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- PDB-6um4: Crystal structure of malate dehydrogenase from Naegleria fowleri ... -

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基本情報

登録情報
データベース: PDB / ID: 6um4
タイトルCrystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863
要素Malate dehydrogenase
キーワードOXIDOREDUCTASE / SSGCID / Structural Genomics / Naegleria fowleri / malate dehydrogenase / NF0021050 / Seattle Structural Genomics Center for Infectious Disease
機能・相同性L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
機能・相同性情報
生物種Naegleria fowleri (フォーラーネグレリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.05 Å
データ登録者Seattle Structural Genomics Center for Infectious Disease (SSGCID)
引用ジャーナル: TO BE PUBLISHED
タイトル: Crystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863
著者: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
履歴
登録2019年10月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年10月23日Provider: repository / タイプ: Initial release
改定 1.12024年3月13日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.22024年4月3日Group: Refinement description / カテゴリ: pdbx_initial_refinement_model

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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: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
E: Malate dehydrogenase
F: Malate dehydrogenase
G: Malate dehydrogenase
H: Malate dehydrogenase
I: Malate dehydrogenase
J: Malate dehydrogenase
K: Malate dehydrogenase
L: Malate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)587,40616
ポリマ－587,15812
非ポリマー2484
水40,3002237
1
A: Malate dehydrogenase
B: Malate dehydrogenase


分子量 (理論値)分子数
合計 (水以外)97,8602
ポリマ－97,8602
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-8 kcal/mol
Surface area25000 Å2
手法PISA
2
C: Malate dehydrogenase
D: Malate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,9223
ポリマ－97,8602
非ポリマー621
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-9 kcal/mol
Surface area24920 Å2
手法PISA
3
E: Malate dehydrogenase
F: Malate dehydrogenase


分子量 (理論値)分子数
合計 (水以外)97,8602
ポリマ－97,8602
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-10 kcal/mol
Surface area24970 Å2
手法PISA
4
G: Malate dehydrogenase
H: Malate dehydrogenase


分子量 (理論値)分子数
合計 (水以外)97,8602
ポリマ－97,8602
非ポリマー00
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-11 kcal/mol
Surface area24980 Å2
手法PISA
5
I: Malate dehydrogenase
J: Malate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,9844
ポリマ－97,8602
非ポリマー1242
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-11 kcal/mol
Surface area24680 Å2
手法PISA
6
K: Malate dehydrogenase
L: Malate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)97,9223
ポリマ－97,8602
非ポリマー621
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-10 kcal/mol
Surface area25160 Å2
手法PISA
単位格子
Length a, b, c (Å)60.330, 137.480, 139.280
Angle α, β, γ (deg.)91.093, 89.998, 91.482
Int Tables number1
Space group name H-MP1
Space group name HallP1
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121

