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- PDB-7po7: Phosphoglycolate phosphatase from Mus musculus -

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基本情報

登録情報
データベース: PDB / ID: 7po7
タイトルPhosphoglycolate phosphatase from Mus musculus
要素Glycerol-3-phosphate phosphatase
キーワードHYDROLASE / PGP / Glycerol-3-phosphate phosphatase / AUM / Apo-enzyme
機能・相同性
機能・相同性情報


glycerol-1-phosphatase / sn-glycerol 3-phosphatase activity / sn-glycerol 1-phosphatase activity / glycerophospholipid metabolic process / ADP phosphatase activity / phosphoglycolate phosphatase activity / glycerol biosynthetic process / negative regulation of gluconeogenesis / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / magnesium ion binding
類似検索 - 分子機能
2-phosphoglycolate phosphatase, eukaryotic / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
ACETATE ION / Glycerol-3-phosphate phosphatase
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.31 Å
データ登録者Schloetzer, J. / Schindelin, H. / Fratz, S.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Nat Commun / 年: 2022
タイトル: Glycolytic flux control by drugging phosphoglycolate phosphatase.
著者: Jeanclos, E. / Schlotzer, J. / Hadamek, K. / Yuan-Chen, N. / Alwahsh, M. / Hollmann, R. / Fratz, S. / Yesilyurt-Gerhards, D. / Frankenbach, T. / Engelmann, D. / Keller, A. / Kaestner, A. / ...著者: Jeanclos, E. / Schlotzer, J. / Hadamek, K. / Yuan-Chen, N. / Alwahsh, M. / Hollmann, R. / Fratz, S. / Yesilyurt-Gerhards, D. / Frankenbach, T. / Engelmann, D. / Keller, A. / Kaestner, A. / Schmitz, W. / Neuenschwander, M. / Hergenroder, R. / Sotriffer, C. / von Kries, J.P. / Schindelin, H. / Gohla, A.
履歴
登録2021年9月8日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年12月21日Provider: repository / タイプ: Initial release
改定 1.12024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.22024年7月3日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.32024年10月23日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Glycerol-3-phosphate phosphatase
B: Glycerol-3-phosphate phosphatase
C: Glycerol-3-phosphate phosphatase
D: Glycerol-3-phosphate phosphatase
E: Glycerol-3-phosphate phosphatase
F: Glycerol-3-phosphate phosphatase
G: Glycerol-3-phosphate phosphatase
H: Glycerol-3-phosphate phosphatase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)279,14740
ポリマ－276,4848
非ポリマー2,66232
水5,170287
1
A: Glycerol-3-phosphate phosphatase
B: Glycerol-3-phosphate phosphatase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,6168
ポリマ－69,1212
非ポリマー4946
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-45 kcal/mol
Surface area25150 Å2
手法PISA
2
C: Glycerol-3-phosphate phosphatase
D: Glycerol-3-phosphate phosphatase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,89211
ポリマ－69,1212
非ポリマー7719
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-41 kcal/mol
Surface area25540 Å2
手法PISA
3
E: Glycerol-3-phosphate phosphatase
F: Glycerol-3-phosphate phosphatase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,80410
ポリマ－69,1212
非ポリマー6838
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-49 kcal/mol
Surface area26190 Å2
手法PISA
4
G: Glycerol-3-phosphate phosphatase
H: Glycerol-3-phosphate phosphatase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)69,83611
ポリマ－69,1212
非ポリマー7159
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-50 kcal/mol
Surface area22880 Å2
手法PISA
単位格子
Length a, b, c (Å)84.262, 91.197, 101.317
Angle α, β, γ (deg.)103.457, 89.980, 104.632
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGPROPRO(chain 'A' and (resid 12 through 103 or resid 105...AA12 - 8912 - 89
12LEULEUTYRTYR(chain 'A' and (resid 12 through 103 or resid 105...AA96 - 10396 - 103
13SERSERASNASN(chain 'A' and (resid 12 through 103 or resid 105...AA105 - 199105 - 199
14ASPASPVALVAL(chain 'A' and (resid 12 through 103 or resid 105...AA201 - 219201 - 219
