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- PDB-7yob: Crystal structure of Aldehyde dehydrogenase 1A1 from mouse -

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基本情報

登録情報
データベース: PDB / ID: 7yob
タイトルCrystal structure of Aldehyde dehydrogenase 1A1 from mouse
要素Aldehyde dehydrogenase 1A1
キーワードOXIDOREDUCTASE (酸化還元酵素)
機能・相同性
機能・相同性情報


fructose catabolic process / 9-cis-retinoic acid metabolic process / Fructose catabolism / Ethanol oxidation / RA biosynthesis pathway / optic cup morphogenesis involved in camera-type eye development / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity ...fructose catabolic process / 9-cis-retinoic acid metabolic process / Fructose catabolism / Ethanol oxidation / RA biosynthesis pathway / optic cup morphogenesis involved in camera-type eye development / 9-cis-retinoic acid biosynthetic process / 3-chloroallyl aldehyde dehydrogenase activity / fructosamine catabolic process / 3-deoxyglucosone dehydrogenase activity / ベンズアルデヒドデヒドロゲナーゼ (NAD+) / benzaldehyde dehydrogenase (NAD+) activity / retinoic acid biosynthetic process / maintenance of lens transparency / embryonic eye morphogenesis / gamma-aminobutyric acid biosynthetic process / aminobutyraldehyde dehydrogenase activity / レチナールデヒドロゲナーゼ / アミノブチルアルデヒドデヒドロゲナーゼ / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / アルデヒドデヒドロゲナーゼ (NAD+) / cellular detoxification of aldehyde / aldehyde dehydrogenase (NAD+) activity / negative regulation of cold-induced thermogenesis / retinal dehydrogenase activity / retinoic acid metabolic process / retinol metabolic process / retinoid metabolic process / NAD binding / response to ethanol / response to oxidative stress / response to xenobiotic stimulus / positive regulation of apoptotic process / 神経繊維 / シナプス / apoptotic process / identical protein binding / 細胞核 / 細胞質基質 / 細胞質
類似検索 - 分子機能
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
類似検索 - ドメイン・相同性
Aldehyde dehydrogenase 1A1
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: 2.89 Å
データ登録者Zhang, X.Y. / Ouyang, Z.Q.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China (NSFC)31870751 中国
引用ジャーナル: Biochem.Biophys.Res.Commun. / 年: 2022
タイトル: Crystal structure of aldehyde dehydrogenase 1A1 from mouse.
著者: Zhang, X. / Ouyang, Z.
履歴
登録2022年8月1日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年8月17日Provider: repository / タイプ: Initial release
改定 2.02022年8月31日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / entity_poly / pdbx_contact_author / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / software / struct_conf / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens / struct_ncs_ens_gen / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / symmetry
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _cell.angle_beta / _cell.volume / _entity_poly.pdbx_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.beg_label_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_refine_tls_group.end_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_close_contact.dist / _pdbx_validate_main_chain_plane.improper_torsion_angle / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_standard_deviation / _pdbx_validate_rmsd_angle.angle_target_value / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_atom_id_1 / _pdbx_validate_rmsd_angle.auth_atom_id_2 / _pdbx_validate_rmsd_angle.auth_atom_id_3 / _pdbx_validate_rmsd_angle.auth_comp_id_1 / _pdbx_validate_rmsd_angle.auth_comp_id_2 / _pdbx_validate_rmsd_angle.auth_comp_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_angle.linker_flag / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.cycle_id / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_ncs_dom.details / _struct_ncs_dom.id / _struct_ncs_dom.pdbx_ens_id / _struct_ncs_ens.id / _struct_ncs_ens_gen.dom_id_1 / _struct_ncs_ens_gen.dom_id_2 / _struct_ncs_ens_gen.ens_id / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id / _symmetry.space_group_name_Hall
解説: Model orientation/position / 詳細: replace the unplausible assembly of chain F / Provider: author / タイプ: Coordinate replacement
改定 2.12023年3月1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_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name
改定 2.22023年11月29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