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
11LEULEUGLYGLY(chain 'A' and (resid 94 through 105 or resid 107...AA94 - 10494 - 104
12GLYGLYLEULEU(chain 'A' and (resid 94 through 105 or resid 107...AA107 - 158107 - 158
13GLUGLUSERSER(chain 'A' and (resid 94 through 105 or resid 107...AA160 - 166160 - 166
14ASNASNPHEPHE(chain 'A' and (resid 94 through 105 or resid 107...AA168 - 171168 - 171
15GLYGLYPROPRO(chain 'A' and (resid 94 through 105 or resid 107...AA173 - 184173 - 184
16METMETLEULEU(chain 'A' and (resid 94 through 105 or resid 107...AA189 - 220189 - 220
17VALVALTHRTHR(chain 'A' and (resid 94 through 105 or resid 107...AA222 - 292222 - 292
18LYSLYSASPASP(chain 'A' and (resid 94 through 105 or resid 107...AA294 - 304294 - 304
19GLNGLNASPASP(chain 'A' and (resid 94 through 105 or resid 107...AA306 - 398306 - 398
110ILEILEILEILE(chain 'A' and (resid 94 through 105 or resid 107...AA400 - 408400 - 408
111GLUGLUVALVAL(chain 'A' and (resid 94 through 105 or resid 107...AA410 - 414410 - 414
112ASNASNLEULEU(chain 'A' and (resid 94 through 105 or resid 107...AA416 - 417416 - 417
21LEULEUGLYGLY(chain 'B' and (resid 94 through 105 or resid 107...BB94 - 10494 - 104
22GLYGLYLEULEU(chain 'B' and (resid 94 through 105 or resid 107...BB107 - 158107 - 158
23GLUGLUSERSER(chain 'B' and (resid 94 through 105 or resid 107...BB160 - 166160 - 166
24ASNASNPHEPHE(chain 'B' and (resid 94 through 105 or resid 107...BB168 - 171168 - 171
25GLYGLYPROPRO(chain 'B' and (resid 94 through 105 or resid 107...BB173 - 184173 - 184
26METMETLEULEU(chain 'B' and (resid 94 through 105 or resid 107...BB189 - 220189 - 220
27VALVALTHRTHR(chain 'B' and (resid 94 through 105 or resid 107...BB222 - 292222 - 292
28LYSLYSASPASP(chain 'B' and (resid 94 through 105 or resid 107...BB294 - 304294 - 304
29GLNGLNASPASP(chain 'B' and (resid 94 through 105 or resid 107...BB306 - 398306 - 398
210ILEILEILEILE(chain 'B' and (resid 94 through 105 or resid 107...BB400 - 408400 - 408
211GLUGLUVALVAL(chain 'B' and (resid 94 through 105 or resid 107...BB410 - 414410 - 414
212ASNASNLEULEU(chain 'B' and (resid 94 through 105 or resid 107...BB416 - 417416 - 417
31LEULEUGLYGLY(chain 'C' and (resid 94 through 105 or resid 107...CC94 - 10494 - 104
32GLYGLYLEULEU(chain 'C' and (resid 94 through 105 or resid 107...CC107 - 158107 - 158
33GLUGLUSERSER(chain 'C' and (resid 94 through 105 or resid 107...CC160 - 166160 - 166
34ASNASNPHEPHE(chain 'C' and (resid 94 through 105 or resid 107...CC168 - 171168 - 171
35GLYGLYPROPRO(chain 'C' and (resid 94 through 105 or resid 107...CC173 - 184173 - 184
36METMETLEULEU(chain 'C' and (resid 94 through 105 or resid 107...CC189 - 220189 - 220
37VALVALTHRTHR(chain 'C' and (resid 94 through 105 or resid 107...CC222 - 292222 - 292
38LYSLYSASPASP(chain 'C' and (resid 94 through 105 or resid 107...CC294 - 304294 - 304
39GLNGLNASPASP(chain 'C' and (resid 94 through 105 or resid 107...CC306 - 398306 - 398
310ILEILEILEILE(chain 'C' and (resid 94 through 105 or resid 107...CC400 - 408400 - 408
311GLUGLUVALVAL(chain 'C' and (resid 94 through 105 or resid 107...CC410 - 414410 - 414
312ASNASNLEULEU(chain 'C' and (resid 94 through 105 or resid 107...CC416 - 417416 - 417