15ALAALAARGARG(chain 'A' and (resid 12 through 103 or resid 105...AA221 - 238221 - 238
16ILEILEASPASP(chain 'A' and (resid 12 through 103 or resid 105...AA240 - 242240 - 242
17VALVALLEULEU(chain 'A' and (resid 12 through 103 or resid 105...AA244 - 319244 - 319
21ARGARGPROPRO(chain 'B' and (resid 12 through 89 or resid 96...BB12 - 8912 - 89
22LEULEUTYRTYR(chain 'B' and (resid 12 through 89 or resid 96...BB96 - 10396 - 103
23SERSERASNASN(chain 'B' and (resid 12 through 89 or resid 96...BB105 - 199105 - 199
24ASPASPVALVAL(chain 'B' and (resid 12 through 89 or resid 96...BB201 - 219201 - 219
25ALAALAARGARG(chain 'B' and (resid 12 through 89 or resid 96...BB221 - 238221 - 238
26ILEILEASPASP(chain 'B' and (resid 12 through 89 or resid 96...BB240 - 242240 - 242
27VALVALLEULEU(chain 'B' and (resid 12 through 89 or resid 96...BB244 - 319244 - 319
31ARGARGPROPRO(chain 'C' and (resid 12 through 89 or resid 96...CC12 - 8912 - 89
32LEULEUTYRTYR(chain 'C' and (resid 12 through 89 or resid 96...CC96 - 10396 - 103
33SERSERASNASN(chain 'C' and (resid 12 through 89 or resid 96...CC105 - 199105 - 199
34ASPASPVALVAL(chain 'C' and (resid 12 through 89 or resid 96...CC201 - 219201 - 219
35ALAALAARGARG(chain 'C' and (resid 12 through 89 or resid 96...CC221 - 238221 - 238
36ILEILEASPASP(chain 'C' and (resid 12 through 89 or resid 96...CC240 - 242240 - 242
37VALVALLEULEU(chain 'C' and (resid 12 through 89 or resid 96...CC244 - 319244 - 319
41ARGARGPROPRO(chain 'D' and (resid 12 through 89 or resid 96...DD12 - 8912 - 89
42LEULEUTYRTYR(chain 'D' and (resid 12 through 89 or resid 96...DD96 - 10396 - 103
43SERSERASNASN(chain 'D' and (resid 12 through 89 or resid 96...DD105 - 199105 - 199
44ASPASPVALVAL(chain 'D' and (resid 12 through 89 or resid 96...DD201 - 219201 - 219
45ALAALAARGARG(chain 'D' and (resid 12 through 89 or resid 96...DD221 - 238221 - 238
46ILEILEASPASP(chain 'D' and (resid 12 through 89 or resid 96...DD240 - 242240 - 242
47VALVALLEULEU(chain 'D' and (resid 12 through 89 or resid 96...DD244 - 319244 - 319
51ARGARGPROPRO(chain 'E' and (resid 12 through 89 or resid 96...EE12 - 8912 - 89
52LEULEUTYRTYR(chain 'E' and (resid 12 through 89 or resid 96...EE96 - 10396 - 103
53SERSERASNASN(chain 'E' and (resid 12 through 89 or resid 96...EE105 - 199105 - 199
54ASPASPVALVAL(chain 'E' and (resid 12 through 89 or resid 96...EE201 - 219201 - 219
55ALAALAARGARG(chain 'E' and (resid 12 through 89 or resid 96...EE221 - 238221 - 238
56ILEILEASPASP(chain 'E' and (resid 12 through 89 or resid 96...EE240 - 242240 - 242
57VALVALLEULEU(chain 'E' and (resid 12 through 89 or resid 96...EE244 - 319244 - 319
61ARGARGPROPRO(chain 'F' and (resid 12 through 89 or resid 96...FF12 - 8912 - 89
62LEULEUTYRTYR(chain 'F' and (resid 12 through 89 or resid 96...FF96 - 10396 - 103
63SERSERASNASN(chain 'F' and (resid 12 through 89 or resid 96...FF105 - 199105 - 199
64ASPASPVALVAL(chain 'F' and (resid 12 through 89 or resid 96...FF201 - 219201 - 219
65ALAALAARGARG(chain 'F' and (resid 12 through 89 or resid 96...FF221 - 238221 - 238
66ILEILEASPASP(chain 'F' and (resid 12 through 89 or resid 96...FF240 - 242240 - 242
67VALVALLEULEU(chain 'F' and (resid 12 through 89 or resid 96...FF244 - 319244 - 319
71ARGARGPROPRO(chain 'H' and (resid 12 through 89 or resid 96...HH12 - 8912 - 89
72LEULEUTYRTYR(chain 'H' and (resid 12 through 89 or resid 96...HH96 - 10396 - 103
73SERSERASNASN(chain 'H' and (resid 12 through 89 or resid 96...HH105 - 199105 - 199
74ASPASPVALVAL(chain 'H' and (resid 12 through 89 or resid 96...HH201 - 219201 - 219
75ALAALAARGARG(chain 'H' and (resid 12 through 89 or resid 96...HH221 - 238221 - 238
76ILEILEASPASP(chain 'H' and (resid 12 through 89 or resid 96...HH240 - 242240 - 242
77VALVALLEULEU(chain 'H' and (resid 12 through 89 or resid 96...HH244 - 319244 - 319

