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- PDB-5mrw: Structure of the KdpFABC complex -

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基本情報

登録情報
データベース: PDB / ID: 5mrw
タイトルStructure of the KdpFABC complex
要素(Potassium-transporting ATPase ...) x 4
キーワードHYDROLASE / membrane protein complex potassium transport P-type ATPase SKT channel
機能・相同性
機能・相同性情報


plasma membrane => GO:0005886 / P-type K+ transporter / P-type potassium transmembrane transporter activity / potassium:proton antiporter complex / potassium ion-transporting ATPase complex / potassium ion binding / monoatomic cation transmembrane transport / potassium ion transmembrane transport / potassium ion transport / hydrolase activity ...plasma membrane => GO:0005886 / P-type K+ transporter / P-type potassium transmembrane transporter activity / potassium:proton antiporter complex / potassium ion-transporting ATPase complex / potassium ion binding / monoatomic cation transmembrane transport / potassium ion transmembrane transport / potassium ion transport / hydrolase activity / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane
類似検索 - 分子機能
Potassium-transporting ATPase C chain / Potassium-transporting ATPase A chain / K+ transporting P-type ATPase, F subunit / K+-transporting ATPase, c chain / Potassium-transporting ATPase A subunit / F subunit of K+-transporting ATPase (Potass_KdpF) / P-type ATPase, B chain, subfamily IA / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / P-type ATPase actuator domain ...Potassium-transporting ATPase C chain / Potassium-transporting ATPase A chain / K+ transporting P-type ATPase, F subunit / K+-transporting ATPase, c chain / Potassium-transporting ATPase A subunit / F subunit of K+-transporting ATPase (Potass_KdpF) / P-type ATPase, B chain, subfamily IA / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
: / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Potassium-transporting ATPase KdpC subunit / Potassium-transporting ATPase potassium-binding subunit / Potassium-transporting ATPase ATP-binding subunit / Potassium-transporting ATPase KdpC subunit / Potassium-transporting ATPase KdpF subunit
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 単波長異常分散 / 解像度: 2.9 Å
データ登録者Huang, C. / Pedersen, B.P. / Stokes, D.L.
資金援助 米国, デンマーク, 3件
組織認可番号国
National Institutes of HealthGM108043 米国
Danish Council for Independent ResearchDFF-4002-00052 デンマーク
European Research Council637372 デンマーク
引用ジャーナル: Nature / 年: 2017
タイトル: Crystal structure of the potassium-importing KdpFABC membrane complex.
著者: Huang, C.S. / Pedersen, B.P. / Stokes, D.L.
履歴
登録2016年12月27日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年6月21日Provider: repository / タイプ: Initial release
改定 1.12017年6月28日Group: Database references / カテゴリ: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.year
改定 1.22017年7月5日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.32018年1月31日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42020年7月29日Group: Data collection / Derived calculations / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / 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 / _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 / _struct_conn_type.id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.52024年11月13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_entry_details / pdbx_modification_feature / 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