41LEULEUGLYGLY(chain 'D' and (resid 94 through 105 or resid 107...DD94 - 10494 - 104
42GLYGLYLEULEU(chain 'D' and (resid 94 through 105 or resid 107...DD107 - 158107 - 158
43GLUGLUSERSER(chain 'D' and (resid 94 through 105 or resid 107...DD160 - 166160 - 166
44ASNASNPHEPHE(chain 'D' and (resid 94 through 105 or resid 107...DD168 - 171168 - 171
45GLYGLYPROPRO(chain 'D' and (resid 94 through 105 or resid 107...DD173 - 184173 - 184
46METMETLEULEU(chain 'D' and (resid 94 through 105 or resid 107...DD189 - 220189 - 220
47VALVALTHRTHR(chain 'D' and (resid 94 through 105 or resid 107...DD222 - 292222 - 292
48LYSLYSASPASP(chain 'D' and (resid 94 through 105 or resid 107...DD294 - 304294 - 304
49GLNGLNASPASP(chain 'D' and (resid 94 through 105 or resid 107...DD306 - 398306 - 398
410ILEILEILEILE(chain 'D' and (resid 94 through 105 or resid 107...DD400 - 408400 - 408
411GLUGLUVALVAL(chain 'D' and (resid 94 through 105 or resid 107...DD410 - 414410 - 414
412ASNASNLEULEU(chain 'D' and (resid 94 through 105 or resid 107...DD416 - 417416 - 417
51LEULEUGLYGLY(chain 'E' and (resid 94 through 105 or resid 107...EE94 - 10494 - 104
52GLYGLYLEULEU(chain 'E' and (resid 94 through 105 or resid 107...EE107 - 158107 - 158
53GLUGLUSERSER(chain 'E' and (resid 94 through 105 or resid 107...EE160 - 166160 - 166
54ASNASNPHEPHE(chain 'E' and (resid 94 through 105 or resid 107...EE168 - 171168 - 171
55GLYGLYPROPRO(chain 'E' and (resid 94 through 105 or resid 107...EE173 - 184173 - 184
56METMETLEULEU(chain 'E' and (resid 94 through 105 or resid 107...EE189 - 220189 - 220
57VALVALTHRTHR(chain 'E' and (resid 94 through 105 or resid 107...EE222 - 292222 - 292
58LYSLYSASPASP(chain 'E' and (resid 94 through 105 or resid 107...EE294 - 304294 - 304
59GLNGLNASPASP(chain 'E' and (resid 94 through 105 or resid 107...EE306 - 398306 - 398
510ILEILEILEILE(chain 'E' and (resid 94 through 105 or resid 107...EE400 - 408400 - 408
511GLUGLUVALVAL(chain 'E' and (resid 94 through 105 or resid 107...EE410 - 414410 - 414
512ASNASNLEULEU(chain 'E' and (resid 94 through 105 or resid 107...EE416 - 417416 - 417
61LEULEUGLYGLY(chain 'F' and (resid 94 through 105 or resid 107...FF94 - 10494 - 104
62GLYGLYLEULEU(chain 'F' and (resid 94 through 105 or resid 107...FF107 - 158107 - 158
63GLUGLUSERSER(chain 'F' and (resid 94 through 105 or resid 107...FF160 - 166160 - 166
64ASNASNPHEPHE(chain 'F' and (resid 94 through 105 or resid 107...FF168 - 171168 - 171
65GLYGLYPROPRO(chain 'F' and (resid 94 through 105 or resid 107...FF173 - 184173 - 184
66METMETLEULEU(chain 'F' and (resid 94 through 105 or resid 107...FF189 - 220189 - 220
67VALVALTHRTHR(chain 'F' and (resid 94 through 105 or resid 107...FF222 - 292222 - 292
68LYSLYSASPASP(chain 'F' and (resid 94 through 105 or resid 107...FF294 - 304294 - 304
69GLNGLNASPASP(chain 'F' and (resid 94 through 105 or resid 107...FF306 - 398306 - 398
610ILEILEILEILE(chain 'F' and (resid 94 through 105 or resid 107...FF400 - 408400 - 408
611GLUGLUVALVAL(chain 'F' and (resid 94 through 105 or resid 107...FF410 - 414410 - 414
612ASNASNLEULEU(chain 'F' and (resid 94 through 105 or resid 107...FF416 - 417416 - 417