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要素

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タンパク質 , 1種, 8分子 ABCDEFGH

#1: タンパク質
Glycerol-3-phosphate phosphatase / G3PP / Aspartate-based ubiquitous Mg(2+)-dependent phosphatase / AUM / Phosphoglycolate phosphatase / PGP


分子量: 34560.559 Da / 分子数: 8 / 変異: D34N, C297S / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Pgp / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q8CHP8, glycerol-1-phosphatase, protein-tyrosine-phosphatase

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非ポリマー , 5種, 319分子

#2: 化合物
ChemComp-ACT / ACETATE ION / 酢酸イオン


分子量: 59.044 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C2H3O2
#3: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 8 / 由来タイプ: 合成 / 式: SO4
#4: 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: 15 / 由来タイプ: 合成 / 式: C3H8O3
#5: 化合物 ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Ca
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 287 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN
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: 2.75 Å3/Da / 溶媒含有率: 55.3 % / 解説: Plate
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5 / 詳細: 0.1 M Tris-HCl 0.2 M (NH4)2SO4 12% (w/v) PEG 8000

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: ID23-1 / 波長: 0.972422 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2017年2月11日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.972422 Å / 相対比: 1
反射解像度: 2.31→49.17 Å / Num. obs: 88859 / % possible obs: 71.32 % / Observed criterion σ(I): -3 / 冗長度: 3.1 % / Biso Wilson estimate: 49.53 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.062 / Net I/σ(I): 7.43
反射 シェル解像度: 2.31→2.54 Å / 冗長度: 3.4 % / Rmerge(I) obs: 1.078 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 4443 / CC1/2: 0.281 / Rpim(I) all: 0.684 / % possible all: 14.39