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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: Aldehyde dehydrogenase 1A1
B: Aldehyde dehydrogenase 1A1
C: Aldehyde dehydrogenase 1A1
D: Aldehyde dehydrogenase 1A1
E: Aldehyde dehydrogenase 1A1
G: Aldehyde dehydrogenase 1A1
H: Aldehyde dehydrogenase 1A1
F: Aldehyde dehydrogenase 1A1


分子量 (理論値)分子数
合計 (水以外)442,9088
ポリマ－442,9088
非ポリマー00
水0
1
A: Aldehyde dehydrogenase 1A1
B: Aldehyde dehydrogenase 1A1
C: Aldehyde dehydrogenase 1A1
D: Aldehyde dehydrogenase 1A1


分子量 (理論値)分子数
合計 (水以外)221,4544
ポリマ－221,4544
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: Aldehyde dehydrogenase 1A1
G: Aldehyde dehydrogenase 1A1
H: Aldehyde dehydrogenase 1A1
F: Aldehyde dehydrogenase 1A1


分子量 (理論値)分子数
合計 (水以外)221,4544
ポリマ－221,4544
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)104.062, 156.484, 129.209
Angle α, β, γ (deg.)90.000, 97.970, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 10 through 16 or (resid 17...
21(chain B and (resid 10 through 14 or (resid 15...
31(chain C and (resid 10 through 14 or (resid 15...
41(chain D and (resid 10 through 14 or (resid 15...
51(chain E and (resid 10 through 14 or (resid 15...
61(chain F and (resid 10 through 14 or (resid 15...
71(chain G and (resid 10 through 14 or (resid 15...
81(chain H and (resid 10 through 14 or (resid 15...