71LEULEUGLYGLY(chain 'G' and (resid 94 through 105 or resid 107...GG94 - 10494 - 104
72GLYGLYLEULEU(chain 'G' and (resid 94 through 105 or resid 107...GG107 - 158107 - 158
73GLUGLUSERSER(chain 'G' and (resid 94 through 105 or resid 107...GG160 - 166160 - 166
74ASNASNPHEPHE(chain 'G' and (resid 94 through 105 or resid 107...GG168 - 171168 - 171
75GLYGLYPROPRO(chain 'G' and (resid 94 through 105 or resid 107...GG173 - 184173 - 184
76METMETLEULEU(chain 'G' and (resid 94 through 105 or resid 107...GG189 - 220189 - 220
77VALVALTHRTHR(chain 'G' and (resid 94 through 105 or resid 107...GG222 - 292222 - 292
78LYSLYSASPASP(chain 'G' and (resid 94 through 105 or resid 107...GG294 - 304294 - 304
79GLNGLNASPASP(chain 'G' and (resid 94 through 105 or resid 107...GG306 - 398306 - 398
710ILEILEILEILE(chain 'G' and (resid 94 through 105 or resid 107...GG400 - 408400 - 408
711GLUGLUVALVAL(chain 'G' and (resid 94 through 105 or resid 107...GG410 - 414410 - 414
712ASNASNLEULEU(chain 'G' and (resid 94 through 105 or resid 107...GG416 - 417416 - 417
81LEULEUGLYGLY(chain 'H' and (resid 94 through 105 or resid 107...HH94 - 10494 - 104
82GLYGLYLEULEU(chain 'H' and (resid 94 through 105 or resid 107...HH107 - 158107 - 158
83GLUGLUSERSER(chain 'H' and (resid 94 through 105 or resid 107...HH160 - 166160 - 166
84ASNASNPHEPHE(chain 'H' and (resid 94 through 105 or resid 107...HH168 - 171168 - 171
85GLYGLYPROPRO(chain 'H' and (resid 94 through 105 or resid 107...HH173 - 184173 - 184
86METMETLEULEU(chain 'H' and (resid 94 through 105 or resid 107...HH189 - 220189 - 220
87VALVALTHRTHR(chain 'H' and (resid 94 through 105 or resid 107...HH222 - 292222 - 292
88LYSLYSASPASP(chain 'H' and (resid 94 through 105 or resid 107...HH294 - 304294 - 304
89GLNGLNASPASP(chain 'H' and (resid 94 through 105 or resid 107...HH306 - 398306 - 398
810ILEILEILEILE(chain 'H' and (resid 94 through 105 or resid 107...HH400 - 408400 - 408
811GLUGLUVALVAL(chain 'H' and (resid 94 through 105 or resid 107...HH410 - 414410 - 414
812ASNASNLEULEU(chain 'H' and (resid 94 through 105 or resid 107...HH416 - 417416 - 417
91LEULEUGLYGLY(chain 'I' and (resid 94 through 105 or resid 107...II94 - 10494 - 104
92GLYGLYLEULEU(chain 'I' and (resid 94 through 105 or resid 107...II107 - 158107 - 158
93GLUGLUSERSER(chain 'I' and (resid 94 through 105 or resid 107...II160 - 166160 - 166
94ASNASNPHEPHE(chain 'I' and (resid 94 through 105 or resid 107...II168 - 171168 - 171
95GLYGLYPROPRO(chain 'I' and (resid 94 through 105 or resid 107...II173 - 184173 - 184
96METMETLEULEU(chain 'I' and (resid 94 through 105 or resid 107...II189 - 220189 - 220
97VALVALTHRTHR(chain 'I' and (resid 94 through 105 or resid 107...II222 - 292222 - 292
98LYSLYSASPASP(chain 'I' and (resid 94 through 105 or resid 107...II294 - 304294 - 304
99GLNGLNASPASP(chain 'I' and (resid 94 through 105 or resid 107...II306 - 398306 - 398
910ILEILEILEILE(chain 'I' and (resid 94 through 105 or resid 107...II400 - 408400 - 408
911GLUGLUVALVAL(chain 'I' and (resid 94 through 105 or resid 107...II410 - 414410 - 414
912ASNASNLEULEU(chain 'I' and (resid 94 through 105 or resid 107...II416 - 417416 - 417