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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: Potassium-transporting ATPase potassium-binding subunit
B: Potassium-transporting ATPase ATP-binding subunit
C: Potassium-transporting ATPase KdpC subunit
D: Potassium-transporting ATPase KdpF subunit
E: Potassium-transporting ATPase potassium-binding subunit
F: Potassium-transporting ATPase ATP-binding subunit
G: Potassium-transporting ATPase KdpC subunit
H: Potassium-transporting ATPase KdpF subunit
I: Potassium-transporting ATPase potassium-binding subunit
J: Potassium-transporting ATPase ATP-binding subunit
K: Potassium-transporting ATPase KdpC subunit
L: Potassium-transporting ATPase KdpF subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)465,93425
ポリマ－460,57412
非ポリマー5,36013
水543
1
A: Potassium-transporting ATPase potassium-binding subunit
B: Potassium-transporting ATPase ATP-binding subunit
C: Potassium-transporting ATPase KdpC subunit
D: Potassium-transporting ATPase KdpF subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)155,5069
ポリマ－153,5254
非ポリマー1,9825
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17310 Å2
ΔGint-133 kcal/mol
Surface area52740 Å2
手法PISA
2
E: Potassium-transporting ATPase potassium-binding subunit
F: Potassium-transporting ATPase ATP-binding subunit
G: Potassium-transporting ATPase KdpC subunit
H: Potassium-transporting ATPase KdpF subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)155,2148
ポリマ－153,5254
非ポリマー1,6894
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16750 Å2
ΔGint-138 kcal/mol
Surface area52780 Å2
手法PISA
3
I: Potassium-transporting ATPase potassium-binding subunit
J: Potassium-transporting ATPase ATP-binding subunit
K: Potassium-transporting ATPase KdpC subunit
L: Potassium-transporting ATPase KdpF subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)155,2148
ポリマ－153,5254
非ポリマー1,6894
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16590 Å2
ΔGint-135 kcal/mol
Surface area53340 Å2
手法PISA
単位格子
Length a, b, c (Å)124.720, 166.290, 196.300
Angle α, β, γ (deg.)90.000, 107.410, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain D
21chain H
31chain L
12(chain A and (resseq 1:54 or resseq 56:57 or (resid...
22(chain E and (resseq 1:54 or resseq 56:57 or (resid...
32(chain I and (resseq 1:54 or resseq 56:57 or (resid...
13(chain G and (resseq 4:7 or (resid 8 and (name...
23(chain C and (resseq 4:7 or (resid 8 and (name...
33(chain K and (resseq 4:7 or (resid 8 and (name...
14(chain F and (resseq 9:77 or (resid 78 and (name...
24(chain B and (resseq 9:77 or (resid 78 and (name...
34(chain J and (resseq 9:77 or (resid 78 and (name...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLUGLUchain DDD1 - 271 - 27
211METMETGLUGLUchain HHH1 - 271 - 27
311METMETGLUGLUchain LLL1 - 271 - 27
112METMETASPASP(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 541 - 54
122GLUGLUMETMET(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA56 - 5756 - 57
132ASNASNASNASN(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA5858
142METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
152METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
162METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
172METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
182METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
192METMETSERSER(chain A and (resseq 1:54 or resseq 56:57 or (resid...AA1 - 5571 - 557
212METMETASPASP(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 541 - 54
222GLUGLUMETMET(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE56 - 5756 - 57
232ASNASNASNASN(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE5858
242METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
252METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
262METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
272METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
282METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
292METMETSERSER(chain E and (resseq 1:54 or resseq 56:57 or (resid...EE1 - 5571 - 557
312METMETASPASP(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 541 - 54
322GLUGLUMETMET(chain I and (resseq 1:54 or resseq 56:57 or (resid...II56 - 5756 - 57
332ASNASNASNASN(chain I and (resseq 1:54 or resseq 56:57 or (resid...II5858
342METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
352METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
362METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
372METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
382METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
392METMETSERSER(chain I and (resseq 1:54 or resseq 56:57 or (resid...II1 - 5571 - 557
113LEULEUALAALA(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 71 - 4
123LEULEULEULEU(chain G and (resseq 4:7 or (resid 8 and (name...GG85
133LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
143LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
153LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
163LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
173LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
183LEULEUGLUGLU(chain G and (resseq 4:7 or (resid 8 and (name...GG4 - 1901 - 187
213LEULEUALAALA(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 71 - 4
223LEULEULEULEU(chain C and (resseq 4:7 or (resid 8 and (name...CC85
233LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
243LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
253LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
263LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
273LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
283LEULEUGLUGLU(chain C and (resseq 4:7 or (resid 8 and (name...CC4 - 1901 - 187
313LEULEUALAALA(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 71 - 4
323LEULEULEULEU(chain K and (resseq 4:7 or (resid 8 and (name...KK85
333LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
343LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
353LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
363LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
373LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
383LEULEUGLUGLU(chain K and (resseq 4:7 or (resid 8 and (name...KK4 - 1901 - 187
114PHEPHELEULEU(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 771 - 69
124PHEPHEPHEPHE(chain F and (resseq 9:77 or (resid 78 and (name...FF7870
134PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
144PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
154PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
164PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
174PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
184PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
194PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
1104PHEPHEVALVAL(chain F and (resseq 9:77 or (resid 78 and (name...FF9 - 6821 - 674
214PHEPHELEULEU(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 771 - 69
224PHEPHEPHEPHE(chain B and (resseq 9:77 or (resid 78 and (name...BB7870
234PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
244PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
254PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
264PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
274PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
284PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
294PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
2104PHEPHEVALVAL(chain B and (resseq 9:77 or (resid 78 and (name...BB9 - 6821 - 674
314PHEPHELEULEU(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 771 - 69
324PHEPHEPHEPHE(chain J and (resseq 9:77 or (resid 78 and (name...JJ7870
334PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
344PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
354PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
364PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
374PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
384PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
394PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674
3104PHEPHEVALVAL(chain J and (resseq 9:77 or (resid 78 and (name...JJ9 - 6821 - 674