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
11PROPROLEULEU(chain A and (resid 10 through 16 or (resid 17...AA10 - 1616 - 22
12LYSLYSLYSLYS(chain A and (resid 10 through 16 or (resid 17...AA1723
13ALAALASERSER(chain A and (resid 10 through 16 or (resid 17...AA8 - 50114 - 507
14ALAALASERSER(chain A and (resid 10 through 16 or (resid 17...AA8 - 50114 - 507
15ALAALASERSER(chain A and (resid 10 through 16 or (resid 17...AA8 - 50114 - 507
16ALAALASERSER(chain A and (resid 10 through 16 or (resid 17...AA8 - 50114 - 507
21PROPROALAALA(chain B and (resid 10 through 14 or (resid 15...BB10 - 1416 - 20
22ASPASPASPASP(chain B and (resid 10 through 14 or (resid 15...BB1521
23ALAALASERSER(chain B and (resid 10 through 14 or (resid 15...BB8 - 50114 - 507
24ALAALASERSER(chain B and (resid 10 through 14 or (resid 15...BB8 - 50114 - 507
25ALAALASERSER(chain B and (resid 10 through 14 or (resid 15...BB8 - 50114 - 507
26ALAALASERSER(chain B and (resid 10 through 14 or (resid 15...BB8 - 50114 - 507
31PROPROALAALA(chain C and (resid 10 through 14 or (resid 15...CC10 - 1416 - 20
32ASPASPASPASP(chain C and (resid 10 through 14 or (resid 15...CC1521
33ALAALASERSER(chain C and (resid 10 through 14 or (resid 15...CC8 - 50114 - 507
34ALAALASERSER(chain C and (resid 10 through 14 or (resid 15...CC8 - 50114 - 507
35ALAALASERSER(chain C and (resid 10 through 14 or (resid 15...CC8 - 50114 - 507
36ALAALASERSER(chain C and (resid 10 through 14 or (resid 15...CC8 - 50114 - 507
41PROPROALAALA(chain D and (resid 10 through 14 or (resid 15...DD10 - 1416 - 20
42ASPASPASPASP(chain D and (resid 10 through 14 or (resid 15...DD1521
43ALAALASERSER(chain D and (resid 10 through 14 or (resid 15...DD8 - 50114 - 507
44ALAALASERSER(chain D and (resid 10 through 14 or (resid 15...DD8 - 50114 - 507
45ALAALASERSER(chain D and (resid 10 through 14 or (resid 15...DD8 - 50114 - 507
46ALAALASERSER(chain D and (resid 10 through 14 or (resid 15...DD8 - 50114 - 507
51PROPROALAALA(chain E and (resid 10 through 14 or (resid 15...EE10 - 1416 - 20
52ASPASPASPASP(chain E and (resid 10 through 14 or (resid 15...EE1521
53ALAALASERSER(chain E and (resid 10 through 14 or (resid 15...EE8 - 50114 - 507
54ALAALASERSER(chain E and (resid 10 through 14 or (resid 15...EE8 - 50114 - 507
55ALAALASERSER(chain E and (resid 10 through 14 or (resid 15...EE8 - 50114 - 507
56ALAALASERSER(chain E and (resid 10 through 14 or (resid 15...EE8 - 50114 - 507
61PROPROALAALA(chain F and (resid 10 through 14 or (resid 15...FH10 - 1416 - 20
62ASPASPASPASP(chain F and (resid 10 through 14 or (resid 15...FH1521
63ALAALASERSER(chain F and (resid 10 through 14 or (resid 15...FH8 - 50114 - 507
64ALAALASERSER(chain F and (resid 10 through 14 or (resid 15...FH8 - 50114 - 507
65ALAALASERSER(chain F and (resid 10 through 14 or (resid 15...FH8 - 50114 - 507
66ALAALASERSER(chain F and (resid 10 through 14 or (resid 15...FH8 - 50114 - 507
71PROPROALAALA(chain G and (resid 10 through 14 or (resid 15...GF10 - 1416 - 20
72ASPASPASPASP(chain G and (resid 10 through 14 or (resid 15...GF1521
73PROPROSERSER(chain G and (resid 10 through 14 or (resid 15...GF10 - 50116 - 507
74PROPROSERSER(chain G and (resid 10 through 14 or (resid 15...GF10 - 50116 - 507
75PROPROSERSER(chain G and (resid 10 through 14 or (resid 15...GF10 - 50116 - 507
76PROPROSERSER(chain G and (resid 10 through 14 or (resid 15...GF10 - 50116 - 507
81PROPROALAALA(chain H and (resid 10 through 14 or (resid 15...HG10 - 1416 - 20
82ASPASPASPASP(chain H and (resid 10 through 14 or (resid 15...HG1521
83ALAALASERSER(chain H and (resid 10 through 14 or (resid 15...HG8 - 50114 - 507
84ALAALASERSER(chain H and (resid 10 through 14 or (resid 15...HG8 - 50114 - 507
85ALAALASERSER(chain H and (resid 10 through 14 or (resid 15...HG8 - 50114 - 507
86ALAALASERSER(chain H and (resid 10 through 14 or (resid 15...HG8 - 50114 - 507

NCS oper:
IDCodeMatrixベクター
1given(-0.994622739484, 0.025589826097, -0.100353210719), (0.0234065290723, -0.888375363262, -0.458520826514), (-0.10088478824, -0.458404160922, 0.882999368489)115.61854429, 39.194571808, 15.8121837614
2given(0.606864027517, 0.751352854253, 0.259200579689), (0.751118296926, -0.64878451268, 0.122065392838), (0.259879503094, 0.12061320206, -0.958078858633)7.54528164651, -4.42927831632, -33.8949320895
3given(-0.602561526163, -0.781726076994, -0.160698312797), (-0.779813904464, 0.533891463151, 0.326879457873), (-0.169734738908, 0.32227976375, -0.931303319163)110.973270072, 59.2781337869, -13.2166546
4given(0.652849206752, -0.560368099466, -0.509681769679), (-0.682430515341, -0.143083745199, -0.716809342567), (0.328749912508, 0.81579080343, -0.475824400452)70.5806502498, 62.6483905439, 17.2741195888
5given(0.119283431819, -0.975126988332, 0.186812257413), (0.648559095602, 0.218991971437, 0.728981217836), (-0.751759644039, 0.03420340732, 0.658549591544)135.161370201, -12.1607226518, -19.8575936628
6given(-0.163663725147, 0.78763822281, 0.594003548003), (-0.7072603561, -0.513449140431, 0.485955521503), (0.687747754457, -0.340581869981, 0.641098288939)95.9080027502, 82.4697011177, 32.3778962215
7given(-0.611788507095, 0.742979702886, -0.271470041968), (0.748415824202, 0.432570140722, -0.50274926896), (-0.256102668222, -0.510748699906, -0.820699207307)116.266082346, -32.9799799697, 79.9682821027

