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- PDB-5t96: Crystal structure of the infectious salmon anemia virus (ISAV) HE... -

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基本情報

登録情報
データベース: PDB / ID: 5t96
タイトルCrystal structure of the infectious salmon anemia virus (ISAV) HE viral receptor complex
要素HE protein
キーワードVIRAL PROTEIN / 4-0-acetylsialic acid / hydrolase / hemagglutinin / coiled-coil / viral receptor-complex / infectious salmon anemia virus / ISAV
機能・相同性Haemagglutinin-esterase glycoprotein, infectious salmon anaemia virus-type / Infectious salmon anaemia virus haemagglutinin / metal ion binding / Chem-79J / FORMIC ACID / HE protein
機能・相同性情報
生物種Infectious salmon anemia virus (ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2 Å
データ登録者Cook, J.D. / Sultana, A. / Lee, J.E.
引用ジャーナル: Proc. Natl. Acad. Sci. U.S.A. / 年: 2017
タイトル: Structure of the infectious salmon anemia virus receptor complex illustrates a unique binding strategy for attachment.
著者: Cook, J.D. / Sultana, A. / Lee, J.E.
履歴
登録2016年9月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年3月22日Provider: repository / タイプ: Initial release
改定 1.12017年4月5日Group: Database references
改定 1.22017年4月19日Group: Database references
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年10月4日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
改定 2.22024年11月13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: HE protein
B: HE protein
C: HE protein
D: HE protein
E: HE protein
F: HE protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)229,45154
ポリマ－225,1716
非ポリマー4,27948
水29,4371634
1
A: HE protein
B: HE protein
C: HE protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)114,81729
ポリマ－112,5863
非ポリマー2,23226
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area12970 Å2
ΔGint-69 kcal/mol
Surface area36760 Å2
手法PISA
2
D: HE protein
E: HE protein
F: HE protein
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)114,63325
ポリマ－112,5863
非ポリマー2,04822
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-54 kcal/mol
Surface area35460 Å2
手法PISA
単位格子
Length a, b, c (Å)82.480, 87.568, 95.534
Angle α, β, γ (deg.)97.140, 113.500, 114.680
Int Tables number1
Space group name H-MP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細 (eV)
11(chain A and (resseq 18:20 or resseq 22:41 or resseq...
21(chain B and (resseq 18:20 or resseq 22:41 or resseq...
31(chain C and (resseq 18:20 or resseq 22:41 or resseq...
41(chain D and (resseq 18:20 or resseq 22:41 or resseq...
51(chain F and (resseq 18:20 or resseq 22:41 or resseq...

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
11LEULEULEULEU(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA18 - 202 - 4
12ASNASNPROPRO(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA22 - 416 - 25
13SERSERPHEPHE(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA43 - 12827 - 112
14GLYGLYGLYGLY(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA130 - 145114 - 129
15SERSERGLYGLY(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA147 - 191131 - 175
16ASNASNSERSER(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA194 - 234178 - 218
17HISHISHISHIS(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA235219
18ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
19ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
110ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
111ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
112ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
113ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
114ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
115ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
116ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
117ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
118ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
119ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
120ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
121ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
122ARGARGHOHHOH(chain A and (resseq 18:20 or resseq 22:41 or resseq...AA - CB17 - 7831
21LEULEULEULEU(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB18 - 202 - 4
22ASNASNPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB22 - 416 - 25
23SERSERPHEPHE(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB43 - 12827 - 112
24GLYGLYGLYGLY(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB130 - 145114 - 129
25SERSERGLYGLY(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB147 - 191131 - 175
26ASNASNSERSER(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB194 - 234178 - 218
27HISHISHISHIS(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB235219
28ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
29ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
210ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
211ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
212ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
213ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
214ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
215ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
216ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
217ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
218ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
219ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
220ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
221ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
222ARGARGPROPRO(chain B and (resseq 18:20 or resseq 22:41 or resseq...BB17 - 3461 - 330
31LEULEULEULEU(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC18 - 202 - 4
32ASNASNPROPRO(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC22 - 416 - 25
33SERSERPHEPHE(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC43 - 12827 - 112
34GLYGLYGLYGLY(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC130 - 145114 - 129
35SERSERGLYGLY(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC147 - 191131 - 175
36ASNASNSERSER(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC194 - 234178 - 218
37HISHISHISHIS(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC235219
38ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
39ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
310ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
311ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
312ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
313ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
314ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
315ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
316ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
317ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
318ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
319ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
320ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
321ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
322ARGARGVALVAL(chain C and (resseq 18:20 or resseq 22:41 or resseq...CC17 - 3411 - 325
41LEULEULEULEU(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD18 - 202 - 4
42ASNASNPROPRO(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD22 - 416 - 25
43SERSERPHEPHE(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD43 - 12827 - 112
44GLYGLYGLYGLY(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD130 - 145114 - 129
45SERSERGLYGLY(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD147 - 191131 - 175
46ASNASNSERSER(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD194 - 234178 - 218
47HISHISHISHIS(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD235219
48ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
49ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
410ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
411ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
412ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
413ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
414ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
415ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
416ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
417ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
418ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
419ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
420ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
421ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
422ARGARGHOHHOH(chain D and (resseq 18:20 or resseq 22:41 or resseq...DD - FB17 - 7691
51LEULEULEULEU(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF18 - 202 - 4
52ASNASNPROPRO(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF22 - 416 - 25
53SERSERPHEPHE(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF43 - 12827 - 112
54GLYGLYGLYGLY(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF130 - 145114 - 129
55SERSERGLYGLY(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF147 - 191131 - 175
56ASNASNSERSER(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF194 - 234178 - 218
57HISHISHISHIS(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF235219
58ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
59ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
510ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
511ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
512ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
513ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
514ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
515ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
516ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
517ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
518ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
519ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
520ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
521ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316
522ARGARGARGARG(chain F and (resseq 18:20 or resseq 22:41 or resseq...FF17 - 3321 - 316

