.585-42.2929
1750.7923-0.42860.40160.7773-0.98871.70570.0653-0.1514-0.05190.0101-0.02380.0408-0.0517-0.0038-0.04150.2266-0.03050.04490.2197-0.02080.242891.005686.5138-68.5753
1761.05820.54980.01650.42310.15310.4889-0.0511-0.10180.0140.0643-0.0113-0.0162-0.10790.04160.06240.2574-0.03520.03830.2035-0.02490.240393.404885.3386-66.6811
1772.4365.97150.771716.26134.76045.3491-0.18130.0001-0.1122-0.12220.1646-0.24350.6170.34050.01670.26550.0394-0.01770.2825-0.040.239597.502186.557-79.6554
1780.1068-0.13390.22530.68870.38652.1058-0.00150.05270.02110.0294-0.0106-0.0264-0.1351-0.10610.01210.2455-0.09340.03640.23990.01160.2679.634779.2867-54.8843
1790.2747-0.2770.17490.80520.79112.0061-0.03570.0018-0.00990.00180.019-0.0618-0.0408-0.02230.01670.2604-0.07510.02730.2340.01620.267278.435372.6577-52.638
1802.29010.4993-2.90532.15732.19187.6955-0.03040.2044-0.0361-0.33780.2805-0.1578-0.3733-0.1204-0.25010.3004-0.08430.03780.33790.05430.262476.83464.1172-68.3607
1810.01540.09970.29320.80152.37747.0757-0.00130.02630.01610.15260.0534-0.00630.41290.1092-0.05210.2853-0.02840.02160.2960.02240.300469.142377.008-54.3591
1822.08121.1738-1.66730.7662-0.9715.28520.1160.31210.3281-0.05290.08130.1103-0.214-0.1975-0.19730.3329-0.00120.01490.27920.09190.251673.821276.374-64.0802
1831.0368-0.4151-0.52280.6938-0.45921.1248-0.0462-0.0123-0.1111-0.04110.01750.03030.1363-0.01360.02870.28260.0091-0.03040.2803-0.08380.212885.113835.4780.971
1840.9504-0.2484-0.52731.3809-0.29920.504-0.1924-0.0684-0.0536-0.17880.0838-0.07150.0592-0.02030.10860.32770.0181-0.02770.27570.00840.213989.413232.0473-7.1189
1850.2659-0.5386-0.30892.42712.23242.3599-0.095-0.08770.02980.14620.0749-0.0750.19160.040.02010.35380.05020.08370.25790.01320.210695.215323.5305-5.0488
1862.3243-2.8032-0.40243.6750.5120.0736-0.1986-0.387-0.15810.21090.16610.08560.03150.02710.03260.32580.07320.01380.47810.02620.161576.935430.302112.4841
1876.0699-0.1043-2.27871.0464-0.18880.9619-0.1824-0.0310.03170.07350.1126-0.1346-0.05860.00950.06990.2638-0.0229-0.06420.3148-0.07720.171794.689338.45684.8474
1880.85840.3925-0.3390.273-0.25980.3251-0.1223-0.07760.03350.11490.0117-0.0544-0.09530.03650.11060.36310.102-0.08340.4183-0.08280.174191.386637.761516.7919
1890.8818-0.2906-0.47421.1349-1.67214.853-0.017-0.06750.19120.01390.0116-0.07350.140.28370.00540.28760.0052-0.01260.24950.0030.2574104.78834.2968-0.3318
1900.59720.18220.25770.7329-0.23710.5135-0.0457-0.08480.05140.06780.0122-0.0932-0.0981-0.00230.03340.3177-0.0382-0.02730.2538-0.02010.237494.179265.0563-11.5085
