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- PDB-2fbw: Avian respiratory complex II with carboxin bound -

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基本情報

登録情報
データベース: PDB / ID: 2fbw
タイトルAvian respiratory complex II with carboxin bound
要素
  • (Succinate dehydrogenase [ubiquinone] ...) x 3
  • Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
キーワードOXIDOREDUCTASE / COMPLEX II / MEMBRANE PROTEIN / HEME PROTEIN / IRON SULFUR PROTEIN / CYTOCHROME B / REDOX ENZYME / RESPIRATORY CHAIN / OXALOACETATE NITROPROPIONATE UBIQUINONE
機能・相同性
機能・相同性情報


: / Citric acid cycle (TCA cycle) / The tricarboxylic acid cycle / succinate dehydrogenase activity / 酸化還元酵素; CH-OHの結合に対し酸化酵素として働く; キノンあるいはその類似化合物を用いる / succinate metabolic process / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase ...: / Citric acid cycle (TCA cycle) / The tricarboxylic acid cycle / succinate dehydrogenase activity / 酸化還元酵素; CH-OHの結合に対し酸化酵素として働く; キノンあるいはその類似化合物を用いる / succinate metabolic process / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / metal ion binding
類似検索 - 分子機能
Single helix bin / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit ...Single helix bin / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 3 helical TM bundles of succinate and fumarate reductases / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / Rhinovirus 14, subunit 4 / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
AZIDE ION / Chem-CBE / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / : / IRON/SULFUR CLUSTER / Unknown ligand / (~{Z})-2-oxidanylbut-2-enedioic acid ...AZIDE ION / Chem-CBE / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / : / IRON/SULFUR CLUSTER / Unknown ligand / (~{Z})-2-oxidanylbut-2-enedioic acid / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
類似検索 - 構成要素
生物種Gallus gallus (ニワトリ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.06 Å
データ登録者Huang, L.S. / Sun, G. / Cobessi, D. / Wang, A.C. / Shen, J.T. / Tung, E.Y. / Anderson, V.E. / Berry, E.A.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM62563 米国
引用
ジャーナル: J.Biol.Chem. / 年: 2006
タイトル: 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme.
著者: Huang, L.S. / Sun, G. / Cobessi, D. / Wang, A.C. / Shen, J.T. / Tung, E.Y. / Anderson, V.E. / Berry, E.A.
#1: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2005
タイトル: Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A
著者: Huang, L.S. / Borders, T.M. / Shen, J.T. / Wang, C.J. / Berry, E.A.
#2: ジャーナル: Cell(Cambridge,Mass.) / 年: 2005
タイトル: Crystal structure of mitochondrial respiratory membrane protein complex II.
著者: Sun, F. / Huo, X. / Zhai, Y. / Wang, A. / Xu, J. / Su, D. / Bartlam, M. / Rao, Z.
履歴
登録2005年12月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02005年12月20日Provider: repository / タイプ: Initial release
改定 1.12008年5月1日Group: Version format compliance
改定 1.22011年7月13日Group: Non-polymer description / Version format compliance
改定 1.32014年10月29日Group: Non-polymer description
改定 1.42020年7月29日Group: Advisory / Derived calculations / Structure summary
カテゴリ: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 2.02021年2月17日Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / audit_author / cell / chem_comp / database_PDB_caveat / diffrn / diffrn_source / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_audit_support / pdbx_chem_comp_identifier / pdbx_database_related / pdbx_database_remark / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / pdbx_xplor_file / refine / refine_analyze / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_biol / struct_conf / struct_conn / struct_mon_prot_cis / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range / symmetry
Item: _audit_author.identifier_ORCID / _cell.volume ..._audit_author.identifier_ORCID / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _diffrn_source.pdbx_wavelength / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_free_error / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_all / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_data_cutoff_high_absF / _refine.pdbx_data_cutoff_low_absF / _refine.pdbx_isotropic_thermal_model / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine.solvent_model_param_bsol / _refine.solvent_model_param_ksol / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.number_all / _reflns.number_obs / _reflns.pdbx_CC_half / _reflns.pdbx_CC_star / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_Rsym_value / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.d_res_high / _reflns_shell.d_res_low / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.pdbx_Rsym_value / _reflns_shell.pdbx_redundancy / _software.classification / _software.name / _software.version / _struct.pdbx_CASP_flag / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet.id / _struct_sheet.number_strands / _symmetry.space_group_name_Hall
解説: Ligand geometry
詳細: The ligand CBE had bad geometry and orientation of the dihydrooxathiin ring was wrong. In additin the structure has been further refined with new software and procedures including TLS refinement.
Provider: author / タイプ: Coordinate replacement
改定 2.12023年8月30日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.22024年11月13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: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
B: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
C: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
N: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
O: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
P: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
Q: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)253,554290
ポリマ－246,5848
非ポリマー6,970282
水21,6721203
1
A: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
B: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
C: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)126,708156
ポリマ－123,2924
非ポリマー3,416152
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
N: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
O: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
P: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
Q: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)126,847134
ポリマ－123,2924
非ポリマー3,555130
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)118.700, 200.753, 67.631
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111(chain 'A' and (resid 15 through 38 or resid 40...
221(chain 'N' and (resid 15 through 38 or resid 40...
112(chain 'B' and (resid 8 through 64 or resid 67...
222(chain 'O' and (resid 8 through 64 or resid 67...
113(chain 'C' and (resid 2 through 10 or resid 12...
223(chain 'P' and (resid 2 through 10 or resid 12...
114(chain 'C' and resid 201)
224(chain 'P' and resid 201)
115(chain 'D' and resid 5 through 101)
225(chain 'Q' and resid 5 through 101)

