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- PDB-6j55: Crystal structure of an iron superoxide dismutate (FeSOD) from a ... -

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基本情報

登録情報
データベース: PDB / ID: 6j55
タイトルCrystal structure of an iron superoxide dismutate (FeSOD) from a pathogenic Acanthamoeba castellanii
要素Superoxide dismutase
キーワードOXIDOREDUCTASE / iron superoxide dismutase / Acanthamoeba castellanii
機能・相同性
機能・相同性情報


superoxide dismutase / superoxide dismutase activity / metal ion binding
類似検索 - 分子機能
Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain
類似検索 - ドメイン・相同性
: / Superoxide dismutase
類似検索 - 構成要素
生物種Acanthamoeba castellanii (カステラーニアメーバ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.33000486301 Å
データ登録者Lee, K.H. / Dao, T.O. / Asaithambi, K. / Na, B.K.
資金援助 韓国, 2件
組織認可番号国
National Research Foundation (Korea)NRF-2015R1D1A1A01060694 韓国
National Research Foundation (Korea)NRF-2016M3D3A1A01913246 韓国
引用ジャーナル: Acta Crystallogr.,Sect.F / 年: 2019
タイトル: Crystal structure of an iron superoxide dismutase from the pathogenic amoeba Acanthamoeba castellanii.
著者: Dao, O. / Asaithambi, K. / Na, B.K. / Lee, K.H.
履歴
登録2019年1月10日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02019年7月17日Provider: repository / タイプ: Initial release
改定 1.12019年11月20日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
改定 1.22023年11月22日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_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 1.32024年3月20日Group: Source and taxonomy / カテゴリ: entity_src_gen