1913.22982.7357.45966.8317.484817.7868-0.12810.35570.5547-0.7268-0.8531-0.5394-0.07980.43950.98120.52340.04820.08020.39360.25980.413299.478175.0685-18.565
1920.43210.2415-0.10030.4021-0.81393.2904-0.0845-0.0742-0.07560.0703-0.0549-0.1678-0.080.09850.13940.2752-0.0044-0.0030.22190.01040.268382.261850.6927-13.0921
1931.721-0.69281.96420.582-1.07452.516-0.059-0.25790.0464-0.15220.20270.18930.1189-0.4435-0.14370.30840.0017-0.03130.33250.0390.192872.445745.9427-12.4437
1941.1608-0.8473-0.40080.8931-0.361.8868-0.0027-0.1414-0.0297-0.05870.14610.02170.08870.1014-0.14340.3334-0.0026-0.02780.2563-0.0310.229481.450742.6573-8.6352
1952.6277-3.0255-1.041910.0257-4.25848.5179-0.02050.06610.06410.10360.0872-0.1928-0.3175-0.2289-0.06670.2322-0.0398-0.02910.24050.04520.239377.760552.6315-28.6162
1960.1429-0.0024-0.00160.0052-0.00440.04680.0047-0.09240.06650.00760.00080.0343-0.12350.025-0.00550.3469-0.0086-0.00180.27240.02020.29973.151653.7373-13.225
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION2A20 - 52
3X-RAY DIFFRACTION3A53 - 71
4X-RAY DIFFRACTION4A72 - 90
5X-RAY DIFFRACTION5A91 - 108
6X-RAY DIFFRACTION6A109 - 153
7X-RAY DIFFRACTION7A154 - 181
8X-RAY DIFFRACTION8A182 - 272
9X-RAY DIFFRACTION9A273 - 276
10X-RAY DIFFRACTION10B0 - 15
11X-RAY DIFFRACTION11B16 - 68
12X-RAY DIFFRACTION12B69 - 77
13X-RAY DIFFRACTION13B78 - 94
14X-RAY DIFFRACTION14B95 - 99
15X-RAY DIFFRACTION15C1 - 19
16X-RAY DIFFRACTION16C20 - 52
17X-RAY DIFFRACTION17C53 - 80
18X-RAY DIFFRACTION18C81 - 89
19X-RAY DIFFRACTION19C90 - 108
20X-RAY DIFFRACTION20C109 - 153
21X-RAY DIFFRACTION21C154 - 181
22X-RAY DIFFRACTION22C182 - 263
23X-RAY DIFFRACTION23C264 - 276
24X-RAY DIFFRACTION24D0 - 5
25X-RAY DIFFRACTION25D6 - 15
26X-RAY DIFFRACTION26D16 - 68
27X-RAY DIFFRACTION27D69 - 91
28X-RAY DIFFRACTION28D92 - 99
29X-RAY DIFFRACTION29E1 - 19
30X-RAY DIFFRACTION30E20 - 52
31X-RAY DIFFRACTION31E53 - 84
32X-RAY DIFFRACTION32E85 - 100
33X-RAY DIFFRACTION33E101 - 114
34X-RAY DIFFRACTION34E115 - 153
35X-RAY DIFFRACTION35E154 - 181
36X-RAY DIFFRACTION36E182 - 272
37X-RAY DIFFRACTION37E273 - 276
38X-RAY DIFFRACTION38F0 - 15
39X-RAY DIFFRACTION39F16 - 68
40X-RAY DIFFRACTION40F69 - 77
41X-RAY DIFFRACTION41F78 - 92
42X-RAY DIFFRACTION42F93 - 99
43X-RAY DIFFRACTION43G1 - 19
44X-RAY DIFFRACTION44G20 - 71
45X-RAY DIFFRACTION45G72 - 89
46X-RAY DIFFRACTION46G90 - 108
47X-RAY DIFFRACTION47G109 - 129
48X-RAY DIFFRACTION48G130 - 153