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4bkm

4bkm


解像度: 2.31→19.97 Å / SU ML: 0.2856 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 30.4273 / 立体化学のターゲット値: CDL v1.2
Rfactor反射数%反射
Rfree0.2296 2230 2.52 %
Rwork0.2079 86432 -
obs0.2085 88662 71.26 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 70.62 Å2
精密化ステップサイクル: LAST / 解像度: 2.31→19.97 Å
タンパク質核酸リガンド溶媒全体
原子数18013 0 163 287 18463
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.003318534
X-RAY DIFFRACTIONf_angle_d0.78925132
X-RAY DIFFRACTIONf_chiral_restr0.04932890
X-RAY DIFFRACTIONf_plane_restr0.00453265
X-RAY DIFFRACTIONf_dihedral_angle_d15.855511260
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.360.227430.319266X-RAY DIFFRACTION0.89
2.36-2.410.3315120.2916361X-RAY DIFFRACTION4.81
2.41-2.470.3277370.30851292X-RAY DIFFRACTION17.23
2.47-2.540.3558820.30132707X-RAY DIFFRACTION35.82
2.54-2.610.3267950.30054126X-RAY DIFFRACTION54.34
2.61-2.70.29461270.30745281X-RAY DIFFRACTION69.52
2.7-2.790.32791940.29986229X-RAY DIFFRACTION82.85
2.79-2.910.31241570.28047111X-RAY DIFFRACTION93.71
2.91-3.040.27771860.26547456X-RAY DIFFRACTION98.18
3.04-3.20.30071850.2487427X-RAY DIFFRACTION98.33
3.2-3.40.24962040.21997504X-RAY DIFFRACTION98.3
3.4-3.660.21991750.19627455X-RAY DIFFRACTION97.98
3.66-4.020.20062200.18247337X-RAY DIFFRACTION97.8
4.02-4.60.18531820.16247394X-RAY DIFFRACTION97.28
4.6-5.770.1851860.17457409X-RAY DIFFRACTION97.62
5.77-19.970.21971850.19647277X-RAY DIFFRACTION96.05
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)
13.425318779720.6807882852292.171579861392.374444820660.003062099501592.71895301068-0.2409005526820.248862961024-0.393467049613-0.2693964683020.08533776736490.482592705640.51726666223-0.664858540853-0.1972519208970.822839475836-0.0291363574110.1439092912561.20216445262-0.2399878596530.901691348177-7.54250243544-17.6929025235-30.9109687354
21.81703527341-1.1436659935-0.5517422693042.434982660971.544087774463.28039271463-0.1599107434120.405283542251-0.2987275078460.138105806071-0.016909717719-0.01845290188860.5122047680560.2473234050720.1216278964890.519562340604-0.09987386870530.1658821385770.667939182233-0.07022780194480.3115457486513.63148275786-3.96555814243-12.8651476717
34.179443234780.02774851553740.465289035163.48951043074-0.4664812127683.11183123062-0.1990375537060.671089061806-0.431332410021-0.387893152374-0.3008900800050.100534656760.378598641392-0.06025443372130.131746122730.839415446162-0.1357000840540.02498709540961.33727141467-0.227548425730.799140852365-9.96945338873-7.37541832652-32.4133048148
41.613805708960.841705052595-0.6577175193442.74766069087-0.3977899466641.254710898610.2373695794461.12887213718-0.500368730727-0.73993364728-0.144653492786-0.733578006515-0.5744724314290.187996650683-0.4246689474811.10736808712-0.388384543869-0.06737993723841.067841570250.4579075200791.00110554532-7.9777184711550.322829079-7.38952079976
54.803568243030.73144326579-0.2105006703656.835397814910.2595390297763.96252484972-0.484358032538-0.009362014809250.001120857271850.3547325508390.295228231635-1.09991995257-0.18283787551.32513504203-0.1938837923820.822497999225-0.359506834852-0.03911220264531.01795184224-0.1568098478610.887217292256-2.9122458025235.07990286325.02785507307
63.196779855170.278491817596-0.9407544225222.7880483529-0.0251465546774.049065182660.009318843907620.1578496435570.633436615023-0.09755208676440.395315044862-0.343822734202-0.4611037077420.232726747101-0.146883323940.690513524917-0.268504867032-0.1337441640830.5250283188520.1561373002690.575284946023-12.434423936640.15214476184.56986148802
74.524556352761.05096652254-0.3138670030362.69321056870.2845117375754.10265985141-0.103394604564-0.1323021361441.067318116430.7393496207240.147239483035-0.13172709351-0.350386835276-0.0933035188872-0.0641796274110.609271459734-0.140880951581-0.1688528063060.429683330453-0.07837234182150.459662646446-16.534763348235.96153431649.78595927971