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要素

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タンパク質 / 糖 , 2種, 12分子 ABCDEF

#1: タンパク質
HE protein / Hemagglutinin / Hemagglutinin-esterase glycoprotein


分子量: 37528.578 Da / 分子数: 6 / 断片: UNP residues 17-353 / 由来タイプ: 組換発現
由来: (組換発現) Infectious salmon anemia virus (ウイルス)
遺伝子: HE / プラスミド: pMT-puro / 細胞株 (発現宿主): S2
発現宿主: Drosophila melanogaster (キイロショウジョウバエ)
参照: UniProt: Q9J0Y0
#3: 糖
ChemComp-79J / 4-O-acetyl-5-acetamido-3,5-dideoxy-L-glycero-alpha-D-galacto-non-2-ulopyranosonic acid / 4-O-acetyl-5-(acetylamino)-3,5-dideoxy-L-glycero-alpha-D-galacto-non-2-ulopyranosonic acid / 4-O-acetyl-5-acetamido-3,5-dideoxy-L-glycero-alpha-D-galacto-non-2-ulosonic acid / 4-O-acetyl-5-acetamido-3,5-dideoxy-L-glycero-D-galacto-non-2-ulosonic acid / 4-O-acetyl-5-acetamido-3,5-dideoxy-L-glycero-galacto-non-2-ulosonic acid


タイプ: D-saccharide, alpha linking / 分子量: 351.307 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C13H21NO10

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非ポリマー , 4種, 1676分子

#2: 化合物
ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Mg
#4: 化合物
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C3H8O3
#5: 化合物...
ChemComp-FMT / FORMIC ACID


分子量: 46.025 Da / 分子数: 28 / 由来タイプ: 合成 / 式: CH2O2
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1634 / 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: 2.49 Å3/Da / 溶媒含有率: 50.51 %
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 / pH: 7.5
詳細: [0.2 M] magnesium formate, 20% PEG 3350, w/ a [0.8 M] sodium phosphate, [0.8 M] potassium phosphate, [0.1 M] HEPES pH 7.5 solution as a 1:6 ratio drop additive

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: CLSI / ビームライン: 08ID-1 / 波長: 0.97949 Å
検出器タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2016年4月28日 / 詳細: 9 CCDS, 9 TILED FIBER-OPTIC TAPERS
放射モノクロメーター: DOUBLE CRYSTAL 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: 0.97949 Å / 相対比: 1
反射解像度: 2→48.4 Å / Num. obs: 138068 / % possible obs: 97.9 % / 冗長度: 3.8 % / Biso Wilson estimate: 25.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Net I/σ(I): 14.9 / Num. measured all: 528952
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.033.90.3972603167160.8720.2340.4613.596.6
10.95-48.43.70.02731608440.9990.0160.03238.198.5