NCSアンサンブル:
ID
1
2
3
4
5

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要素

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Succinate dehydrogenase [ubiquinone] ... , 3種, 6分子 ANBODQ

#1: タンパク質 Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial


分子量: 68256.922 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ)
参照: UniProt: F1NPJ4, UniProt: Q9YHT1*PLUS, succinate dehydrogenase
#2: タンパク質 Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Iron-sulfur subunit of complex II / Ip


分子量: 28685.221 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / 参照: UniProt: Q9YHT2, succinate dehydrogenase
#4: タンパク質 Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / CybS / Succinate dehydrogenase complex subunit D / Succinate-ubiquinone oxidoreductase cytochrome b ...CybS / Succinate dehydrogenase complex subunit D / Succinate-ubiquinone oxidoreductase cytochrome b small subunit / Succinate-ubiquinone reductase membrane anchor subunit


分子量: 10971.604 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / 参照: UniProt: Q5ZIS0

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タンパク質 / 糖 , 2種, 5分子 CP

#17: 糖 ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / オクチルβ-D-グルコピラノシド


タイプ: D-saccharide / 分子量: 292.369 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C14H28O6 / コメント: 可溶化剤*YM
識別子タイププログラム
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: タンパク質 Succinate dehydrogenase cytochrome b560 subunit, mitochondrial


分子量: 15378.134 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Gallus gallus (ニワトリ) / 参照: UniProt: A0A3Q2U2Y6, UniProt: D0VWW3*PLUS

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非ポリマー , 14種, 1482分子

#5: 化合物 ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / FAD


分子量: 785.550 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C27H33N9O15P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: FAD*YM
#6: 化合物 ChemComp-Y3P / (~{Z})-2-oxidanylbut-2-enedioic acid / 2-ヒドロキシフマル酸


分子量: 132.072 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H4O5 / タイプ: SUBJECT OF INVESTIGATION
#7: 化合物 ChemComp-K / POTASSIUM ION / カリウムカチオン


分子量: 39.098 Da / 分子数: 2 / 由来タイプ: 合成 / 式: K
#8: 化合物 ChemComp-AZI / AZIDE ION / アザイド


分子量: 42.020 Da / 分子数: 3 / 由来タイプ: 合成 / 式: N3
#9: 化合物...
ChemComp-UNL / UNKNOWN LIGAND


分子数: 256 / 由来タイプ: 合成
#10: 化合物 ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


分子量: 175.820 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe2S2
#11: 化合物 ChemComp-SF4 / IRON/SULFUR CLUSTER


分子量: 351.640 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe4S4
#12: 化合物 ChemComp-F3S / FE3-S4 CLUSTER


分子量: 295.795 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Fe3S4 / タイプ: SUBJECT OF INVESTIGATION
#13: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Na
#14: 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: 2 / 由来タイプ: 合成 / 式: C3H8O3
#15: 化合物 ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


分子量: 616.487 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C34H32FeN4O4
#16: 化合物 ChemComp-CBE / 2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE / 5,6-DIHYDRO-2-METHYL-1,4-OXATHIIN-3-CARBOXANILID / CARBOXIN / CBX / カルボキシン