NCSアンサンブル:
ID
1
2
3
4

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要素

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Potassium-transporting ATPase ... , 4種, 12分子 AEIBFJCGKDHL

#1: タンパク質 Potassium-transporting ATPase potassium-binding subunit / ATP phosphohydrolase [potassium-transporting] A chain / Potassium-binding and translocating subunit ...ATP phosphohydrolase [potassium-transporting] A chain / Potassium-binding and translocating subunit A / Potassium-translocating ATPase A chain


分子量: 59247.684 Da / 分子数: 3 / 変異: Q116R / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: kdpA, b0698, JW0686 / 発現宿主: Escherichia coli (大腸菌) / Variant (発現宿主): TK2498 / 参照: UniProt: P03959
#2: タンパク質 Potassium-transporting ATPase ATP-binding subunit / ATP phosphohydrolase [potassium-transporting] B chain / Potassium-binding and translocating subunit ...ATP phosphohydrolase [potassium-transporting] B chain / Potassium-binding and translocating subunit B / Potassium-translocating ATPase B chain


分子量: 71417.680 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: kdpB, b0697, JW0685 / 発現宿主: Escherichia coli (大腸菌) / Variant (発現宿主): TK2498 / 参照: UniProt: P03960, EC: 3.6.3.12
#3: タンパク質 Potassium-transporting ATPase KdpC subunit / ATP phosphohydrolase [potassium-transporting] C chain / Potassium-binding and translocating subunit ...ATP phosphohydrolase [potassium-transporting] C chain / Potassium-binding and translocating subunit C / Potassium-translocating ATPase C chain


分子量: 20005.709 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: kdpC, JD73_10370 / 発現宿主: Escherichia coli (大腸菌) / Variant (発現宿主): TK2498 / 参照: UniProt: A0A085P4P2, UniProt: P03961*PLUS
#4: タンパク質・ペプチド Potassium-transporting ATPase KdpF subunit / ATP phosphohydrolase [potassium-transporting] F chain / Potassium-binding and translocating subunit ...ATP phosphohydrolase [potassium-transporting] F chain / Potassium-binding and translocating subunit F / Potassium-translocating ATPase F chain


分子量: 2853.463 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: kdpF, b4513, JW0687 / 発現宿主: Escherichia coli (大腸菌) / Variant (発現宿主): TK2498 / 参照: UniProt: P36937

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糖 , 1種, 4分子

#7: 糖
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


タイプ: D-saccharide / 分子量: 292.369 Da / 分子数: 4 / 由来タイプ: 組換発現 / 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

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非ポリマー , 3種, 12分子

#5: 化合物 ChemComp-K / POTASSIUM ION


分子量: 39.098 Da / 分子数: 3 / 由来タイプ: 合成 / 式: K
#6: 化合物
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


分子量: 678.940 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C36H73NO8P / コメント: DMPC, リン脂質*YM
#8: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 3 / 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: 4.22 Å3/Da / 溶媒含有率: 70.83 %
解説: Crystals appeared within a week and grew to full size (100 x 300 x 40 um) after three weeks.
結晶化温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5
詳細: 20% (w/v) PEG3350, 0.5-1.0 M NaCl, 0.05 mM sodium citrate pH 5.5.