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位相決定

位相決定手法: 分子置換
Phasing MR
最高解像度最低解像度
Rotation6.48 Å48.4 Å
Translation6.48 Å48.4 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10_2155精密化
Aimless0.5.17データスケーリング
XDSデータ削減
PDB_EXTRACT3.2データ抽出
Cootモデル構築
PHASER2.6.0位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5T9Y

5t9y


解像度: 2→48.396 Å / SU ML: 0.17 / 交差検証法: FREE R-VALUE / σ(F): 1.89 / 位相誤差: 18.04 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.1826 2000 1.45 %Random selection
Rwork0.1385 136056 --
obs0.1391 138056 97.9 %-
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 max: 203.08 Å2 / Biso mean: 37.1833 Å2 / Biso min: 13.23 Å2
精密化ステップサイクル: final / 解像度: 2→48.396 Å
タンパク質核酸リガンド溶媒全体
原子数14631 0 494 1634 16759
Biso mean--49.45 37.67 -
残基数----1942
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0115172
X-RAY DIFFRACTIONf_angle_d1.07220617
X-RAY DIFFRACTIONf_chiral_restr0.0612402
X-RAY DIFFRACTIONf_plane_restr0.0072656
X-RAY DIFFRACTIONf_dihedral_angle_d10.3279003
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A8364X-RAY DIFFRACTION4.997TORSIONAL
12B8364X-RAY DIFFRACTION4.997TORSIONAL
13C8364X-RAY DIFFRACTION4.997TORSIONAL
14D8364X-RAY DIFFRACTION4.997TORSIONAL
15F8364X-RAY DIFFRACTION4.997TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.22461440.17969550969497
2.05-2.10540.21921380.16829570970897
2.1054-2.16740.22051420.15279724986697
2.1674-2.23740.22231400.15019623976397
2.2374-2.31730.22111430.14659596973997
2.3173-2.41010.1741350.13939759989498
2.4101-2.51980.1951550.149699985498
2.5198-2.65260.19061410.14089752989398
2.6526-2.81880.20441430.14639714985798
2.8188-3.03640.22171340.14749752988698
3.0364-3.34190.16731470.14379761990899
3.3419-3.82530.17091480.13149848999699
3.8253-4.81880.14431450.11089845999099
4.8188-48.41050.16861450.139698631000899
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)
12.09630.17290.80771.37841.34412.6323-0.02110.0178-0.1789-0.1497-0.0591-0.22180.4334-0.01280.05340.39450.01490.110.14010.0090.295855.0945-0.09233.9983
20.5891-0.1134-0.11530.9682-0.14650.6636-0.00760.1606-0.0148-0.3193-0.0159-0.10760.1691-0.04840.00630.2724-0.00550.0410.1955-0.00160.150545.142818.777-3.0267
30.76180.73540.03925.63863.10264.18060.03230.09-0.2831-0.16640.0513-0.61810.46870.2886-0.19280.38950.09510.14320.23920.01840.442966.3977-1.11754.3788
47.092-5.44746.30274.6135-5.05095.65950.23690.0803-0.1877-0.16940.12040.1284-0.0821-0.0281-0.33920.32070.10110.10510.28510.01570.519377.5418-3.267812.2772
55.4157-1.2544.18227.1764-3.33865.66950.459-0.613-0.87930.2683-0.09-0.24960.57520.4648-0.43630.40120.0945-0.10710.43490.03820.3086106.7749-27.888934.8934
60.8692-0.17480.04431.2954-0.0511.41590.0153-0.0855-0.05560.0182-0.0225-0.12670.171-0.02140.04180.1988-0.0201-0.00560.14210.01970.16647.53956.616730.3254
70.7324-0.17430.24740.822-0.25690.9003-0.0187-0.0672-0.0914-0.00580.02450.04610.2333-0.1837-0.02740.2418-0.06980.0150.2099-0.00240.189334.63334.559823.0218
82.43342.39011.88063.17820.69313.21960.15150.33220.00940.37090.3247-0.25820.26990.1929-0.41810.41120.13530.02260.2258-0.03220.4971.4493-8.173626.9683