49X-RAY DIFFRACTION49G154 - 181
50X-RAY DIFFRACTION50G182 - 272
51X-RAY DIFFRACTION51G273 - 276
52X-RAY DIFFRACTION52H0 - 15
53X-RAY DIFFRACTION53H16 - 68
54X-RAY DIFFRACTION54H69 - 77
55X-RAY DIFFRACTION55H78 - 94
56X-RAY DIFFRACTION56H95 - 99
57X-RAY DIFFRACTION57I1 - 28
58X-RAY DIFFRACTION58I29 - 71
59X-RAY DIFFRACTION59I72 - 89
60X-RAY DIFFRACTION60I90 - 108
61X-RAY DIFFRACTION61I109 - 129
62X-RAY DIFFRACTION62I130 - 153
63X-RAY DIFFRACTION63I154 - 181
64X-RAY DIFFRACTION64I182 - 272
65X-RAY DIFFRACTION65I273 - 276
66X-RAY DIFFRACTION66J0 - 15
67X-RAY DIFFRACTION67J16 - 68
68X-RAY DIFFRACTION68J69 - 77
69X-RAY DIFFRACTION69J78 - 88
70X-RAY DIFFRACTION70J89 - 99
71X-RAY DIFFRACTION71K1 - 19
72X-RAY DIFFRACTION72K20 - 52
73X-RAY DIFFRACTION73K53 - 80
74X-RAY DIFFRACTION74K81 - 100
75X-RAY DIFFRACTION75K101 - 116
76X-RAY DIFFRACTION76K117 - 162
77X-RAY DIFFRACTION77K163 - 181
78X-RAY DIFFRACTION78K182 - 247
79X-RAY DIFFRACTION79K248 - 276
80X-RAY DIFFRACTION80L0 - 15
81X-RAY DIFFRACTION81L16 - 68
82X-RAY DIFFRACTION82L69 - 77
83X-RAY DIFFRACTION83L78 - 94
84X-RAY DIFFRACTION84L95 - 99
85X-RAY DIFFRACTION85M1 - 27
86X-RAY DIFFRACTION86M28 - 70
87X-RAY DIFFRACTION87M71 - 89
88X-RAY DIFFRACTION88M90 - 110
89X-RAY DIFFRACTION89M111 - 132
90X-RAY DIFFRACTION90M133 - 158
91X-RAY DIFFRACTION91M159 - 181
92X-RAY DIFFRACTION92M182 - 272
93X-RAY DIFFRACTION93M273 - 276
94X-RAY DIFFRACTION94N0 - 15
95X-RAY DIFFRACTION95N16 - 67
96X-RAY DIFFRACTION96N68 - 77
97X-RAY DIFFRACTION97N78 - 94
98X-RAY DIFFRACTION98N95 - 99
99X-RAY DIFFRACTION99O1 - 19
100X-RAY DIFFRACTION100O20 - 52
101X-RAY DIFFRACTION101O53 - 80
102X-RAY DIFFRACTION102O81 - 100
103X-RAY DIFFRACTION103O101 - 114
104X-RAY DIFFRACTION104O115 - 153
105X-RAY DIFFRACTION105O154 - 181
106X-RAY DIFFRACTION106O182 - 272
107X-RAY DIFFRACTION107O273 - 276
108X-RAY DIFFRACTION108P0 - 15
109X-RAY DIFFRACTION109P16 - 68
110X-RAY DIFFRACTION110P69 - 77
111X-RAY DIFFRACTION111P78 - 94
112X-RAY DIFFRACTION112P95 - 99
113X-RAY DIFFRACTION113Q1 - 20
114X-RAY DIFFRACTION114Q21 - 52
115X-RAY DIFFRACTION115Q53 - 70
116X-RAY DIFFRACTION116Q71 - 90
117X-RAY DIFFRACTION117Q91 - 108
118X-RAY DIFFRACTION118Q109 - 153
119X-RAY DIFFRACTION119Q154 - 181
120X-RAY DIFFRACTION120Q182 - 263
121X-RAY DIFFRACTION121Q264 - 276
122X-RAY DIFFRACTION122R0 - 15
123X-RAY DIFFRACTION123R16 - 68
124X-RAY DIFFRACTION124R69 - 77
125X-RAY DIFFRACTION125R78 - 92
126X-RAY DIFFRACTION126R93 - 99
127X-RAY DIFFRACTION127S1 - 19