分子量: 235.302 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C12H13NO2S / タイプ: SUBJECT OF INVESTIGATION
#18: 化合物 ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE / ウンデシルβ-マルトシド


分子量: 496.589 Da / 分子数: 1 / 由来タイプ: 天然 / 式: C23H44O11 / コメント: 可溶化剤*YM
#19: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1203 / 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Y
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: 3.29 Å3/Da / 溶媒含有率: 62.3 %
解説: LOW COMPLETENESS IN OUTER SHELLS IS DUE TO DETECTOR GEOMETRY WHICH WAS A COMPROMISE BETWEEN RESOLVING SPOTS AND COLLECTING HIGH RESOLUTION DATA. OPTICAL RESOLUTION FOR THE DATASET: 1.63 A
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: 50 G/L PEG-3350, 25 ML/L ISOPROPANOL, 15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA, CARBOXIN, pH 7.50, VAPOR ...詳細: 50 G/L PEG-3350, 25 ML/L ISOPROPANOL, 15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA, CARBOXIN, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: ALS / ビームライン: 8.2.2 / 波長: 0.98 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2005年2月17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: 0.98 Å / 相対比: 1
反射解像度: 2.06→64.09 Å / Num. obs: 167170 / % possible obs: 85.33 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 4.19 % / Biso Wilson estimate: 22.23 Å2 / CC1/2: 0.959 / CC star: 0.989 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.097 / Rrim(I) all: 0.216 / Net I/σ(I): 6
反射 シェル解像度: 2.06→2.12 Å / 冗長度: 2.99 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / Num. unique obs: 8064 / CC1/2: 0.103 / Rpim(I) all: 0.401 / Rrim(I) all: 0.754 / % possible all: 49.4

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_3150精密化
DENZOデータ削減
SCALEPACKデータスケーリング
AMoRE位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 1YQ3