83.755683323830.0332740014542-0.8278729668273.429739573470.1329142983522.34229927578-0.4492768509520.255034107371-0.210958893422-0.08526712171080.2552467409880.1382417243970.228444416488-0.02001876464930.247589540980.378464386939-0.1589823170080.04490960790060.44576062146-0.03855127271240.205848478387-19.96611673849.90439477666-0.319491390479
94.24077527504-0.9992691933820.1626252788882.91058450838-0.205944216252.34580758485-0.08390154304990.3606568837560.381045797031-0.2163755402520.0573524998981-0.170070716197-0.359406573813-0.02449520083180.2086276283760.430538917442-0.1413712757370.02070699045940.6065326539430.1081875522630.231917349887-9.2071161915615.971819103-6.73534095189
101.92759017521-0.272877904201-0.1835021174951.996677446132.276518803882.63238187013-0.07281530856160.6766414223290.584754213294-0.9612680577580.1256089211380.0278008219569-0.6141558768270.00520008056771-0.09286117415660.773053396875-0.32901695574-0.07383736254891.084361261660.3247385977070.473518134954-15.091325979733.7954981033-9.32119256134
114.246995655340.3874099503870.2750345664053.214824984420.3389287141252.433826897140.3173347117150.8832833377440.514036747591-0.7844765855310.577017459976-0.858687951901-1.49189766040.972409704273-0.326864929131.07593637966-0.4970635330430.2052211204351.4025240020.2545720453360.914576308936-0.98908702118140.4946312041-11.4330023341
123.227497700270.5389920532271.058014317965.018619187970.3152250437363.722362421330.00340769146814-0.07552983124-0.1357539509080.0383535147265-0.07335874764910.2531509253420.209705491225-0.1805096312380.1398411259330.2272324690650.009343261767410.06002300703460.178765141620.008174272745910.36736989384414.0948293812-31.663045545536.6234392765
132.459308517740.2553099346180.6381171330312.81119911096-0.6060808529571.68933678929-0.19317452164-0.04459357837480.2209655472030.225377188230.0971747921324-0.173912647019-0.2646244639580.1232379349750.06073813971430.2860010594280.0048960857559-0.08612009174430.2159600739290.02072292958850.2821387722123.6499363586-3.594880705348.9150531206
140.991960258289-0.781421513256-0.1028521135913.944548334960.5208186066491.388805010530.04699681980780.1151669188620.0964915917942-0.491829155195-0.0407149087281-0.199649479183-0.195960546930.00740782767860.04177870400870.274919630265-0.0641842223833-0.04779656289150.2407342995250.04949581392490.25412354999417.3799684069-12.036965081936.0008542467
157.361693693571.83437209919-0.3007196209067.33486138119-1.336629452513.777344163790.375841933453-0.1363312367710.388906294484-1.00609505775-0.2363714577780.58317911546-0.0671234945574-0.1811336989110.002798804143190.4726138811770.000189295631036-0.1079306357750.2692622048440.03847385425470.32672950288312.0271613196-21.229280489126.9507834297
164.70403570598-0.37811976417-0.9420899487984.11110062916-0.85854880673.050633241330.2299117859290.6238737894360.580488193925-0.877492989267-0.1525866400220.95410502033-0.26249242111-0.210593225072-0.08531531187450.5639578868170.0589821462746-0.245377184950.485951820767-0.001161504253440.6233069029174.37233976624-23.872645719524.1540590466
175.760193216-0.055616592199-1.031323555055.90453405062-0.4760031720873.638301726510.2712888519-0.3602052369180.722365055871-0.300787991566-0.117068956972-0.0669275126358-0.21660071430.370674284151-0.07353972959670.3881642990850.06148764572440.01358535583650.309689701227-0.06427930586160.5173166256966.8066262668133.629853756436.6450364985
182.11508348216-1.620763207160.3591964519143.72275845942-1.024662319831.58612552152-0.115355680134-0.211832459168-0.01372815929180.3220730601650.2054469460040.315084869569-0.1688740072-0.314297647516-0.049866671550.2793928943940.0351774242496-0.0170431498910.3018243486830.05892318232840.311652740618-1.008717055057.5372373171944.6406331436
195.237978394661.07552535095-0.08008764253014.246425174750.04217222635313.495001063980.2057077834760.596383863720.0107833634128-0.919526064062-0.210824361107-0.6474800669090.1132611694790.0890141906908-0.09668201769550.5832509978880.09675189266680.1591843100770.4718306616610.0545018286080.5274277848210.696761142325.409288537525.1056913696