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要素

#1: タンパク質
Aldehyde dehydrogenase 1A1 / 3-deoxyglucosone dehydrogenase / ALDH-E1 / ALHDII / Aldehyde dehydrogenase family 1 member A1 / ...3-deoxyglucosone dehydrogenase / ALDH-E1 / ALHDII / Aldehyde dehydrogenase family 1 member A1 / Aldehyde dehydrogenase / cytosolic / Retinal dehydrogenase 1 / RALDH 1 / RalDH1


分子量: 55363.477 Da / 分子数: 8 / 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: Aldh1a1, Ahd-2, Ahd2, Aldh1 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P24549, アミノブチルアルデヒドデヒドロゲナーゼ, ベンズアルデヒドデヒドロゲナーゼ (NAD+), アルデヒドデヒドロゲナーゼ (NAD+), ...参照: UniProt: P24549, アミノブチルアルデヒドデヒドロゲナーゼ, ベンズアルデヒドデヒドロゲナーゼ (NAD+), アルデヒドデヒドロゲナーゼ (NAD+), レチナールデヒドロゲナーゼ

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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: 2.35 Å3/Da / 溶媒含有率: 47.71 %
結晶化温度: 289 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: 0.2 M potassium iodide (pH 7.0) and 20% (w/v) polyethylene glycol 3,350

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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: NFPSS / ビームライン: BL18U / 波長: 0.97915 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2022年1月6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: 0.97915 Å / 相対比: 1
反射解像度: 2.89→127.96 Å / Num. obs: 85287 / % possible obs: 93.24 % / 冗長度: 1.9 % / Biso Wilson estimate: 69.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03502 / Rpim(I) all: 0.03502 / Rrim(I) all: 0.04952 / Net I/σ(I): 8.31
反射 シェル解像度: 2.89→2.995 Å / Rmerge(I) obs: 0.2951 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 9049 / CC1/2: 0.853 / Rpim(I) all: 0.2951 / Rrim(I) all: 0.4173

-
解析

ソフトウェア
名称バージョン分類
PHENIX1.19_4092精密化
XDSデータ削減
Aimless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: 5L2N