1yq3


解像度: 2.06→64.09 Å / SU ML: 0.2326 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 23.144 / 立体化学のターゲット値: CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.2151 8237 4.94 %RANDOM
Rwork0.1706 158638 --
obs0.1728 166875 85.18 %-
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: 39.05 Å2
精密化ステップサイクル: LAST / 解像度: 2.06→64.09 Å
タンパク質核酸リガンド溶媒全体
原子数16968 0 964 1203 19135
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006818220
X-RAY DIFFRACTIONf_angle_d0.861624581
X-RAY DIFFRACTIONf_chiral_restr0.04972674
X-RAY DIFFRACTIONf_plane_restr0.00533086
X-RAY DIFFRACTIONf_dihedral_angle_d12.185610737
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.080.2932840.24851738X-RAY DIFFRACTION28.12
2.08-2.10.34441670.25193148X-RAY DIFFRACTION50.49
2.1-2.130.27271730.24663281X-RAY DIFFRACTION53.32
2.13-2.160.29371860.23433487X-RAY DIFFRACTION56.69
2.16-2.180.26821920.22853788X-RAY DIFFRACTION60.5
2.18-2.210.29862210.22343902X-RAY DIFFRACTION63.9
2.21-2.250.2712070.21624329X-RAY DIFFRACTION68.6
2.25-2.280.30472460.22014538X-RAY DIFFRACTION73.62
2.28-2.310.25552810.20564957X-RAY DIFFRACTION80.87
2.31-2.350.25333130.20255573X-RAY DIFFRACTION89.86
2.35-2.390.2432940.19285690X-RAY DIFFRACTION92.37
2.39-2.440.26773110.19645723X-RAY DIFFRACTION92.33
2.44-2.480.22112870.19095749X-RAY DIFFRACTION92.34
2.48-2.530.25432950.18665716X-RAY DIFFRACTION92.24
2.53-2.590.24682950.18755778X-RAY DIFFRACTION92.8
2.59-2.650.26833020.17565764X-RAY DIFFRACTION93.29
2.65-2.720.25993230.17465786X-RAY DIFFRACTION93.47
2.72-2.790.22933170.185816X-RAY DIFFRACTION94.02
2.79-2.870.21862950.16465886X-RAY DIFFRACTION94.98
2.87-2.960.20263180.16815961X-RAY DIFFRACTION96.04
2.96-3.070.20122960.16616103X-RAY DIFFRACTION97.95
3.07-3.190.2153500.16436100X-RAY DIFFRACTION99.12
3.19-3.340.2013220.16246194X-RAY DIFFRACTION99.51
3.34-3.510.19533200.15376191X-RAY DIFFRACTION99.65
3.51-3.730.1832880.15096248X-RAY DIFFRACTION99.77
3.73-4.020.19112940.14326231X-RAY DIFFRACTION99.77
4.02-4.430.18092990.1396222X-RAY DIFFRACTION99.86
4.43-5.070.17393360.13476211X-RAY DIFFRACTION99.92
5.07-6.380.17413170.15256245X-RAY DIFFRACTION99.83
6.38-64.090.19563080.19246283X-RAY DIFFRACTION99.22
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)
10.8033289877680.321693097267-0.1335985371160.437129387764-0.1738408741331.229807176190.0238593835337-0.2068889456440.02316334488780.1070016865570.03049851858670.0759887067492-0.0623419593192-0.181935449739-0.001617520740880.1992266239610.02992389162380.02145431957030.3039552010230.03131180255930.21191958502411.290680687154.312010574535.3916882312
20.9157474370680.3751365757210.2397123453160.669538377827-0.2158940871671.11884729158-0.07309847220220.0715483473571-0.00445817733006-0.05695993452640.09216347995390.0266608469097-0.0954068567827-0.06848393159517.96784120077E-60.2578685516410.03528401192740.01251518037290.3037338970620.02507614299520.21942108569813.807357384857.707638581220.4419348876
31.400086559980.09093582936160.2029817538330.465660346931-0.2315126493061.04373245460.00236698089181-0.143442403994-0.03490539820210.0621325113861-0.0103369745898-0.0978783068059-0.08397659785760.09186795317064.25551047833E-50.224805461158-0.0001384348022250.003597966625230.2891349191330.006049532334490.22083963381427.510580451753.829504192235.7382597551
41.236871458850.479290678036-0.5369468438270.475141980695-0.2528171203730.8694900220380.1618739205580.3614964927190.549557485066-0.237406806670.08297725072780.13016487683-0.504111336508-0.1567819084230.09015335613140.4452738510320.06170689141410.003771370614260.4998967171870.07393023736320.28263961983810.704833821466.0241276766.25256752951
50.6434249400490.0565525270695-0.5587856777750.826151911601-0.1873862067870.596821678623-0.08820873147920.2261263376020.0718549274472-0.2599384089030.105824168497-0.205827605862-0.1909425458940.2890108380920.0001124808415040.294453975824-0.05099772500390.032898344880.3127164834610.03766783608550.25973416217333.408738451764.021196568913.1788254295
61.335781178790.01583931364640.1007190088971.40928167276-0.03980143680281.30403479898-0.00988472775817-0.2362638086390.2934568271010.1735369004010.0511281338728-0.0536789327865-0.3750115545870.0839177742633-0.001010902520220.270372701933-0.01824116822850.01564736067920.245872185531-0.00453447103490.26149377018525.090216169673.912344405733.1512113226