204.412419227-0.9310731700730.9660846555785.133018268261.386999015923.08563327853-0.0420777338211-0.107199468175-1.143929917340.3446849172160.0641166066943-1.066134355070.5313249205760.5007462631590.07613261290540.5011145984710.01888906720140.03408354258070.495657208410.112114323611.0752414229349.6169020519-31.860562438631.7547769408
213.79910002742-3.89137561588-0.6063959251874.09450678005-0.1090369488494.807410837860.1830911267971.35998125113-1.44362864039-1.992300316980.0711472264632-0.7596220198330.2640972569461.009988789380.1845164631760.675057959127-0.02086872244270.3175252748840.631613068298-0.2679384270831.0115860216743.6447018443-30.700912654918.9150332088
223.105870998410.905308604847-0.2021418392174.86170136541-1.347756626931.88337665074-0.2716584372380.101891045545-0.00927961051396-0.4650015294130.3661886989310.2428495326060.151609739158-0.356389606788-0.05759814097510.375655696262-0.0362122770.06084221638270.3920144124540.03752337804770.38672032699741.6252427687-3.3758994823719.7867954776
234.41562036976-0.628879289559-0.1245701292443.45161634589-0.7751939507664.940603743060.0300620735694-0.67334990576-0.142056461050.661240315387-0.12364707882-1.256696653810.3211848766950.6178430409280.008047130853210.426013218955-0.0182129858272-0.1310851841230.5505103541480.08631943301750.87750852075549.5418189211-23.406382837338.5563198702
243.650149417650.391601659525-0.98862938436.06870482339-0.3345557973373.00718651757-0.182209872935-0.2241643064940.747820499274-0.2088595315380.05017566200840.438502439187-0.347763065594-0.2302010180060.08526121138760.2860738771310.105555991852-0.1212367227330.283175563696-0.08831984789660.47969685095556.919985681934.235449012728.6057423547
253.46360810770.446597398206-0.808042825462.78830755807-0.4392800613852.73179257521-0.3056720022820.0195518499095-0.2003477462420.02420488992960.168291325483-0.05402799569640.23038075821-0.0254571576950.1244124236460.3071233800320.02404659908430.06936487634930.275410750193-0.01208073537980.26713076201862.63024777996.5881094522119.1317945001
261.79997984217-0.490309763394-0.09034177577313.331779549980.007964576569521.4792440833-0.0397032578721-0.4577040289050.1042158546630.275519848155-0.1197441335110.8495537063740.0224296914328-0.3984883014440.1423167690380.2772585770710.03885191803980.1009691484320.528915058195-0.05698800826960.40368332472755.137426576224.379111218937.9267906325
277.405117811841.55757680134-0.7654684620350.3309254532880.0003692234909045.5654629621-0.4759993783360.3955496469342.08296843667-0.8922741193890.1016061434421.25089989609-0.9447787981990.06110786479171.357014312070.6746740188940.288934645064-0.8821221746030.754515558311-0.2771006488641.0409331757742.856057328942.5170324051-17.317264427
282.84720511771.028086436250.9451732444023.012029897381.44609436883.41090025969-0.258642756046-0.318635653737-0.033471506237-0.17943850750.0129727062591-0.203538602917-0.5881058682850.4146564377890.1500849940320.5211470484310.0722290228114-0.1783594942370.632782401762-0.0005891690899520.33030718874746.326154493522.9442329838-25.6954276874
294.827280625012.423501044742.378743412445.235095715481.741762014772.702796033450.0299057351369-1.49791042237-0.05483134440630.615567098574-0.4675253206650.308199915837-0.295787111444-0.2710973633110.2955487425980.586457365198-0.158152453881-0.2181450139171.58887022308-0.114087936180.42532634234845.951174895932.9535047195-4.29539468189
300.225784407074-0.380978102106-0.1193324857373.281002061160.1690118555150.0573813723380.453885887922-0.914272830556-0.01116923181010.821589984904-0.9547939147741.29627653212-0.6180297629190.1655373262650.3362274722641.04887766319-0.319978379025-0.04183957660921.889532909-0.3451014089940.83903623298236.185041600233.58049627172.64442261452