5l2n


解像度: 2.89→127.96 Å / SU ML: 0.39 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 27.93 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2493 2000 2.35 %
Rwork0.195 83246 -
obs0.1963 85246 93.24 %
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: 177.11 Å2 / Biso mean: 76.2045 Å2 / Biso min: 28.52 Å2
精密化ステップサイクル: final / 解像度: 2.89→127.96 Å
タンパク質核酸リガンド溶媒全体
原子数29957 0 0 0 29957
残基数----3950
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A17880X-RAY DIFFRACTION14.585TORSIONAL
12B17880X-RAY DIFFRACTION14.585TORSIONAL
13C17880X-RAY DIFFRACTION14.585TORSIONAL
14D17880X-RAY DIFFRACTION14.585TORSIONAL
15E17880X-RAY DIFFRACTION14.585TORSIONAL
16F17880X-RAY DIFFRACTION14.585TORSIONAL
17G17880X-RAY DIFFRACTION14.585TORSIONAL
18H17880X-RAY DIFFRACTION14.585TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.89-2.960.34191510.263562906441100
2.96-3.040.30611520.250163206472100
3.04-3.130.29921530.239663726525100
3.13-3.240.3351530.244763596512100
3.24-3.350.30521520.2363106462100
3.35-3.480.31671090.22874565467471
3.49-3.610.26881200.21344985510599
3.7-3.840.2803970.21674056415395
3.84-4.080.22611510.18656290644199
4.08-4.390.21331520.17916306645899
4.39-4.830.2111510.15096318646999
4.83-5.530.24861530.17716384653799
5.53-6.970.23991530.20786345649899
6.97-127.960.21921530.17566346649998
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.19220.73940.71343.40311.50553.37160.1458-1.05760.40130.643-0.13320.2459-0.2986-0.3180.09530.6417-0.06260.02710.6344-0.15460.442546.20637.619429.0014
22.1074-0.4285-0.62861.19170.19572.34910.0841-0.14080.29610.1343-0.0333-0.1687-0.40550.0148-0.06680.405-0.12-0.00420.296-0.02790.427549.962136.084513.8511
31.7339-0.64870.28021.12280.23532.65780.3377-0.1874-0.33110.2824-0.32910.04730.0183-0.6096-0.00110.4115-0.0093-0.03390.45930.00740.48531.055427.8252.5382
44.57710.296-0.55143.54541.07898.33440.1441-0.22990.03680.3387-0.78290.31690.4884-1.82410.60220.3334-0.1191-0.02251.00080.01050.713716.962121.08390.2037
52.26020.87951.16331.70261.08352.9184-0.034-0.65390.24720.1316-0.29470.6617-0.4789-1.08020.27140.50130.09220.10050.9406-0.1030.629118.95633.985211.3188
63.8368-1.1907-0.36711.8431.64485.98770.11280.13330.2763-0.1853-0.20540.1532-0.3631-0.47290.00090.3793-0.0006-0.03270.40880.0460.450825.028427.5597-8.0551
71.6930.26310.94730.233-0.02670.48540.1135-0.02460.30140.1675-0.1051-0.2224-0.27680.0126-0.03250.5409-0.1122-0.00770.43220.02590.528748.105728.6939-5.0826
81.70543.1496-0.09766.79961.82911.59650.2519-0.0916-0.02530.8965-0.09920.02470.54230.3219-0.13580.48380.102-0.12060.30690.02870.381167.7798-6.383419.5012
91.2232-0.78120.98141.0943-0.66921.31610.2819-0.0273-0.5215-0.1671-0.0160.19040.58130.0485-0.33040.55990.0221-0.12180.3171-0.07370.568465.0496-7.24329.1183
100.5411-0.29240.71980.3802-0.24661.57240.0780.08540.0327-0.0253-0.0146-0.02970.19650.2248-0.01040.4136-0.0244-0.03090.2802-0.05850.44564.76755.1256.9687
111.64050.8477-0.15932.1512-0.90160.61860.07240.20480.3233-0.03620.0325-0.6501-0.09770.6837-0.08460.4536-0.02810.06230.8122-0.12920.746588.221911.86354.4236