70.54828696290.22010775729-0.2303979133240.859121617032-0.7502590462360.686612857790.1202290635620.3485225563210.322943068355-0.433984788938-0.0429258952406-0.3346173442010.07314039142770.3360134906560.1754754421940.3386244212530.02271122062890.07504475105620.437706078037-0.06961289849990.32432653521631.889563137940.00307347850.930842281746
80.0455382660296-0.0402044018623-0.05832147811290.04653084000270.04470397678680.0713088759491-0.0358946947881-0.0369417028085-0.06089569246440.170476907553-0.103977001505-0.307795497222-0.003920498757680.416045111303-0.0003528182463370.247851319277-0.03144313764660.03962203030160.413943562591-0.01413786205810.38959336657234.11856926644.602213824111.1558952345
90.200814489134-0.0064299422601-0.1619867977620.1743552202570.01514503119510.126097056217-0.01509684346550.0394770992709-0.19161938532-0.06869425514910.0460114276039-0.07857774729420.08758756233880.051826999762.242594563E-50.2039607178320.00954673769340.02219990448840.2524507493570.02900752981170.23172130774725.577886197141.173030554313.7626206737
101.200824428310.04331192424360.4019922219130.2454441457980.28987945170.5901091673050.0334413865421-0.183616231327-0.479886423158-0.03199315510460.0951814778015-0.3214836129330.2051272077490.3391640314140.01715726138380.2416194561240.02156267561240.02965238925050.312994199595-0.02132782626070.31138149378225.866181174434.55396419237.14107007603
110.04702217057530.01854016293020.06179711600510.2454065735060.03900102592120.266305831450.0467536530322-0.230181448667-0.03763448984540.0747347308543-0.03800649468650.372943529442-0.0040600293351-0.01740918493580.05317292319710.222557325409-0.01962968669650.01656408544130.308634658999-0.01376374401540.3506555813280.77606539958337.57437908824.4931720751
120.14557547094-0.02176809448430.01892881015980.07762779288220.09213650303690.2454978390990.0444794208175-0.177068690169-0.03004013006520.000345234575217-0.2099134946380.09320090756660.102370384234-0.351873262663-0.01408624299850.313259196244-0.01634050669750.03837858020890.4524569548340.07305109074880.4087490861585.386692228737.120721248442.1437983152
130.268118774545-0.3108700657730.0368971758350.534860068098-0.4555098730590.8529517280310.0588066634898-0.165837435069-0.1356979401570.0341218728089-0.06808729937870.0984009237470.140818289018-0.0198526590665-4.38127284395E-50.237339928481-0.01125625460490.004958393747440.226702493387-0.006125826520420.3056884671658.5592396075527.210552075921.6280284198
140.8167436929260.0834822474564-0.6369263402020.0473843896494-0.1191559313761.02110247446-0.0771538377085.14638495596E-50.04307546289550.3526252662880.1098998990180.3480749541130.262019898617-0.172995760416-0.01363604141060.3524406256320.006581327556470.03991632285810.1298708377960.02822907818340.2503419858793.0670710507519.565896886528.2920912827
150.07004988537170.04850736772870.04818455720470.0604883458036-0.001478439560340.07969628164690.1688714061040.46986856174-0.0901620386018-0.312457577199-0.1239876112390.184538677845-0.260171519882-0.398459267941-0.0001404168070320.3457481770120.01544317518670.005614041538590.4369327983650.003064761600770.3617845216750.69250640553438.88676549786.88751994635
160.4196195698330.197352133593-0.1678380904780.606126649332-0.3361412166850.2740378249880.1011677740230.124778966498-0.210178510245-0.414497865708-0.002658369054220.4541876721970.23339745679-0.2535989054420.02108225781750.345993800572-0.0009390905301040.01872785046920.252339695381-0.07101619464060.30391168072718.1553796228.50023597133.00194752041
170.2924018337880.2709500339060.1418042047941.024639413150.01110499880290.344303310631-0.06472812405760.266274334312-0.311173902416-0.3356085884850.1878579671450.04745731597510.1711666437690.07347109295510.9399940717240.4918994119820.0472707208775-0.1350833388970.178302491784-0.1003004214130.57942808089311.0510644048-7.247774395923.50545701811
180.40227977539-0.136841185978-0.01011602519920.330428503089-0.02176040425760.1732330493250.0454680445358-0.1466590299130.04235862908890.0319990530180.05245305917-0.0174224538907-0.141524761544-0.04008497557550.008460576773660.3792604316330.026078973641-0.01820546594570.2264231659510.04932566486420.47080829002920.18990485491.2288246397617.7343599722