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


分子量 (理論値)分子数
合計 (水以外)284,11624
ポリマ－283,44612
非ポリマー67012
水15,889882
1
A: Superoxide dismutase
B: Superoxide dismutase
E: Superoxide dismutase
H: Superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,7058
ポリマ－94,4824
非ポリマー2234
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-59 kcal/mol
Surface area31950 Å2
手法PISA
2
C: Superoxide dismutase
D: Superoxide dismutase
F: Superoxide dismutase
G: Superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,7058
ポリマ－94,4824
非ポリマー2234
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-56 kcal/mol
Surface area32170 Å2
手法PISA
3
I: Superoxide dismutase
J: Superoxide dismutase
K: Superoxide dismutase
L: Superoxide dismutase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)94,7058
ポリマ－94,4824
非ポリマー2234
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-58 kcal/mol
Surface area32230 Å2
手法PISA
単位格子
Length a, b, c (Å)127.486, 127.486, 327.064
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
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
11PHEPHELEULEU(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA3 - 1111 - 19
12THRTHRSERSER(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA13 - 2021 - 28
13THRTHRASNASN(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA23 - 3731 - 45
14THRTHRVALVAL(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA39 - 4347 - 51
15GLYGLYGLUGLU(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA45 - 4953 - 57
16LYSLYSTHRTHR(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA51 - 8859 - 96
17GLNGLNTHRTHR(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA90 - 9198 - 99
18ILEILEPROPRO(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA94 - 96102 - 104
19LEULEUILEILE(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA98 - 102106 - 110
110GLUGLULYSLYS(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA104 - 113112 - 121
111PHEPHELEULEU(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA116 - 152124 - 160
112VALVALLEULEU(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA154 - 179162 - 187
113TRPTRPTRPTRP(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA182 - 188190 - 196
114PHEPHEASPASP(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA190 - 192198 - 200
115GLNGLNLEULEU(chain A and (resseq 3:11 or resseq 13:21 or resseq...AA194 - 195202 - 203
21PHEPHELEULEU(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB3 - 1111 - 19
22THRTHRSERSER(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB13 - 2021 - 28
23THRTHRASNASN(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB23 - 3731 - 45
24THRTHRVALVAL(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB39 - 4347 - 51
25GLYGLYGLUGLU(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB45 - 4953 - 57
26LYSLYSTHRTHR(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB51 - 8859 - 96
27GLNGLNTHRTHR(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB90 - 9198 - 99
28ILEILEPROPRO(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB94 - 96102 - 104
29LEULEUILEILE(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB98 - 102106 - 110
210GLUGLULYSLYS(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB104 - 113112 - 121
211PHEPHELEULEU(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB116 - 152124 - 160
212VALVALLEULEU(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB154 - 179162 - 187
213TRPTRPTRPTRP(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB182 - 188190 - 196
214PHEPHEASPASP(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB190 - 192198 - 200
215GLNGLNLEULEU(chain B and (resseq 3:11 or resseq 13:21 or resseq...BB194 - 195202 - 203
31PHEPHELEULEU(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC3 - 1111 - 19
32THRTHRSERSER(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC13 - 2021 - 28
33THRTHRASNASN(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC23 - 3731 - 45
34THRTHRVALVAL(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC39 - 4347 - 51
35GLYGLYGLUGLU(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC45 - 4953 - 57
36LYSLYSTHRTHR(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC51 - 8859 - 96
37GLNGLNTHRTHR(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC90 - 9198 - 99
38ILEILEPROPRO(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC94 - 96102 - 104
39LEULEUILEILE(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC98 - 102106 - 110
310GLUGLULYSLYS(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC104 - 113112 - 121
311PHEPHELEULEU(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC116 - 152124 - 160
312VALVALLEULEU(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC154 - 179162 - 187
313TRPTRPTRPTRP(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC182 - 188190 - 196
314PHEPHEASPASP(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC190 - 192198 - 200
315GLNGLNLEULEU(chain C and (resseq 3:11 or resseq 13:21 or resseq...CC194 - 195202 - 203
41PHEPHELEULEU(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD3 - 1111 - 19
42THRTHRSERSER(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD13 - 2021 - 28
43THRTHRASNASN(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD23 - 3731 - 45
44THRTHRVALVAL(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD39 - 4347 - 51
45GLYGLYGLUGLU(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD45 - 4953 - 57
46LYSLYSTHRTHR(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD51 - 8859 - 96
47GLNGLNTHRTHR(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD90 - 9198 - 99
48ILEILEPROPRO(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD94 - 96102 - 104
49LEULEUILEILE(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD98 - 102106 - 110
410GLUGLULYSLYS(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD104 - 113112 - 121
411PHEPHELEULEU(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD116 - 152124 - 160
412VALVALLEULEU(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD154 - 179162 - 187
413TRPTRPTRPTRP(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD182 - 188190 - 196
414PHEPHEASPASP(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD190 - 192198 - 200
415GLNGLNLEULEU(chain D and (resseq 3:11 or resseq 13:21 or resseq...DD194 - 195202 - 203
51PHEPHELEULEU(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE3 - 1111 - 19
52THRTHRSERSER(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE13 - 2021 - 28
53THRTHRASNASN(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE23 - 3731 - 45
54THRTHRVALVAL(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE39 - 4347 - 51
55GLYGLYGLUGLU(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE45 - 4953 - 57
56LYSLYSTHRTHR(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE51 - 8859 - 96
57GLNGLNTHRTHR(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE90 - 9198 - 99
58ILEILEPROPRO(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE94 - 96102 - 104
59LEULEUILEILE(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE98 - 102106 - 110
510GLUGLULYSLYS(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE104 - 113112 - 121
511PHEPHELEULEU(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE116 - 152124 - 160
512VALVALLEULEU(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE154 - 179162 - 187
513TRPTRPTRPTRP(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE182 - 188190 - 196
514PHEPHEASPASP(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE190 - 192198 - 200
515GLNGLNLEULEU(chain E and (resseq 3:11 or resseq 13:21 or resseq...EE194 - 195202 - 203
61PHEPHELEULEU(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF3 - 1111 - 19
62THRTHRSERSER(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF13 - 2021 - 28
63THRTHRASNASN(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF23 - 3731 - 45
64THRTHRVALVAL(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF39 - 4347 - 51
65GLYGLYGLUGLU(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF45 - 4953 - 57
66LYSLYSTHRTHR(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF51 - 8859 - 96
67GLNGLNTHRTHR(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF90 - 9198 - 99
68ILEILEPROPRO(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF94 - 96102 - 104
69LEULEUILEILE(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF98 - 102106 - 110