124.561.2033-1.83165.3946-0.20961.40690.12640.8647-0.1105-0.1485-0.0214-1.15860.11690.4541-0.02740.51070.1278-0.03871.1283-0.20180.989998.8361.2778.92
131.4267-2.0810.48792.2748-1.06892.45380.22520.39060.3111-0.587-0.1273-0.90850.2671.1086-0.03970.5537-0.1430.12581.1428-0.08940.850593.053616.654-5.0585
141.83370.8981-0.25540.69770.6350.7870.02-0.05950.1144-0.0035-0.0142-0.06070.16120.57570.02260.512-0.01190.0950.5669-0.010.606966.393615.2853-6.3346
151.9766-0.3610.6811.50640.40641.39750.28540.9086-0.1769-0.7703-0.0754-0.41190.03140.6177-0.16680.81180.24250.17131.0424-0.02040.656973.69188.4078-39.2447
161.7646-0.00810.91521.20840.42292.6150.25790.5632-0.132-0.3288-0.1485-0.22520.31690.6053-0.12370.51660.07360.09140.6121-0.00930.49466.809612.3501-28.3712
171.9766-0.29590.08111.38350.10312.24860.34120.3244-0.6958-0.2537-0.07610.30760.5917-0.1802-0.23120.73620.0166-0.15070.3588-0.05760.644542.7265-1.2156-25.3202
184.4513-0.3946-0.29882.04540.39170.61190.03770.868-0.9599-0.6767-0.13370.49630.55850.15990.12771.16250.2061-0.18950.7205-0.23310.73347.6541-9.6306-39.8385
192.04381.17820.65532.23830.10483.69940.1411-0.058-0.97790.0895-0.14140.0851.15430.34050.0260.66980.0334-0.09960.36820.06190.703942.777-4.7753-18.2449
200.01460.2229-0.13180.4581-0.24510.16680.45860.3864-0.0847-0.602-0.2676-0.07910.78230.3835-0.13330.76130.07210.03040.46750.07890.622253.30457.4527-20.0872
211.362-0.10750.12930.2456-0.59781.12850.0864-0.2281-0.07970.1943-0.1713-0.15430.23970.20060.05320.4444-0.04060.09860.4805-0.0190.623471.198522.978-5.8451
220.9911-0.87460.43192.9112-0.35221.0923-0.03240.36570.3325-1.0457-0.06610.0938-0.53820.23790.10470.9207-0.09-0.05380.45030.04490.478445.861351.0942-30.4591
231.1828-0.61940.66651.964-0.38712.0931-0.00010.3510.3584-0.2928-0.1207-0.271-0.45230.4330.11950.4693-0.07910.00310.37910.07810.414352.495941.6023-23.2334
242.308-0.6731.24712.1098-0.13491.2785-0.5908-0.3490.45810.06340.3869-0.4677-0.52410.38790.25540.7861-0.1341-0.08080.4610.01390.638257.751950.4497-6.582
251.632-1.14540.6851.1646-0.85732.1822-0.19580.42490.9427-0.025-0.139-0.9707-0.90450.85320.0721.1083-0.4559-0.06881.04020.27291.413875.592159.8961-15.9698
261.1219-0.8502-0.12142.9477-1.8851.6206-0.50220.43110.85420.20670.1355-0.8585-1.30360.29290.38951.2441-0.3016-0.03821.01550.17461.413572.992566.1811-12.4078
273.2479-2.541.11713.1456-1.20595.0537-0.2985-0.27021.3664-0.02080.1215-1.0051-1.38370.70510.2880.6105-0.23530.03520.6405-0.09851.019975.759250.76560.041
283.3587-0.62011.98830.73540.29592.0241-0.09040.42960.7707-0.56840.0337-0.2452-0.79740.21630.26490.645-0.22240.08740.73560.04310.792668.813442.4018-7.4642
292.318-0.16260.04310.8827-1.1211.72310.19420.0841-0.190.29030.11720.0097-0.18320.0772-0.1770.4901-0.0370.0070.308-0.08030.415545.870123.0831-7.1997
301.42940.1958-1.32223.5643-3.18195.0168-0.175-0.1695-0.9481-0.39930.18990.28731.0363-1.1855-0.04040.6676-0.3418-0.11171.08920.17130.911964.76194.893249.2292
311.8804-0.26881.73791.0446-0.13132.7590.0495-0.5129-0.38290.03870.09420.27050.2841-0.8931-0.15110.5124-0.20610.03880.74430.09240.406376.753112.287454.6501