190.2882193707-0.01090917264440.3215519622190.00608267021994-0.02175977692510.404138377789-0.145203552828-0.1596815848910.00661312390689-0.4168945751370.08632271577370.3989569645180.148319781499-0.0700149365047-0.1186118775060.286817872771-0.05254864205740.01924025828490.1848897635650.04347237069320.4293145231422.533404939352.7990337726221.5647059057
200.03824141282090.02059458592590.0621578465780.06364765955390.1400101569480.289245922789-0.023175009302-0.00239082901445-0.23793252224-0.03744082242-0.08387947307690.1095151462170.1697158515580.0713532447484-0.01716472773070.4018023872310.01465674510340.002739564447360.203153002229-0.06478765519320.5541878542161.79878224805-0.1843767862513.0327864834
210.1471249371240.290457418554-0.1700552337980.91107963805-0.1068654507010.6300943546840.05828676688930.363636803765-0.456308541829-0.1134755744340.06906633257380.854795962425-0.0172466223098-0.1445819324670.7980912644090.420254843759-0.0049595350303-0.1729147785160.212648840513-0.08279347355750.719098132067-3.628162463441.382724741233.76384094314
221.35995086637-0.2633966111731.501508928060.0798027975258-0.1997741200181.970028241430.186725252303-0.219356662949-0.12928568417-0.646557667622-0.234625610482-0.05496775512130.0826515274467-0.320645444917-0.02632891273390.5585749120230.00379689206003-0.03395897551740.248085779038-0.01184418323820.7625714443299.93745562117-17.63016651389.71793560532
230.4458387721310.129225400366-0.09799188133550.7680777779250.4998924109070.8105736043420.0483081645560.276078070882-0.163129786962-0.1607304235280.120423417168-0.120688781045-0.001374361510290.6147395472910.2882336037140.1573153420770.0173246981750.01330994433460.298177273483-0.04710767949510.12189012769654.5526091297-55.283182640913.5363563603
240.8495806420210.210595530558-0.06741864917170.4300335004160.2592979711471.12855968979-0.00410232569591-0.0867472549507-0.005867721177390.06768979226150.0371277536914-0.03734491987330.07589615669430.1390763931960.0003207982479780.199807267870.03852766796840.008376026580120.264579270833-0.02890202482760.16522871754145.2821459634-55.763377621428.0453409285
251.214876204910.087539720852-0.1397342421270.4024083008870.09754606153820.9160577824220.000724049592041-0.137509312010.01548959495860.044024589599-0.001182125219120.06992147717190.0712621920853-0.04745481223615.21604143187E-60.2470715457380.005195195859140.01102389138540.299112598673-0.01081521003890.21942230763131.7936575579-53.666467246632.7337463553
261.40002032341-0.1199081400960.4200907501510.394167117631-0.2369922038140.2508493208180.1603009045490.477777200668-0.146054430394-0.356416228275-0.00247549786611-0.1658189981250.3217222658030.3643276412140.8563638264060.2248566378060.05887187401850.03554319894510.362439891611-0.09683727426040.20388281809648.5608810755-65.71198133583.52463566481
270.6066141031930.007142356803030.2806055832660.4042429944740.1644503011090.8640902852030.01644876238090.0295419882512-0.126914367516-0.09463794244080.03083853795750.0875098666020.163831848752-0.05369894652876.94217299685E-50.188837444701-0.009704474808790.0004330862663790.186662832777-0.02906853225810.21165408493427.7497654638-66.454545470216.1365338686
281.389818143450.18510855821-0.1800080022221.26071889038-0.2966473084730.3457136673530.0460628681698-0.198285830227-0.297804947170.2673827388880.0563733845195-0.08454874983980.350753646930.09603848411860.005084180259190.4018809939970.0451957695237-0.004679724771940.275117820670.05030874316260.29711539781737.6469989455-76.801159022435.6092991704
290.489107835732-0.002004811333770.3167136736870.1163746485840.2357882321860.6395903628250.104630274910.194358727227-0.464666840445-0.172764582353-0.05521938673810.16186822484-0.0854659445225-0.0777478424862-0.003573704621710.3192000865590.0332135563604-0.03843574640970.2813260944660.01658879699470.24702609012327.4819548458-39.8239358-2.12101413671
300.176688203284-0.0465058669380.160526524180.04863393475720.06445581854180.3191441389160.0590378424145-0.0127871670982-0.0309653509988-0.0304882666429-0.06377676861620.2429545037990.049439973872-0.274407395531-0.003430358632970.188389426970.000756277316984-0.02634129754930.1864815740050.001438039396430.19760387039330.3598472985-44.70503351269.6360945226