128X-RAY DIFFRACTION128S20 - 52
129X-RAY DIFFRACTION129S53 - 84
130X-RAY DIFFRACTION130S85 - 99
131X-RAY DIFFRACTION131S100 - 116
132X-RAY DIFFRACTION132S117 - 179
133X-RAY DIFFRACTION133S180 - 203
134X-RAY DIFFRACTION134S204 - 272
135X-RAY DIFFRACTION135S273 - 276
136X-RAY DIFFRACTION136T0 - 15
137X-RAY DIFFRACTION137T16 - 68
138X-RAY DIFFRACTION138T69 - 77
139X-RAY DIFFRACTION139T78 - 94
140X-RAY DIFFRACTION140T95 - 99
141X-RAY DIFFRACTION141U1 - 19
142X-RAY DIFFRACTION142U20 - 65
143X-RAY DIFFRACTION143U66 - 90
144X-RAY DIFFRACTION144U91 - 108
145X-RAY DIFFRACTION145U109 - 128
146X-RAY DIFFRACTION146U129 - 153
147X-RAY DIFFRACTION147U154 - 181
148X-RAY DIFFRACTION148U182 - 272
149X-RAY DIFFRACTION149U273 - 276
150X-RAY DIFFRACTION150V0 - 15
151X-RAY DIFFRACTION151V16 - 68
152X-RAY DIFFRACTION152V69 - 77
153X-RAY DIFFRACTION153V78 - 88
154X-RAY DIFFRACTION154V89 - 99
155X-RAY DIFFRACTION155W1 - 19
156X-RAY DIFFRACTION156W20 - 52
157X-RAY DIFFRACTION157W53 - 65
158X-RAY DIFFRACTION158W66 - 89
159X-RAY DIFFRACTION159W90 - 108
160X-RAY DIFFRACTION160W109 - 153
161X-RAY DIFFRACTION161W154 - 181
162X-RAY DIFFRACTION162W182 - 272
163X-RAY DIFFRACTION163W273 - 276
164X-RAY DIFFRACTION164X0 - 15
165X-RAY DIFFRACTION165X16 - 68
166X-RAY DIFFRACTION166X69 - 77
167X-RAY DIFFRACTION167X78 - 94
168X-RAY DIFFRACTION168X95 - 99
169X-RAY DIFFRACTION169Y1 - 19
170X-RAY DIFFRACTION170Y20 - 52
171X-RAY DIFFRACTION171Y53 - 71
172X-RAY DIFFRACTION172Y72 - 90
173X-RAY DIFFRACTION173Y91 - 165
174X-RAY DIFFRACTION174Y166 - 181
175X-RAY DIFFRACTION175Y182 - 229
176X-RAY DIFFRACTION176Y230 - 272
177X-RAY DIFFRACTION177Y273 - 276
178X-RAY DIFFRACTION178Z0 - 15
179X-RAY DIFFRACTION179Z16 - 68
180X-RAY DIFFRACTION180Z69 - 77
181X-RAY DIFFRACTION181Z78 - 88
182X-RAY DIFFRACTION182Z89 - 99
183X-RAY DIFFRACTION183a1 - 19
184X-RAY DIFFRACTION184a20 - 52
185X-RAY DIFFRACTION185a53 - 70
186X-RAY DIFFRACTION186a71 - 89
187X-RAY DIFFRACTION187a90 - 108
188X-RAY DIFFRACTION188a109 - 153
189X-RAY DIFFRACTION189a154 - 181
190X-RAY DIFFRACTION190a182 - 272
191X-RAY DIFFRACTION191a273 - 276
192X-RAY DIFFRACTION192b0 - 30
193X-RAY DIFFRACTION193b31 - 44
194X-RAY DIFFRACTION194b45 - 68
195X-RAY DIFFRACTION195b69 - 77
196X-RAY DIFFRACTION196b78 - 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

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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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