92.3674-3.2971.79814.4641-1.78952.0686-0.8323-0.92650.93630.72660.5293-1.2244-0.17160.30660.21690.3870.0445-0.20470.5357-0.11180.6431114.5919-21.766635.9921
101.2283-0.21790.39982.2812-0.36481.4622-0.10540.02620.0078-0.0597-0.0294-0.46470.02220.26620.12590.14920.00330.02580.21070.01830.337467.895423.692716.6222
111.5171-0.46830.27761.0644-0.24030.8106-0.0099-0.02510.04640.04-0.0374-0.1009-0.0565-0.05050.04120.1416-0.0083-0.00480.16950.00030.162649.514529.948222.6412
120.7419-1.74551.32235.3099-2.49753.8089-0.06310.1232-0.1446-0.0441-0.09430.0023-0.20060.06370.19180.1338-0.005-0.02420.2402-0.05170.143634.667934.890720.1931
131.26330.0479-0.02770.8117-0.11670.687-0.025-0.120.08520.0786-0.0405-0.2481-0.04820.05560.0490.156-0.0002-0.03360.172-0.00250.197256.126131.126226.2699
149.0688-6.6003-2.90164.95362.86313.4782-0.1322-0.0432-0.15250.0806-0.1604-0.0490.33590.21020.19960.30970.0740.02130.30430.1240.528580.58965.715926.0067
155.291-6.78614.70359.2761-5.75095.22580.33710.51670.5694-0.1956-0.5226-0.72690.35960.64930.15020.3084-0.0008-0.0840.39380.00090.4622111.3602-23.708227.5397
161.0089-0.2120.14960.87670.34121.395-0.04430.22090.142-0.2091-0.04840.0951-0.2322-0.33180.09580.30110.0077-0.0740.32470.00370.186264.33749.8706-29.938
170.9002-0.40960.00170.80.22911.0467-0.03340.1232-0.0957-0.09120.0007-0.00130.0345-0.08830.04410.197-0.0522-0.01390.2122-0.00090.173575.522437.1222-18.4578
181.3619-0.17650.02840.95850.22271.9639-0.06850.0494-0.2632-0.01630.0686-0.11120.21450.1999-0.01050.1671-0.00590.0020.1633-0.01120.238687.610528.7062-12.1124
190.735-0.16540.06020.60270.18981.6902-0.0730.2539-0.0607-0.1914-0.08510.12830.106-0.41010.09380.2247-0.0736-0.03420.3279-0.03070.22663.257635.9544-26.551
200.95240.250.46590.7606-0.19651.6220.04950.23790.1775-0.2518-0.11060.1343-0.4442-0.51960.13820.34180.0985-0.11140.4979-0.01830.276753.158451.389-28.2724
216.9587-4.83792.04828.1898-4.20933.47730.02740.5791-0.06860.47650.29-0.249-0.6411-0.8846-0.31990.41520.1982-0.07070.7363-0.00230.305843.929459.7115-24.6647
226.6721-3.61611.29955.6303-0.56114.99440.44551.20990.8759-0.7246-0.8151-0.2308-0.11420.78770.2670.53590.08690.05480.64390.23120.506421.505193.6429-33.7047
230.9702-0.2016-0.00891.11120.50230.8710.01310.11010.2119-0.36280.0685-0.1046-0.40630.0542-0.09740.3788-0.06020.04910.19760.02610.207282.759264.8642-17.8113
245.2355-0.30742.41731.54160.41574.0537-0.0612-0.1049-0.0792-0.14250.259-0.2764-0.27470.1511-0.14690.2367-0.09310.08860.2522-0.02280.216599.17150.9891-16.4726
250.8599-0.1595-0.12091.41960.3470.96870.07230.1890.3301-0.440.0459-0.1495-0.4770.0728-0.09250.4816-0.08780.07020.25130.04090.263884.99267.1838-23.2904
265.0916-1.4426-2.17321.26571.20121.6447-0.0001-0.08390.5432-0.2523-0.13770.1479-0.7839-0.57840.15230.79290.307-0.13170.64130.03420.469751.236475.435-23.8261
271.01870.2048-1.12184.03571.25521.8505-0.52430.00851.0630.55190.2403-0.3989-0.2881-0.31890.31470.6260.20360.040.53560.02950.457416.242894.7859-25.2452
280.15490.0308-0.39243.5351-0.86152.6706-0.01590.08190.0196-0.2188-0.03970.24930.0299-0.30360.06030.12620.0085-0.04740.2451-0.0210.219558.21450.7837-1.2353