310.6089949003970.3281938277750.07857941417210.4886278663640.2144710582570.3857010069270.0213879575375-0.1189832973290.34366135984-0.0573567571310.02876005955050.110891347502-0.0285761479277-0.01879592666610.00480166425410.2094023232910.005704741595720.004719439869520.1928237000850.007522018299440.1843617138633.4429981169-34.1383106835.84865424738
320.303685856431-0.3947331776590.3807658488871.508771283660.6920117340561.987828894540.0679152311491-0.3191274815020.027036242073-0.124337038547-0.0538728627697-0.350023989219-0.265595688092-0.04752972463620.3167916343480.124557148443-0.0407918410580.01728413580490.2798496258180.00772151679330.24005221481258.5349695084-37.3064132821.4999011437
330.372386741930.150552151970.1548427797890.06346670968850.06196878222850.0922723040389-0.19270934991-0.1469073769740.2701586239120.169093619979-0.006803552753210.0401142876916-0.1317462593240.470613625441-0.001612694108920.3223667114010.0289138258924-0.01773494737450.501974279198-0.03566832159070.30135131375953.8379649534-36.851095861139.1759518025
340.483274696782-0.2344484576780.2620013729120.873423890520.1536813673720.6278118705490.0112374476303-0.1500762933930.2372756505870.105938702629-0.0340451625853-0.101313479826-0.1710981722060.153233935424-8.80806638293E-50.239110335649-0.03947017446140.02479289955770.285662520978-0.01249034162140.3009577018850.7394433215-26.961343503218.6038539302
351.07512041869-0.04169193270970.7696881267460.00601185814912-0.0191756953470.9225394966840.0959905042824-0.4742030709650.05736861768940.234484295579-0.0165336599191-0.749339568108-0.2477110644540.0893449843181-0.01767534201290.288394279085-0.0454282596539-0.04454189126530.281020305768-0.005876989918710.49054318574957.105086531-19.137709905625.0748041495
360.1402074738320.0359544479345-0.001548453572350.1430584228090.1106082906960.092221721997-0.04122229670090.291958283806-0.527995523195-0.01879643725260.210569495028-0.2573625722310.3487206159530.0817332670594-5.76478913633E-50.49889965407-0.01359191676050.04372402651370.5775531065630.05084343459980.41992603153758.6896183769-38.65643236193.91310077198
370.06918919227880.02359628388920.02154009144670.008818857127670.01487855860440.03027605329720.3038376442120.447770350427-0.0312537968889-0.5683052068240.128446633994-0.03800082783520.2870056493340.5587161455140.001032210665120.452826199909-0.06122492231710.09242106806780.6870219373570.03907427207510.31700428292149.5486481777-38.7329796195-6.11941256525
380.07289795498990.0598834247204-0.01976318312410.0552547505874-0.0005867826267090.0160566199088-0.06760027702140.03600105880130.2963216408210.00696297346723-0.0307363015612-0.058839462134-0.5613008419230.0799534262809-0.00763925418230.402040969355-0.003303146806430.006160133704360.1874079714570.05152269796690.30966089198437.699660976-24.02478618152.45967362978
390.226965260254-0.04258085209690.2704152599110.00740639486435-0.05007280328640.331302030995-0.04947562534180.133738410870.3922681822820.009235631902640.0275525190509-0.0370055066615-0.280941057650.2673823322760.02695609146680.413234331395-0.05031410211540.0826384370980.2370825244180.05921283629240.45566246060848.7108482587-1.650301100533.33910072722
400.346479942751-0.351119550165-0.3264424787140.5890634240370.8031739737471.290918571110.3436823228860.135255657180.1840954511-0.4097788834020.1448850907130.259877008412-1.11256432264-0.2263114933930.6655084541481.09014231278-0.08030998447870.01503949639720.5868427927660.4387086399761.291364723947.492024752221.1089611271-4.26810001228
410.394331623601-0.1478184435-0.5319679223580.5543364321050.1568705920420.736029907959-0.0166050332024-0.06656226605110.426210959734-0.1016207113420.05873372373720.0325901817108-0.3038588559380.1102659224510.2078746990130.473501187455-0.0795186810612-0.006051068726410.197930604224-0.006495303532690.55166746050240.95197965841.6995767250310.9818645976
420.4848616440250.220890234264-0.1502454689690.108074473896-0.1196354935520.394995284369-0.04238344287150.1240589567450.297283672512-0.2859233557570.09002045923030.15409831768-0.0874892317034-0.02972664063150.009482468343360.3628101839520.005084422016720.01345450947480.161879751568-0.02024826293880.42828805976336.9299210028-3.9855408909518.2983067211