610GLUGLULYSLYS(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF104 - 113112 - 121
611PHEPHELEULEU(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF116 - 152124 - 160
612VALVALLEULEU(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF154 - 179162 - 187
613TRPTRPTRPTRP(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF182 - 188190 - 196
614PHEPHEASPASP(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF190 - 192198 - 200
615GLNGLNLEULEU(chain F and (resseq 3:11 or resseq 13:21 or resseq...FF194 - 195202 - 203
71PHEPHELEULEU(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG3 - 1111 - 19
72THRTHRSERSER(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG13 - 2021 - 28
73THRTHRASNASN(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG23 - 3731 - 45
74THRTHRVALVAL(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG39 - 4347 - 51
75GLYGLYGLUGLU(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG45 - 4953 - 57
76LYSLYSTHRTHR(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG51 - 8859 - 96
77GLNGLNTHRTHR(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG90 - 9198 - 99
78ILEILEPROPRO(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG94 - 96102 - 104
79LEULEUILEILE(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG98 - 102106 - 110
710GLUGLULYSLYS(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG104 - 113112 - 121
711PHEPHELEULEU(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG116 - 152124 - 160
712VALVALLEULEU(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG154 - 179162 - 187
713TRPTRPTRPTRP(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG182 - 188190 - 196
714PHEPHEASPASP(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG190 - 192198 - 200
715GLNGLNLEULEU(chain G and (resseq 3:11 or resseq 13:21 or resseq...GG194 - 195202 - 203
81PHEPHELEULEU(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH3 - 1111 - 19
82THRTHRSERSER(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH13 - 2021 - 28
83THRTHRASNASN(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH23 - 3731 - 45
84THRTHRVALVAL(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH39 - 4347 - 51
85GLYGLYGLUGLU(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH45 - 4953 - 57
86LYSLYSTHRTHR(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH51 - 8859 - 96
87GLNGLNTHRTHR(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH90 - 9198 - 99
88ILEILEPROPRO(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH94 - 96102 - 104
89LEULEUILEILE(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH98 - 102106 - 110
810GLUGLULYSLYS(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH104 - 113112 - 121
811PHEPHELEULEU(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH116 - 152124 - 160
812VALVALLEULEU(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH154 - 179162 - 187
813TRPTRPTRPTRP(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH182 - 188190 - 196
814PHEPHEASPASP(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH190 - 192198 - 200
815GLNGLNLEULEU(chain H and (resseq 3:11 or resseq 13:21 or resseq...HH194 - 195202 - 203
91PHEPHELEULEU(chain I and (resseq 3:11 or resseq 13:21 or resseq...II3 - 1111 - 19
92THRTHRSERSER(chain I and (resseq 3:11 or resseq 13:21 or resseq...II13 - 2021 - 28
93THRTHRASNASN(chain I and (resseq 3:11 or resseq 13:21 or resseq...II23 - 3731 - 45
94THRTHRVALVAL(chain I and (resseq 3:11 or resseq 13:21 or resseq...II39 - 4347 - 51
95GLYGLYGLUGLU(chain I and (resseq 3:11 or resseq 13:21 or resseq...II45 - 4953 - 57
96LYSLYSTHRTHR(chain I and (resseq 3:11 or resseq 13:21 or resseq...II51 - 8859 - 96
97GLNGLNTHRTHR(chain I and (resseq 3:11 or resseq 13:21 or resseq...II90 - 9198 - 99
98ILEILEPROPRO(chain I and (resseq 3:11 or resseq 13:21 or resseq...II94 - 96102 - 104
99LEULEUILEILE(chain I and (resseq 3:11 or resseq 13:21 or resseq...II98 - 102106 - 110
910GLUGLULYSLYS(chain I and (resseq 3:11 or resseq 13:21 or resseq...II104 - 113112 - 121
911PHEPHELEULEU(chain I and (resseq 3:11 or resseq 13:21 or resseq...II116 - 152124 - 160
912VALVALLEULEU(chain I and (resseq 3:11 or resseq 13:21 or resseq...II154 - 179162 - 187
913TRPTRPTRPTRP(chain I and (resseq 3:11 or resseq 13:21 or resseq...II182 - 188190 - 196
914PHEPHEASPASP(chain I and (resseq 3:11 or resseq 13:21 or resseq...II190 - 192198 - 200
915GLNGLNLEULEU(chain I and (resseq 3:11 or resseq 13:21 or resseq...II194 - 195202 - 203
101PHEPHELEULEU(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ3 - 1111 - 19
102THRTHRSERSER(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ13 - 2021 - 28
103THRTHRASNASN(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ23 - 3731 - 45
104THRTHRVALVAL(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ39 - 4347 - 51
105GLYGLYGLUGLU(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ45 - 4953 - 57
106LYSLYSTHRTHR(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ51 - 8859 - 96
107GLNGLNTHRTHR(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ90 - 9198 - 99
108ILEILEPROPRO(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ94 - 96102 - 104
109LEULEUILEILE(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ98 - 102106 - 110
1010GLUGLULYSLYS(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ104 - 113112 - 121
1011PHEPHELEULEU(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ116 - 152124 - 160
1012VALVALLEULEU(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ154 - 179162 - 187
1013TRPTRPTRPTRP(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ182 - 188190 - 196
1014PHEPHEASPASP(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ190 - 192198 - 200
1015GLNGLNLEULEU(chain J and (resseq 3:11 or resseq 13:21 or resseq...JJ194 - 195202 - 203
111PHEPHELEULEU(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK3 - 1111 - 19
112THRTHRSERSER(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK13 - 2021 - 28
113THRTHRASNASN(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK23 - 3731 - 45
114THRTHRVALVAL(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK39 - 4347 - 51
115GLYGLYGLUGLU(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK45 - 4953 - 57
116LYSLYSTHRTHR(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK51 - 8859 - 96
117GLNGLNTHRTHR(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK90 - 9198 - 99
118ILEILEPROPRO(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK94 - 96102 - 104
119LEULEUILEILE(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK98 - 102106 - 110
1110GLUGLULYSLYS(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK104 - 113112 - 121
1111PHEPHELEULEU(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK116 - 152124 - 160
1112VALVALLEULEU(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK154 - 179162 - 187
1113TRPTRPTRPTRP(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK182 - 188190 - 196
1114PHEPHEASPASP(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK190 - 192198 - 200
1115GLNGLNLEULEU(chain K and (resseq 3:11 or resseq 13:21 or resseq...KK194 - 195202 - 203
121PHEPHELEULEU(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL3 - 1111 - 19
122THRTHRSERSER(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL13 - 2021 - 28
123THRTHRASNASN(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL23 - 3731 - 45
124THRTHRVALVAL(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL39 - 4347 - 51
125GLYGLYGLUGLU(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL45 - 4953 - 57
126LYSLYSTHRTHR(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL51 - 8859 - 96
127GLNGLNTHRTHR(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL90 - 9198 - 99
128ILEILEPROPRO(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL94 - 96102 - 104
129LEULEUILEILE(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL98 - 102106 - 110
1210GLUGLULYSLYS(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL104 - 113112 - 121
1211PHEPHELEULEU(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL116 - 152124 - 160
1212VALVALLEULEU(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL154 - 179162 - 187
1213TRPTRPTRPTRP(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL182 - 188190 - 196
1214PHEPHEASPASP(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL190 - 192198 - 200
1215GLNGLNLEULEU(chain L and (resseq 3:11 or resseq 13:21 or resseq...LL194 - 195202 - 203