290.9799-0.1456-0.20410.80780.44270.7959-0.0243-0.05710.00670.04970.0926-0.1239-0.03960.1155-0.07460.1381-0.0169-0.02430.1713-0.00560.157681.432150.81823.4649
300.8675-0.0398-0.4140.64720.23450.79280.0333-0.1003-0.00520.06980.0439-0.086-0.06280.0947-0.06950.1668-0.0026-0.03680.1791-0.01720.183576.836954.07659.4858
312.4606-0.13640.85232.164-1.61063.2786-0.00990.13920.1236-0.16650.12060.2486-0.1868-0.5851-0.17060.23740.1092-0.04820.331-0.04470.294251.473659.9512-2.0425
323.4117-1.49032.5241.9435-2.25582.863-0.0121-0.06460.1734-0.17390.10520.4443-0.4763-0.4214-0.04460.4410.2324-0.11390.5358-0.02750.541744.152268.8381-10.3126
336.3829-6.73197.4227.024-7.77198.5871.06710.5962-0.5802-1.7075-0.53590.6340.91470.533-0.43270.68060.0942-0.04870.4082-0.05960.51217.527384.4605-28.9495
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 56 )A17 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 266 )A57 - 266
3X-RAY DIFFRACTION3chain 'A' and (resid 267 through 290 )A267 - 290
4X-RAY DIFFRACTION4chain 'A' and (resid 291 through 306 )A291 - 306
5X-RAY DIFFRACTION5chain 'A' and (resid 307 through 341 )A307 - 341
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 80 )B17 - 80
7X-RAY DIFFRACTION7chain 'B' and (resid 81 through 290 )B81 - 290
8X-RAY DIFFRACTION8chain 'B' and (resid 291 through 306 )B291 - 306
9X-RAY DIFFRACTION9chain 'B' and (resid 307 through 346 )B307 - 346
10X-RAY DIFFRACTION10chain 'C' and (resid 17 through 52 )C17 - 52
11X-RAY DIFFRACTION11chain 'C' and (resid 53 through 140 )C53 - 140
12X-RAY DIFFRACTION12chain 'C' and (resid 141 through 169 )C141 - 169
13X-RAY DIFFRACTION13chain 'C' and (resid 170 through 290 )C170 - 290
14X-RAY DIFFRACTION14chain 'C' and (resid 291 through 306 )C291 - 306
15X-RAY DIFFRACTION15chain 'C' and (resid 307 through 341 )C307 - 341
16X-RAY DIFFRACTION16chain 'D' and (resid 17 through 56 )D17 - 56
17X-RAY DIFFRACTION17chain 'D' and (resid 57 through 140 )D57 - 140
18X-RAY DIFFRACTION18chain 'D' and (resid 141 through 208 )D141 - 208
19X-RAY DIFFRACTION19chain 'D' and (resid 209 through 266 )D209 - 266
20X-RAY DIFFRACTION20chain 'D' and (resid 267 through 290 )D267 - 290
21X-RAY DIFFRACTION21chain 'D' and (resid 291 through 306 )D291 - 306
22X-RAY DIFFRACTION22chain 'D' and (resid 307 through 337 )D307 - 337
23X-RAY DIFFRACTION23chain 'E' and (resid 17 through 140 )E17 - 140
24X-RAY DIFFRACTION24chain 'E' and (resid 141 through 169 )E141 - 169
25X-RAY DIFFRACTION25chain 'E' and (resid 170 through 290 )E170 - 290
26X-RAY DIFFRACTION26chain 'E' and (resid 291 through 306 )E291 - 306
27X-RAY DIFFRACTION27chain 'E' and (resid 307 through 341 )E307 - 341
28X-RAY DIFFRACTION28chain 'F' and (resid 17 through 56 )F17 - 56
29X-RAY DIFFRACTION29chain 'F' and (resid 57 through 169 )F57 - 169
30X-RAY DIFFRACTION30chain 'F' and (resid 170 through 266 )F170 - 266
31X-RAY DIFFRACTION31chain 'F' and (resid 267 through 290 )F267 - 290
32X-RAY DIFFRACTION32chain 'F' and (resid 291 through 306 )F291 - 306
33X-RAY DIFFRACTION33chain 'F' and (resid 307 through 332 )F307 - 332

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://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