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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: APS / ビームライン: 23-ID-D / 波長: 1.03666 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2015年10月22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: 1.03666 Å / 相対比: 1
反射解像度: 2.9→50 Å / Num. obs: 167947 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / 冗長度: 18.8 % / Biso Wilson estimate: 94.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.201 / Net I/σ(I): 11.28
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.9-318.54.910.960.488198.9
3-3.519.3452.5911.950.865199.2
3.5-418.850.7075.920.986199.3
4-518.5370.19315.90.998199.5
5-619.2240.12823.210.998199.7
6-717.7520.09828.690.998199.8
7-817.5920.06738.710.999199.7
8-918.3780.05346.40.999199.8
9-1217.7450.04350.030.999199.8
12-1516.0070.04247.761199.7
15-19.97418.1350.03752.30.999196.1

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位相決定

位相決定手法: 単波長異常分散

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
SHARP位相決定
PHENIX精密化
PDB_EXTRACT3.22データ抽出
XDSデータ削減
精密化構造決定の手法: 単波長異常分散 / 解像度: 2.9→20 Å / SU ML: 0.5 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 39.8
Rfactor反射数%反射Selection details
Rfree0.2749 8341 5 %Random
Rwork0.243 ---
obs0.2446 166954 99.12 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 488.57 Å2 / Biso mean: 151.7128 Å2 / Biso min: 61.96 Å2
精密化ステップサイクル: final / 解像度: 2.9→20 Å
タンパク質核酸リガンド溶媒全体
原子数32334 0 329 3 32666
Biso mean--195.59 109.22 -
残基数----4335
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00233254
X-RAY DIFFRACTIONf_angle_d0.44845199
X-RAY DIFFRACTIONf_chiral_restr0.0375432
X-RAY DIFFRACTIONf_plane_restr0.0035700
X-RAY DIFFRACTIONf_dihedral_angle_d8.77619780
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11D342X-RAY DIFFRACTION4.608TORSIONAL
12H342X-RAY DIFFRACTION4.608TORSIONAL
13L342X-RAY DIFFRACTION4.608TORSIONAL
21A7559X-RAY DIFFRACTION4.608TORSIONAL
22E7559X-RAY DIFFRACTION4.608TORSIONAL
23I7559X-RAY DIFFRACTION4.608TORSIONAL
31G2611X-RAY DIFFRACTION4.608TORSIONAL
32C2611X-RAY DIFFRACTION4.608TORSIONAL
33K2611X-RAY DIFFRACTION4.608TORSIONAL
41F9259X-RAY DIFFRACTION4.608TORSIONAL
42B9259X-RAY DIFFRACTION4.608TORSIONAL
43J9259X-RAY DIFFRACTION4.608TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.93290.54162770.56225248552599
2.9329-2.96730.60172790.54225305558499
2.9673-3.00330.54152730.51445187546099
3.0033-3.04120.53912780.50865276555499
3.0412-3.08110.49912740.48495240551499
3.0811-3.12310.47632780.44815284556299
3.1231-3.16760.45132730.42495213548699
3.1676-3.21470.45432770.40445256553399
3.2147-3.26470.41932730.38585255552899
3.2647-3.3180.38772780.3575257553599
3.318-3.37490.37682770.34345291556899
3.3749-3.4360.38442760.32365230550699
3.436-3.50170.34632790.31375297557699
3.5017-3.57280.35792780.29715269554799
3.5728-3.65010.31462750.27925264553999
3.6501-3.73440.3142750.26815221549699
3.7344-3.82720.26092740.25165277555199
3.8272-3.92990.29642770.2415262553998
3.9299-4.04460.27392790.23525299557899
4.0446-4.1740.25612800.21815314559499
4.174-4.32180.24832790.21185282556199
4.3218-4.49290.24842790.21535305558499
4.4929-4.69490.27022790.19295282556199
4.6949-4.93890.22322810.184953295610100
4.9389-5.2430.21922800.193753275607100
5.243-5.63940.22852800.200753195599100
5.6394-6.19150.26362830.224753595642100
6.1915-7.05270.26292820.216253585640100
7.0527-8.75910.21452830.181553765659100
8.7591-19.97410.20182850.194354315716100
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)