430.4486319075020.198529925749-0.2310968093860.0943665383656-0.05157434328840.313240731219-0.00322542813973-0.03759169261250.6486443727920.0421582750708-0.0821760264311-0.110549065809-0.606702243749-0.05538660634050.000232201099630.620514404744-0.05880582851460.04913672525420.406532981033-0.0592196048070.70303466984356.6224569622-2.4332101076318.4347707439
440.06469988025890.0209743331443-0.09606069723020.0662258630059-0.09415975491030.2042953445770.20692118272-0.08038139446090.2560045555890.0878579257777-0.190339647485-0.330645129986-0.101734318167-0.0439505300727-0.0001237799966430.503824999116-0.09279013595550.04847132186320.3650590344640.02204922219830.6043850682457.45513254530.4536269908269.90762918523
450.2654859115230.384043446432-0.1721042980570.553930511502-0.247176895340.6155092213650.0264543562780.1223131603850.234898722442-0.399878815634-0.143723057229-0.362438202856-0.09005489708540.352677670369-0.3976790601320.5206451601-0.1583141538590.106834807870.4705671886330.1208360818720.60786768140862.944669092-1.119358165880.67540311102
460.5563432911530.2559358092270.2248848898860.139699398373-0.06059106987591.552313421090.20833499861-0.1708335549210.4572567014520.35985085783-0.1727948208580.366035867729-0.445389491426-0.1346927441580.003279761858940.811191181431-0.1148355903210.1505483738120.2982924295490.04033289325420.93725141070449.210329598517.84930064756.50838373844
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 143 )
2X-RAY DIFFRACTION2chain 'A' and (resid 144 through 253 )
3X-RAY DIFFRACTION3chain 'A' and (resid 254 through 429 )
4X-RAY DIFFRACTION4chain 'A' and (resid 430 through 464 )
5X-RAY DIFFRACTION5chain 'A' and (resid 465 through 516 )
6X-RAY DIFFRACTION6chain 'A' and (resid 517 through 621 )
7X-RAY DIFFRACTION7chain 'B' and (resid 8 through 39 )
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 54 )
9X-RAY DIFFRACTION9chain 'B' and (resid 55 through 86 )
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 115 )
11X-RAY DIFFRACTION11chain 'B' and (resid 116 through 135 )
12X-RAY DIFFRACTION12chain 'B' and (resid 136 through 152 )
13X-RAY DIFFRACTION13chain 'B' and (resid 153 through 230 )
14X-RAY DIFFRACTION14chain 'B' and (resid 231 through 247 )
15X-RAY DIFFRACTION15chain 'C' and (resid 2 through 17 )
16X-RAY DIFFRACTION16chain 'C' and (resid 18 through 33 )
17X-RAY DIFFRACTION17chain 'C' and (resid 34 through 80 )
18X-RAY DIFFRACTION18chain 'C' and (resid 81 through 140 )
19X-RAY DIFFRACTION19chain 'D' and (resid 3 through 29 )
20X-RAY DIFFRACTION20chain 'D' and (resid 30 through 58 )
21X-RAY DIFFRACTION21chain 'D' and (resid 59 through 89 )
22X-RAY DIFFRACTION22chain 'D' and (resid 90 through 103 )
23X-RAY DIFFRACTION23chain 'N' and (resid 10 through 55 )
24X-RAY DIFFRACTION24chain 'N' and (resid 56 through 253 )
25X-RAY DIFFRACTION25chain 'N' and (resid 254 through 429 )
26X-RAY DIFFRACTION26chain 'N' and (resid 430 through 464 )
27X-RAY DIFFRACTION27chain 'N' and (resid 465 through 561 )
28X-RAY DIFFRACTION28chain 'N' and (resid 562 through 621 )
29X-RAY DIFFRACTION29chain 'O' and (resid 8 through 39 )
30X-RAY DIFFRACTION30chain 'O' and (resid 40 through 73 )
31X-RAY DIFFRACTION31chain 'O' and (resid 74 through 115 )
32X-RAY DIFFRACTION32chain 'O' and (resid 116 through 135 )
33X-RAY DIFFRACTION33chain 'O' and (resid 136 through 152 )
34X-RAY DIFFRACTION34chain 'O' and (resid 153 through 230 )
35X-RAY DIFFRACTION35chain 'O' and (resid 231 through 248 )
36X-RAY DIFFRACTION36chain 'P' and (resid 2 through 17 )
37X-RAY DIFFRACTION37chain 'P' and (resid 18 through 22 )
38X-RAY DIFFRACTION38chain 'P' and (resid 23 through 33 )
39X-RAY DIFFRACTION39chain 'P' and (resid 34 through 62 )
40X-RAY DIFFRACTION40chain 'P' and (resid 63 through 80 )
41X-RAY DIFFRACTION41chain 'P' and (resid 81 through 109 )
42X-RAY DIFFRACTION42chain 'P' and (resid 110 through 140 )
43X-RAY DIFFRACTION43chain 'Q' and (resid 3 through 29 )
44X-RAY DIFFRACTION44chain 'Q' and (resid 30 through 58 )
45X-RAY DIFFRACTION45chain 'Q' and (resid 59 through 89 )
46X-RAY DIFFRACTION46chain 'Q' and (resid 90 through 103 )

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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