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要素

#1: タンパク質
Superoxide dismutase


分子量: 23620.486 Da / 分子数: 12 / 由来タイプ: 組換発現
由来: (組換発現) Acanthamoeba castellanii (カステラーニアメーバ)
プラスミド: pQE30 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): M15[pREP4] / 参照: UniProt: Q5IZD9, superoxide dismutase
#2: 化合物
ChemComp-FE2 / FE (II) ION


分子量: 55.845 Da / 分子数: 12 / 由来タイプ: 組換発現 / 式: Fe
#3: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 882 / 由来タイプ: 天然 / 式: H2O

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.74 Å3/Da / 溶媒含有率: 55.1 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: 12% (w/v) polyethylene glycol 4000, 5% (w/v) 2-propanol and 100 mM HEPES pH 7.5 and 1 mM hexammine cobalt (III) chloride as an additive

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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: PAL/PLS / ビームライン: 7A (6B, 6C1) / 波長: 0.97933 Å
検出器タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2017年4月24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: 0.97933 Å / 相対比: 1
反射解像度: 2.33→50 Å / Num. obs: 128266 / % possible obs: 100 % / 冗長度: 29.6 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.019 / Rrim(I) all: 0.115 / Χ2: 1.028 / Net I/σ(I): 9.1
反射 シェル

Diffraction-ID: 1 / % possible all: 100

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.33-2.3721.20.67763620.9240.150.6931.373
2.37-2.4121.60.64364640.9410.1410.6581.414
2.41-2.4621.60.54663810.9520.120.5591.46
2.46-2.5121.60.51663910.9590.1140.5291.469
2.51-2.5621.60.48564090.9670.1060.4961.467
2.56-2.6221.60.44563780.9720.0980.4551.403
2.62-2.6921.60.37164080.9780.0810.381.362
2.69-2.7621.60.31564010.9830.0690.3231.258
2.76-2.8421.60.28564170.9860.0630.2921.229
2.84-2.9421.70.22363730.9910.0490.2281.164
2.94-3.0421.60.21364520.9910.0470.2181.449
3.04-3.1621.70.18163860.9940.040.1861.297
3.16-3.3123.80.15164030.9950.0310.1541.218
3.31-3.4843.10.14564070.9980.0220.1471.194
3.48-3.744.70.12764250.9980.0190.1291.024
3.7-3.9844.60.10464280.9990.0160.1050.677
3.98-4.3844.50.0964180.9990.0140.0910.762
4.38-5.0244.30.07964160.9990.0120.080.634
5.02-6.3244.10.07764470.9990.0120.0780.597
6.32-5043.40.06565000.9990.010.0650.311