101LEULEUGLYGLY(chain 'J' and (resid 94 through 105 or resid 107...JJ94 - 10494 - 104
102GLYGLYLEULEU(chain 'J' and (resid 94 through 105 or resid 107...JJ107 - 158107 - 158
103GLUGLUSERSER(chain 'J' and (resid 94 through 105 or resid 107...JJ160 - 166160 - 166
104ASNASNPHEPHE(chain 'J' and (resid 94 through 105 or resid 107...JJ168 - 171168 - 171
105GLYGLYPROPRO(chain 'J' and (resid 94 through 105 or resid 107...JJ173 - 184173 - 184
106METMETLEULEU(chain 'J' and (resid 94 through 105 or resid 107...JJ189 - 220189 - 220
107VALVALTHRTHR(chain 'J' and (resid 94 through 105 or resid 107...JJ222 - 292222 - 292
108LYSLYSASPASP(chain 'J' and (resid 94 through 105 or resid 107...JJ294 - 304294 - 304
109GLNGLNASPASP(chain 'J' and (resid 94 through 105 or resid 107...JJ306 - 398306 - 398
1010ILEILEILEILE(chain 'J' and (resid 94 through 105 or resid 107...JJ400 - 408400 - 408
1011GLUGLUVALVAL(chain 'J' and (resid 94 through 105 or resid 107...JJ410 - 414410 - 414
1012ASNASNLEULEU(chain 'J' and (resid 94 through 105 or resid 107...JJ416 - 417416 - 417
111LEULEUGLYGLY(chain 'K' and (resid 94 through 105 or resid 107...KK94 - 10494 - 104
112GLYGLYLEULEU(chain 'K' and (resid 94 through 105 or resid 107...KK107 - 158107 - 158
113GLUGLUSERSER(chain 'K' and (resid 94 through 105 or resid 107...KK160 - 166160 - 166
114ASNASNPHEPHE(chain 'K' and (resid 94 through 105 or resid 107...KK168 - 171168 - 171
115GLYGLYPROPRO(chain 'K' and (resid 94 through 105 or resid 107...KK173 - 184173 - 184
116METMETLEULEU(chain 'K' and (resid 94 through 105 or resid 107...KK189 - 220189 - 220
117VALVALTHRTHR(chain 'K' and (resid 94 through 105 or resid 107...KK222 - 292222 - 292
118LYSLYSASPASP(chain 'K' and (resid 94 through 105 or resid 107...KK294 - 304294 - 304
119GLNGLNASPASP(chain 'K' and (resid 94 through 105 or resid 107...KK306 - 398306 - 398
1110ILEILEILEILE(chain 'K' and (resid 94 through 105 or resid 107...KK400 - 408400 - 408
1111GLUGLUVALVAL(chain 'K' and (resid 94 through 105 or resid 107...KK410 - 414410 - 414
1112ASNASNLEULEU(chain 'K' and (resid 94 through 105 or resid 107...KK416 - 417416 - 417
121LEULEUGLYGLY(chain 'L' and (resid 94 through 105 or resid 107...LL94 - 10494 - 104
122GLYGLYLEULEU(chain 'L' and (resid 94 through 105 or resid 107...LL107 - 158107 - 158
123GLUGLUSERSER(chain 'L' and (resid 94 through 105 or resid 107...LL160 - 166160 - 166
124ASNASNPHEPHE(chain 'L' and (resid 94 through 105 or resid 107...LL168 - 171168 - 171
125GLYGLYPROPRO(chain 'L' and (resid 94 through 105 or resid 107...LL173 - 184173 - 184
126METMETLEULEU(chain 'L' and (resid 94 through 105 or resid 107...LL189 - 220189 - 220
127VALVALTHRTHR(chain 'L' and (resid 94 through 105 or resid 107...LL222 - 292222 - 292
128LYSLYSASPASP(chain 'L' and (resid 94 through 105 or resid 107...LL294 - 304294 - 304
129GLNGLNASPASP(chain 'L' and (resid 94 through 105 or resid 107...LL306 - 398306 - 398
1210ILEILEILEILE(chain 'L' and (resid 94 through 105 or resid 107...LL400 - 408400 - 408
1211GLUGLUVALVAL(chain 'L' and (resid 94 through 105 or resid 107...LL410 - 414410 - 414
1212ASNASNLEULEU(chain 'L' and (resid 94 through 105 or resid 107...LL416 - 417416 - 417