322.1558-0.96281.48462.09680.05071.9926-0.2226-0.4869-0.02220.3630.09840.1213-0.4986-0.89170.17750.51680.0682-0.00170.7873-0.05640.514172.576229.81156.9104
332.948-0.51591.48961.91430.21863.7628-0.26750.5440.8987-0.62150.4422-0.0581-0.9696-0.49130.52531.03530.2603-0.15340.92350.06970.858570.131748.717239.7457
343.1720.7293-0.58423.9621-0.8642.73220.0421-0.47260.4962-0.0887-0.00610.9763-0.5037-1.2368-0.10080.6780.2121-0.09141.2334-0.07920.810156.419333.86143.0512
353.4943-0.44521.49442.25090.84461.9210.1218-0.66960.65470.3083-0.22780.1925-0.7321-0.7660.16190.82030.1914-0.03190.7317-0.02840.579174.1445.432551.7018
360.7714-0.67020.80161.7584-1.75872.5518-0.132-0.30470.22360.13780.16350.1466-0.1248-0.5303-0.0610.6395-0.0104-0.0420.596-0.05760.50989.709724.366161.4378
371.8859-0.5744-0.38272.7658-0.40113.9051-0.2492-0.42330.40520.26550.14930.0129-0.9944-0.51290.10480.67490.1183-0.10570.611-0.12310.684987.57845.50988.641
381.5033-0.17430.95490.9260.07093.2171-0.1761-0.42580.0430.11180.04710.1103-0.0901-0.40630.09450.4326-0.01840.01460.48330.00570.428293.11529.44582.823
392.2058-0.6658-0.44892.7102-1.48530.9385-0.3003-0.8878-0.13820.96750.01750.34790.4254-0.4580.22660.9056-0.0380.08441.0234-0.02130.538589.82318.802105.16
402.4166-0.3465-0.54241.82522.76585.0873-0.2351-0.0634-0.30790.3942-0.19410.55220.6436-0.99320.4640.651-0.1994-0.04070.65110.12070.616291.2976.38286.11
410.8457-0.4160.83081.337-1.08410.99340.009-0.21770.030.4158-0.0126-0.05350.1439-0.5524-0.05570.6822-0.1295-0.01810.64940.11770.626492.97726.46767.126
422.209-0.30340.09451.67520.11912.558-0.09590.18160.7866-0.03020.16-0.6732-0.81920.8235-0.11660.7404-0.2682-0.080.69340.04770.8066125.648336.123764.1016
431.7517-0.472-0.2945-0.29350.67381.22810.14230.60141.227-0.1492-0.2321-0.4856-1.33630.7867-0.01581.4844-0.379-0.06991.09880.4081.3848117.717253.245240.6133
441.2355-0.99251.34820.1164-0.30081.8116-0.15710.18570.58550.4931-0.139-0.1732-0.70810.43110.23040.9079-0.1780.05440.62130.10110.61107.393831.201852.4804
453.22530.3775-0.50233.6279-2.68882.7424-0.11591.4697-0.7385-0.24510.31750.05740.5187-0.5588-0.30490.6028-0.11710.02081.0354-0.17610.6186107.79093.284825.2019
461.4491-0.02480.23751.90420.80062.444-0.03860.54190.1615-0.14130.1256-0.2918-0.06070.4507-0.09330.3866-0.1477-0.01180.62970.0620.4185108.718513.055337.3904
471.8887-0.43650.75130.04970.62163.3420.19110.5388-0.70190.00470.046-0.2681.18590.5602-0.25540.88930.0958-0.16460.7085-0.13780.8148121.7507-7.507353.2002
483.0678-0.5120.95222.56941.88612.6450.29860.2535-0.35490.02660.0621-0.30050.42090.5662-0.35560.7448-0.0017-0.17360.53590.02140.5555124.75170.484163.8425
490.72340.32930.7840.7897-1.16641.4885-0.15610.3550.3327-0.31880.0788-0.06140.04380.30380.09660.5653-0.1606-0.02520.62940.08490.709108.783119.616354.6768
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 36 )A8 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 261 )A37 - 261
3X-RAY DIFFRACTION3chain 'A' and (resid 262 through 305 )A262 - 305
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 329 )A306 - 329
5X-RAY DIFFRACTION5chain 'A' and (resid 330 through 404 )A330 - 404