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
HKL-2000データ削減
HKL-2000データスケーリング
MOLREP位相決定
PDB_EXTRACT3.24データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 1ISA

1isa


解像度: 2.33000486301→36.5712467012 Å / SU ML: 0.299197773496 / 交差検証法: FREE R-VALUE / σ(F): 1.35409012865 / 位相誤差: 23.9266752481
Rfactor反射数%反射Selection details
Rfree0.247818808138 6498 5.08896685671 %Random selection
Rwork0.199588225603 ---
obs0.202041589108 127688 99.9945181879 %-
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 mean: 43.0556487553 Å2
精密化ステップサイクル: LAST / 解像度: 2.33000486301→36.5712467012 Å
タンパク質核酸リガンド溶媒全体
原子数19394 0 12 882 20288
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0080250932991319942
X-RAY DIFFRACTIONf_angle_d0.96647499158427163
X-RAY DIFFRACTIONf_chiral_restr0.05743749619872983
X-RAY DIFFRACTIONf_plane_restr0.006887727709123444
X-RAY DIFFRACTIONf_dihedral_angle_d16.008385222411597
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.35650.3090920549922210.2416868546864076X-RAY DIFFRACTION100
2.3565-2.38420.2783739577922480.2247451092993962X-RAY DIFFRACTION100
2.3842-2.41330.2732218148752080.2275767854514056X-RAY DIFFRACTION100
2.4133-2.44380.2914243139832130.2193363323254027X-RAY DIFFRACTION100
2.4438-2.4760.2907352919442040.2167062232884026X-RAY DIFFRACTION99.9763649255
2.476-2.50990.2734930164632220.2219803506444062X-RAY DIFFRACTION100
2.5099-2.54570.2702510533591990.2201888289314049X-RAY DIFFRACTION100
2.5457-2.58370.2924506852522110.2192665168784005X-RAY DIFFRACTION100
2.5837-2.62410.2740071128321990.2168830500294057X-RAY DIFFRACTION100
2.6241-2.66710.2704983801452330.2192752119444038X-RAY DIFFRACTION100
2.6671-2.7130.310993462152020.2162660292684060X-RAY DIFFRACTION100
2.713-2.76240.2471194001842310.2153555064134022X-RAY DIFFRACTION100
2.7624-2.81550.2781754248492090.2190470533694026X-RAY DIFFRACTION100
2.8155-2.87290.288344863822230.2171944952744020X-RAY DIFFRACTION100
2.8729-2.93540.2387574078492260.2067211740074014X-RAY DIFFRACTION99.9764206555
2.9354-3.00360.278620058251960.2116903493854063X-RAY DIFFRACTION100
3.0036-3.07870.2670252747572180.2111256069444030X-RAY DIFFRACTION100
3.0787-3.16190.2266184612192500.2064054852084009X-RAY DIFFRACTION100
3.1619-3.25490.2634955679842020.2012982763824066X-RAY DIFFRACTION100
3.2549-3.35990.2580403817572120.1987252751494050X-RAY DIFFRACTION100
3.3599-3.47990.2521185087962340.2020334335314020X-RAY DIFFRACTION100
3.4799-3.61910.2638635519542290.2027144084224041X-RAY DIFFRACTION100
3.6191-3.78360.2184882312172070.1963292723614022X-RAY DIFFRACTION100
3.7836-3.98290.2516965572442170.1883304486954073X-RAY DIFFRACTION100
3.9829-4.23210.2269972359932150.1848557218364026X-RAY DIFFRACTION100
4.2321-4.55830.2147939994032390.1786675543964036X-RAY DIFFRACTION100
4.5583-5.0160.2191887495952300.180538651174005X-RAY DIFFRACTION100
5.016-5.73940.232348814761940.1875710971544080X-RAY DIFFRACTION100
5.7394-7.22190.2305326168971730.2021078391424099X-RAY DIFFRACTION100
7.2219-36.57570.2319438859762330.1850517239054070X-RAY DIFFRACTION99.8839368617

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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

+
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

+
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