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要素

#1: タンパク質
Malate dehydrogenase / NafoA.00005.a.B1


分子量: 48929.793 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Naegleria fowleri (フォーラーネグレリア)
遺伝子: mRNA1_NF0021050
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
株 (発現宿主): BL21(DE3)
#2: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C2H6O2
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2237 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかN

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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: 1.97 Å3/Da / 溶媒含有率: 37.6 %
結晶化温度: 290 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: Microlytics MCSG1 screen, condition H11: 25% PEG 3350, 200mM NaCl, 100mM HEPES / NaOH pH 7.5: NafoA.00005.a.B1.PS38166 at 16.9mg/ml + 2mM NAD. Cryo: 15% EG: tray: 298888 h11: puck eqq6-5.

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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: APS / ビームライン: 21-ID-F / 波長: 0.97872 Å
検出器タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2018年3月1日
放射モノクロメーター: C(111) / 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: 0.97872 Å / 相対比: 1
反射解像度: 2.05→44.23 Å / Num. obs: 271476 / % possible obs: 96.7 % / 冗長度: 2.645 % / Biso Wilson estimate: 23.36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.108 / Χ2: 0.998 / Net I/σ(I): 8.18 / Num. measured all: 718188 / Scaling rejects: 104
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.12.6560.5122.015295320736199370.8690.6596.1
2.1-2.162.650.4072.445173420265195230.9170.51696.3
2.16-2.222.6560.3392.915055019752190320.9360.42996.4
2.22-2.292.6550.3043.234877419051183700.9480.38596.4
2.29-2.372.6520.2713.534745618528178950.9560.34396.6
2.37-2.452.6520.2164.294589317897173030.9710.27496.7
2.45-2.542.6460.1795.024429117316167360.9790.22796.7
2.54-2.652.6510.1665.414271116644161130.9810.21196.8
2.65-2.762.6490.1416.384097415992154660.9840.17996.7
2.76-2.92.6450.1177.473898415240147410.9880.14996.7
2.9-3.062.6440.0968.853721614488140780.9910.12297.2
3.06-3.242.6430.07211.213534213745133730.9950.09297.3
3.24-3.472.6360.06113.143297712859125120.9950.07797.3
3.47-3.742.630.04716.363075812038116940.9970.05997.1
3.74-4.12.6360.04117.742830111048107350.9970.05297.2
4.1-4.582.6420.03519.7325471995696400.9980.04496.8
4.58-5.292.640.03419.7222512877385280.9980.04397.2
5.29-6.482.6320.03618.5319063743572420.9980.04697.4
6.48-9.172.6210.03221.114636574355840.9980.0497.2
9.17-44.232.5530.02823.47592314729740.9980.03594.5

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17_3644精密化
XDSデータ削減
XSCALEデータスケーリング
PDB_EXTRACT3.25データ抽出
MoRDa位相決定
ARP/wARPモデル構築
BUCCANEERモデル構築
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 1bdm_A as per MorDa