6X-RAY DIFFRACTION6chain 'A' and (resid 405 through 436 )A405 - 436
7X-RAY DIFFRACTION7chain 'A' and (resid 437 through 501 )A437 - 501
8X-RAY DIFFRACTION8chain 'B' and (resid 8 through 36 )B8 - 36
9X-RAY DIFFRACTION9chain 'B' and (resid 37 through 81 )B37 - 81
10X-RAY DIFFRACTION10chain 'B' and (resid 82 through 247 )B82 - 247
11X-RAY DIFFRACTION11chain 'B' and (resid 248 through 347 )B248 - 347
12X-RAY DIFFRACTION12chain 'B' and (resid 348 through 384 )B348 - 384
13X-RAY DIFFRACTION13chain 'B' and (resid 385 through 446 )B385 - 446
14X-RAY DIFFRACTION14chain 'B' and (resid 447 through 501 )B447 - 501
15X-RAY DIFFRACTION15chain 'C' and (resid 8 through 81 )C8 - 81
16X-RAY DIFFRACTION16chain 'C' and (resid 82 through 261 )C82 - 261
17X-RAY DIFFRACTION17chain 'C' and (resid 262 through 327 )C262 - 327
18X-RAY DIFFRACTION18chain 'C' and (resid 328 through 384 )C328 - 384
19X-RAY DIFFRACTION19chain 'C' and (resid 385 through 454 )C385 - 454
20X-RAY DIFFRACTION20chain 'C' and (resid 455 through 479 )C455 - 479
21X-RAY DIFFRACTION21chain 'C' and (resid 480 through 501 )C480 - 501
22X-RAY DIFFRACTION22chain 'D' and (resid 8 through 81 )D8 - 81
23X-RAY DIFFRACTION23chain 'D' and (resid 82 through 247 )D82 - 247
24X-RAY DIFFRACTION24chain 'D' and (resid 248 through 283 )D248 - 283
25X-RAY DIFFRACTION25chain 'D' and (resid 284 through 364 )D284 - 364
26X-RAY DIFFRACTION26chain 'D' and (resid 365 through 407 )D365 - 407
27X-RAY DIFFRACTION27chain 'D' and (resid 408 through 436 )D408 - 436
28X-RAY DIFFRACTION28chain 'D' and (resid 437 through 479 )D437 - 479
29X-RAY DIFFRACTION29chain 'D' and (resid 480 through 501 )D480 - 501
30X-RAY DIFFRACTION30chain 'E' and (resid 8 through 36 )E8 - 36
31X-RAY DIFFRACTION31chain 'E' and (resid 37 through 229 )E37 - 229
32X-RAY DIFFRACTION32chain 'E' and (resid 230 through 305 )E230 - 305
33X-RAY DIFFRACTION33chain 'E' and (resid 306 through 328 )E306 - 328
34X-RAY DIFFRACTION34chain 'E' and (resid 329 through 384 )E329 - 384
35X-RAY DIFFRACTION35chain 'E' and (resid 385 through 454 )E385 - 454
36X-RAY DIFFRACTION36chain 'E' and (resid 455 through 501 )E455 - 501
37X-RAY DIFFRACTION37chain 'F' and (resid 8 through 81 )F8 - 81
38X-RAY DIFFRACTION38chain 'F' and (resid 82 through 329 )F82 - 329
39X-RAY DIFFRACTION39chain 'F' and (resid 330 through 384 )F330 - 384
40X-RAY DIFFRACTION40chain 'F' and (resid 385 through 454 )F385 - 454
41X-RAY DIFFRACTION41chain 'F' and (resid 455 through 501 )F455 - 501
42X-RAY DIFFRACTION42chain 'G' and (resid 10 through 261 )G10 - 261
43X-RAY DIFFRACTION43chain 'G' and (resid 262 through 436 )G262 - 436
44X-RAY DIFFRACTION44chain 'G' and (resid 437 through 501 )G437 - 501
45X-RAY DIFFRACTION45chain 'H' and (resid 8 through 36 )H8 - 36
46X-RAY DIFFRACTION46chain 'H' and (resid 37 through 261 )H37 - 261
47X-RAY DIFFRACTION47chain 'H' and (resid 262 through 384 )H262 - 384
48X-RAY DIFFRACTION48chain 'H' and (resid 385 through 446 )H385 - 446
49X-RAY DIFFRACTION49chain 'H' and (resid 447 through 501 )H447 - 501

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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