10.926-0.27560.55030.34-0.15080.73420.2230.156-0.0643-0.13430.0790.15720.25790.183300.87740.09570.0240.8138-0.09510.8663141.2138-34.3355-21.4678
20.1285-0.19780.35820.2159-0.26560.44640.1499-0.1688-0.07210.2314-0.0484-0.06970.16890.194601.02490.13220.00061.4137-0.15651.1228169.2423-29.2323-1.0695
30.1416-0.087-0.15370.13910.10410.15840.1991-0.0576-0.4255-0.0140.12410.74990.1516-0.232801.36380.05450.04561.36610.07961.781866.3133-34.7871-30.9703
40.22850.08010.22990.18240.09670.1388-0.13030.37930.036-0.52780.12440.01760.0155-0.087501.56570.2479-0.16141.21340.12071.650767.1057-5.6108-35.6346
50.7332-0.547-0.18980.3361-0.0320.40160.10370.5409-0.211-0.27990.01710.0992-0.22360.077201.271-0.0125-0.17141.23790.02631.300193.1447-15.6712-35.3119
60.70570.49940.02160.78870.58751.67130.2743-0.7893-0.1107-0.2099-0.03270.26520.3035-0.27810.00240.7007-0.16-0.01951.24750.20671.0693106.7075-32.5601-2.995
70.51330.53520.02770.66720.02230.96980.0356-0.022-0.0127-0.02570.1068-00.0087-0.455600.58150.22030.08730.9168-0.06790.7705157.6559-23.476843.0288
80.0808-0.16070.0646-0.0152-0.10620.04390.08520.0926-0.03450.30670.2027-0.09860.0862-0.197101.52590.0136-0.08681.39450.04741.2626162.4143-43.072871.7055
90.09360.0585-0.07790.1947-0.27290.27560.1123-0.26640.1537-0.35480.3640.8152-0.2555-0.4704-01.4872-0.2863-0.13961.7282-0.14821.863180.646735.3461-0.1248
100.0525-0.11740.14290.1849-0.1920.1751-0.2804-0.33560.0838-1.11550.4651-0.67770.0380.24830.00011.814-0.28590.2411.9082-0.221.4806202.623918.045-10.136
110.4594-0.0944-0.30940.3820.11540.1832-0.0190.4827-0.1205-0.4060.36710.0362-0.10840.002601.4199-0.031-0.02761.5961-0.19831.2551183.60772.31013.7647
121.3873-0.0096-0.03910.44440.07250.81860.1065-0.02460.11590.42270.0231-0.2233-0.71120.300101.32650.01540.01980.7168-0.0580.9462179.29869.051541.5556
130.0329-0.05340.19180.61430.38760.78660.00530.2173-0.0897-0.22740.0330.0703-0.23090.32601.0648-0.0458-0.02460.93570.0030.8771125.5608-23.2319-86.0464
14-0.02120.12990.1680.11630.03190.1186-0.1382-0.38690.05720.24150.1291-0.2787-0.20150.139801.4478-0.0426-0.06921.102-0.09471.1569121.3135-8.9862-54.3416
150.09130.0684-0.17890.1828-0.11090.2487-0.0591-0.1979-0.23570.0460.1149-1.39270.57511.7192-0.01171.87670.0984-0.04271.9011-0.46962.158148.996-81.9195-128.4143
160.03570.0205-0.1004-0.0037-0.07010.16320.22080.6514-0.11940.03580.2066-0.3578-0.0805-0.108301.85990.2289-0.51171.3395-0.29241.7772122.6725-94.634-123.9122
170.19320.07750.13290.1989-0.05390.1407-0.06410.1534-0.1852-0.06960.25690.3726-0.1552-0.082701.85910.201-0.35641.4828-0.20731.5367121.112-68.0019-114.8072
181.69060.3329-0.29220.974-0.47731.10930.07920.0715-0.24910.16390.3059-0.14650.64150.768601.22150.4415-0.1951.4511-0.35991.172145.0579-57.0859-86.5522
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and not resseq 199:217 and not resseq 305:328 or chain C and not resseq 40:190 or chain M and resseq 1301:1302 or chain N and resid 2A1 - 199
2X-RAY DIFFRACTION1chain A and not resseq 199:217 and not resseq 305:328 or chain C and not resseq 40:190 or chain M and resseq 1301:1302 or chain N and resid 2A199 - 217
3X-RAY DIFFRACTION1chain A and not resseq 199:217 and not resseq 305:328 or chain C and not resseq 40:190 or chain M and resseq 1301:1302 or chain N and resid 2A217 - 557
4X-RAY DIFFRACTION2chain A and resseq 199:217 or chain A and resseq 305:328 or chain C and resseq 40:190A0
5X-RAY DIFFRACTION3chain B and resseq 103:196B103 - 196
6X-RAY DIFFRACTION4chain B and resseq 318:447B318 - 447