解像度: 2.05→44.23 Å / SU ML: 0.222 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 31.3053
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射Selection details
Rfree0.2324 1853 0.68 %0
Rwork0.2106 268817 --
obs0.2108 270670 96.45 %-
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: 33.15 Å2
精密化ステップサイクル: LAST / 解像度: 2.05→44.23 Å
タンパク質核酸リガンド溶媒全体
原子数28960 0 16 2237 31213
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006929671
X-RAY DIFFRACTIONf_angle_d0.840640416
X-RAY DIFFRACTIONf_chiral_restr0.05434597
X-RAY DIFFRACTIONf_plane_restr0.00595384
X-RAY DIFFRACTIONf_dihedral_angle_d17.147910702
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.38181230.314820541X-RAY DIFFRACTION95.81
2.11-2.170.32281010.290820624X-RAY DIFFRACTION95.95
2.17-2.240.29341070.279520625X-RAY DIFFRACTION96.05
2.24-2.320.27441370.268820663X-RAY DIFFRACTION96.2
2.32-2.410.32121150.250620758X-RAY DIFFRACTION96.46
2.41-2.520.27621840.22920531X-RAY DIFFRACTION96.16
2.52-2.650.28491680.223420636X-RAY DIFFRACTION96.51
2.65-2.820.25331500.221120665X-RAY DIFFRACTION96.61
2.82-3.040.2631530.229620840X-RAY DIFFRACTION96.89
3.04-3.340.2631130.204620860X-RAY DIFFRACTION97.17
3.34-3.830.19791650.183320756X-RAY DIFFRACTION97.12
3.83-4.820.16691390.156720738X-RAY DIFFRACTION96.77
4.82-44.230.18731980.172620580X-RAY DIFFRACTION96.14
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)
11.471997630620.2975311940920.07803335355030.7208849275070.06509804075321.52222506383-0.03097789757970.04202768251080.0149331928728-0.06437676426720.0143328637605-0.05928739369390.02188609731640.1499011619380.01738550801180.1345051620720.056046068370.001348545835780.3829818101180.01121246217160.1505604493693.73305345568138.756285829147.746929987
21.12326535393-0.005124554908020.202456925370.597551142174-0.1095526546341.888208877220.01727280693-0.2536233745080.01101364282550.110423853256-0.01969933273290.0579510426672-0.0393386812049-0.2381154630130.005755381895340.1712922195930.0166251044372-0.008684360752960.5185168677090.002972408899570.176690337334-12.7130499751136.426445909178.056930038
31.759836228430.03339871099390.1511963565510.5055025772670.1223043350842.11722244868-0.0123587024393-0.08503221939730.0343682480431-0.0442808630917-0.0187236770194-0.0576969463648-0.02953181226390.09375984641810.02257269520.1401993051810.00418714686450.03409768860640.292744650991-0.01062427159390.1890837762217.2050189899592.3287975159144.336015308
40.9251251863150.1270200473760.3864521280210.5252905448080.1367524216242.01808232194-0.00334853047262-0.1893152278650.02291385224190.116148599039-0.05827158079230.06398770736840.0463520693175-0.1447458858170.05059445150060.173370746314-0.008523986622250.03404253559520.4827505368870.007695462387520.203769144558-9.1225489988791.3217288509174.948888428
51.418100356670.0712478476376-0.16276536350.4884514702150.1185243234172.25761792934-0.0139824214253-0.08643816796470.0485824244183-0.0682536029409-0.014743499377-0.0221953025754-0.09674451815710.1259304980760.01195850705310.1787527111220.02737254893280.02128162546120.421176407870.01330544546030.1338908819825.9851652025146.8714711233146.063523574
61.28769099435-0.02044781780030.2428164033860.412170710159-0.03443840477051.987871601070.00871792222455-0.1693558349880.04668712625520.0853143775693-0.03156920868590.03898626069820.0384284484769-0.1135496013730.01402754042880.2056314514180.007574144229230.01866826437540.5692087263660.007066736131070.140156415447-10.237492150245.2904059669176.403277099
71.007010285470.076796922685-0.2054668222760.40764237103-0.1441137240122.10201444231-0.01265207288530.118664230479-0.0282563388623-0.1020140568360.0006793460096080.0301443106104-0.0380272939856-0.09710929184130.01317212849450.2022177782340.0816970378886-0.008914222766110.5719224858860.002208402320940.13580917259316.3934660261174.63837864275.9984467916
81.50099018078-0.04898457810330.02883864389690.50933552530.1456435934922.052134036190.01798602066510.0459395661601-0.08888878068360.0612863212546-0.0147277695366-0.02272080148120.1155064800610.191609085991-0.008444210129250.1842834010620.0485396525828-0.01286551667490.4313993830290.01328528564550.13112376113832.5232554268172.988923182106.526995107
91.36915192132-0.0314756002268-0.3590061726040.38794711025-0.009302715796491.817591115010.005635676439380.181798480642-0.0640253552178-0.087472842007-0.01621267092550.0383006878856-0.00583619077199-0.118693028420.02480491972640.1668889892360.0358899855468-0.0301126735420.525922283329-0.00687800119280.1950670824917.1958215109128.61736484877.9694698828
101.84022343922-0.0100949070576-0.2652379598620.5563392657410.1653943905411.84493963758-0.009999343536150.0550080742378-0.06716550739940.0760838317096-0.0118368794846-0.0491320350663-0.00957410718430.1401576715280.01465697809660.1614866257690.0140589719703-0.03090015086960.3912449386510.003963109383310.17333303515633.7458518862127.600496565108.232107684
111.31556933728-0.05867662398-0.2707456802230.667922120752-0.07343784092292.013058668990.01122133425340.2662017980370.0213063064831-0.120785480317-0.04625077949050.050777336049-0.0306876497277-0.2878295197260.01369979598310.1795147598520.002985688219590.01315354123870.4619913099840.01534637015240.19517990696221.193687893883.620397778574.550153158
121.62348426532-0.213239946329-0.06974770636930.8423189523790.06035665109611.50768396114-0.0362104287805-0.1144648718360.005802248511870.044623233922-0.00392881938855-0.03325562008740.001005393607060.1228939372640.02677160655870.140957984415-0.025194075913-0.0006277993366050.389877245763-0.002974078949250.1616022899937.40202780581.1155255529104.910363699
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 93 through 501)
2X-RAY DIFFRACTION2(chain 'B' and resid 93 through 418)
3X-RAY DIFFRACTION3(chain 'C' and resid 93 through 418)
4X-RAY DIFFRACTION4(chain 'D' and resid 94 through 501)
5X-RAY DIFFRACTION5(chain 'E' and resid 93 through 418)
6X-RAY DIFFRACTION6(chain 'F' and resid 93 through 418)
7X-RAY DIFFRACTION7(chain 'G' and resid 93 through 418)
8X-RAY DIFFRACTION8(chain 'H' and resid 93 through 418)
9X-RAY DIFFRACTION9(chain 'I' and resid 93 through 418)
10X-RAY DIFFRACTION10(chain 'J' and resid 93 through 501)
11X-RAY DIFFRACTION11(chain 'K' and resid 93 through 418)
12X-RAY DIFFRACTION12(chain 'L' and resid 93 through 501)

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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