313.51986341518-0.5196633696030.7778271637123.13515491837-0.3990402371543.36554007076-0.0584140753965-0.113488090069-0.5443662751160.2015634740670.0189117327997-0.3207058223850.5603093955980.1531762890240.07625650219970.4988010013630.1468268635010.05010969793710.370194559290.04477233588830.41081998933530.529231735-14.5304317027-37.2580224874
324.444631207271.510970854180.8567203382752.759256942510.185518854293.26021610168-0.277085602443-0.738915877350.3418694592440.1884508474550.06185283870050.152380254415-0.270774644763-0.09186142502520.1944946329810.4045392540640.178398353753-0.05674248022130.480236344834-0.06602538621520.23837871387625.230304361513.7494178014-29.9604964844
334.692713501-0.394376512984-0.6034006425033.8873131930.6760892261643.68537284865-0.0317314260476-0.5529955812020.3190578473690.915241231570.194553529364-0.6311504240070.6188660679930.317055449603-0.2457985829910.7750103000950.252677258569-0.0813586078260.6943320143740.0977977382730.48088567196833.7773625803-13.387866359-24.1902317324
342.000005024292.00002162162.000009011351.999995431485.368768929112.00001577029-0.4931012804555.883364587765.08627197661-10.39764653435.630224732052.09199833935-12.6499936239-8.48003034159-5.100984706912.156545820990.23643910042-0.2271017695571.66062676118-0.7183050098441.1944208702535.271303215-26.707348958-43.6272637436
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 259 )
3X-RAY DIFFRACTION3chain 'A' and (resid 260 through 319 )
4X-RAY DIFFRACTION4chain 'B' and (resid 11 through 33 )
5X-RAY DIFFRACTION5chain 'B' and (resid 34 through 48 )
6X-RAY DIFFRACTION6chain 'B' and (resid 49 through 73 )
7X-RAY DIFFRACTION7chain 'B' and (resid 74 through 100 )
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 188 )
9X-RAY DIFFRACTION9chain 'B' and (resid 189 through 226 )
10X-RAY DIFFRACTION10chain 'B' and (resid 227 through 279 )
11X-RAY DIFFRACTION11chain 'B' and (resid 280 through 320 )
12X-RAY DIFFRACTION12chain 'C' and (resid 11 through 100 )
13X-RAY DIFFRACTION13chain 'C' and (resid 101 through 188 )
14X-RAY DIFFRACTION14chain 'C' and (resid 189 through 259 )
15X-RAY DIFFRACTION15chain 'C' and (resid 260 through 279 )
16X-RAY DIFFRACTION16chain 'C' and (resid 280 through 320 )
17X-RAY DIFFRACTION17chain 'D' and (resid 11 through 100 )
18X-RAY DIFFRACTION18chain 'D' and (resid 101 through 248 )
19X-RAY DIFFRACTION19chain 'D' and (resid 249 through 320 )
20X-RAY DIFFRACTION20chain 'E' and (resid 11 through 73 )
21X-RAY DIFFRACTION21chain 'E' and (resid 74 through 100 )
22X-RAY DIFFRACTION22chain 'E' and (resid 101 through 237 )
23X-RAY DIFFRACTION23chain 'E' and (resid 238 through 320 )
24X-RAY DIFFRACTION24chain 'F' and (resid 10 through 100 )
25X-RAY DIFFRACTION25chain 'F' and (resid 101 through 225 )
26X-RAY DIFFRACTION26chain 'F' and (resid 226 through 320 )
27X-RAY DIFFRACTION27chain 'G' and (resid 65 through 100 )
28X-RAY DIFFRACTION28chain 'G' and (resid 101 through 237 )
29X-RAY DIFFRACTION29chain 'G' and (resid 238 through 271 )
30X-RAY DIFFRACTION30chain 'G' and (resid 272 through 309 )
31X-RAY DIFFRACTION31chain 'H' and (resid 11 through 100 )
32X-RAY DIFFRACTION32chain 'H' and (resid 101 through 237 )
33X-RAY DIFFRACTION33chain 'H' and (resid 238 through 320 )
34X-RAY DIFFRACTION34chain 'H' and (resid 321 through 321 )

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万見について

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お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

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

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

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

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

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

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

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

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

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

他の情報も見る