7X-RAY DIFFRACTION5chain B and resseq 287:554 and not resseq 318:447B9 - 318
8X-RAY DIFFRACTION5chain B and resseq 287:554 and not resseq 318:447B447 - 682
9X-RAY DIFFRACTION6chain B and not resseq 103:196 and not resseq 287:554 or chain D or chain N and resid 1B9 - 103
10X-RAY DIFFRACTION6chain B and not resseq 103:196 and not resseq 287:554 or chain D or chain N and resid 1B196 - 682
11X-RAY DIFFRACTION7chain E and not resseq 199:217 and not resseq 305:328 or chain G and not resseq 40:190 or chain M and resseq 1303:1304 or chain N and resid 3E1 - 199
12X-RAY DIFFRACTION7chain E and not resseq 199:217 and not resseq 305:328 or chain G and not resseq 40:190 or chain M and resseq 1303:1304 or chain N and resid 3E199 - 217
13X-RAY DIFFRACTION7chain E and not resseq 199:217 and not resseq 305:328 or chain G and not resseq 40:190 or chain M and resseq 1303:1304 or chain N and resid 3E217 - 557
14X-RAY DIFFRACTION8chain E and resseq 199:217 or chain E and resseq 305:328 or chain G and resseq 40:190E0
15X-RAY DIFFRACTION9chain F and resseq 103:196F103 - 196
16X-RAY DIFFRACTION10chain F and resseq 318:447F318 - 447
17X-RAY DIFFRACTION11chain F and resseq 287:554 and not resseq 318:447F9 - 318
18X-RAY DIFFRACTION11chain F and resseq 287:554 and not resseq 318:447F447 - 682
19X-RAY DIFFRACTION12chain F and not resseq 103:196 and not resseq 287:554 or chain HF9 - 103
20X-RAY DIFFRACTION12chain F and not resseq 103:196 and not resseq 287:554 or chain HF103 - 196
21X-RAY DIFFRACTION12chain F and not resseq 103:196 and not resseq 287:554 or chain HF196 - 682
22X-RAY DIFFRACTION13chain I and not resseq 199:217 and not resseq 305:328 or chain K and not resseq 40:190 or chain M and resseq 1305:1306 or chain N and resid 4I1 - 199
23X-RAY DIFFRACTION13chain I and not resseq 199:217 and not resseq 305:328 or chain K and not resseq 40:190 or chain M and resseq 1305:1306 or chain N and resid 4I199 - 217
24X-RAY DIFFRACTION13chain I and not resseq 199:217 and not resseq 305:328 or chain K and not resseq 40:190 or chain M and resseq 1305:1306 or chain N and resid 4I217 - 557
25X-RAY DIFFRACTION14chain I and resseq 199:217 or chain I and resseq 305:328 or chain K and resseq 40:190I0
26X-RAY DIFFRACTION15chain J and resseq 103:196J103 - 196
27X-RAY DIFFRACTION16chain J and resseq 318:447J318 - 447
28X-RAY DIFFRACTION17chain J and resseq 287:554 and not resseq 318:447J9 - 318
29X-RAY DIFFRACTION17chain J and resseq 287:554 and not resseq 318:447J447 - 682
30X-RAY DIFFRACTION18chain J and not resseq 103:196 and not resseq 287:554 or chain LJ9 - 103
31X-RAY DIFFRACTION18chain J and not resseq 103:196 and not resseq 287:554 or chain LJ103 - 196
32X-RAY DIFFRACTION18chain J and not resseq 103:196 and not resseq 287:554 or chain LJ196 - 682

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万見について

-
お知らせ

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

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

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

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

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

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

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

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

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

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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

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