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- PDB-4yuu: Crystal structure of oxygen-evolving photosystem II from a red alga -

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基本情報

登録情報
データベース: PDB / ID: 4yuu
タイトルCrystal structure of oxygen-evolving photosystem II from a red alga
要素
  • (Cytochrome b559 subunit ...) x 2
  • (PEPTIDE CHAIN ...) x 2
  • (PHOTOSYSTEM II REACTION CENTER PROTEIN ...) x 10
  • (Photosystem II ...) x 6
  • Cytochrome c-550
  • Extrinsic protein in photosystem II
キーワードPHOTOSYNTHESIS / TRANSMEMBRANE ALPHA-HELIX / ELECTRON TRANSPORT / PHOTOSYSTEM II / WATER-SPLITTING / OXYGEN-EVOLVING / IRON BINDING / CALCIUM BINDING / MANGANESE BINDING / CHLORIDE BINDING / THYLAKOID MEMBRANE
機能・相同性
機能・相同性情報


photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / extrinsic component of membrane / chlorophyll binding / photosynthetic electron transport in photosystem II ...photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / extrinsic component of membrane / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / : / photosynthesis / respiratory electron transport chain / electron transfer activity / oxidoreductase activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / metal ion binding
類似検索 - 分子機能
Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ ...Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
類似検索 - ドメイン・相同性
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Unknown ligand / Photosystem II reaction center protein I / Photosystem II protein D1 / Photosystem II reaction center protein H / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Extrinsic protein in photosystem II / Photosystem II extrinsic protein V / Photosystem II reaction center protein K / Photosystem II reaction center protein Psb30 / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein L / Photosystem II reaction center protein J / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II extrinsic protein U, chloroplastic
類似検索 - 構成要素
生物種Cyanidium caldarium (真核生物)
手法X線回折 / シンクロトロン / 解像度: 2.77000368116 Å
データ登録者Ago, H. / Shen, J.-R.
資金援助 日本, 1件
組織認可番号国
JSPS24000018 日本
引用
ジャーナル: J.Biol.Chem. / 年: 2016
タイトル: Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga
著者: Ago, H. / Adachi, H. / Umena, Y. / Tashiro, T. / Kawakami, K. / Kamiya, N. / Tian, L. / Han, G. / Kuang, T. / Liu, Z. / Wang, F. / Zou, H. / Enami, I. / Miyano, M. / Shen, J.-R.
#1: ジャーナル: Biochim. Biophys. Acta / 年: 2009
タイトル: Towards structural elucidation of eukaryotic photosystem II: Purification, crystallization and preliminary X-ray diffraction analysis of photosystem II from a red alga.
著者: Adachi, H. / Umena, Y. / Enami, I. / Henmi, T. / Kamiya, N. / Shen, J.-R.
履歴
登録2015年3月19日登録サイト: RCSB / 処理サイト: PDBJ
改定 1.02016年1月20日Provider: repository / タイプ: Initial release
改定 1.12016年2月3日Group: Database references
改定 1.22016年3月23日Group: Database references
改定 1.32020年2月5日Group: Data collection / Database references / Derived calculations
カテゴリ: atom_type / citation ...atom_type / citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
改定 2.02024年11月6日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer 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 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn_type.id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A1: Photosystem II protein D1
B1: Photosystem II CP47 reaction center protein
C1: Photosystem II CP43 reaction center protein
D1: Photosystem II D2 protein
E1: Cytochrome b559 subunit alpha
F1: Cytochrome b559 subunit beta
H1: Photosystem II reaction center protein H
I1: Photosystem II reaction center protein I
J1: Photosystem II reaction center protein J
K1: Photosystem II reaction center protein K
L1: Photosystem II reaction center protein L
M1: PHOTOSYSTEM II REACTION CENTER PROTEIN M
O1: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
T1: Photosystem II reaction center protein T
U1: Photosystem II 12 kDa extrinsic protein, chloroplastic
V1: Cytochrome c-550
Y1: Photosystem II reaction center protein Ycf12
X1: PHOTOSYSTEM II REACTION CENTER PROTEIN X
S1: PEPTIDE CHAIN UNASSIGNED
W1: PEPTIDE CHAIN UNASSIGNED
a1: Photosystem II protein D1
b1: Photosystem II CP47 reaction center protein
c1: Photosystem II CP43 reaction center protein
d1: Photosystem II D2 protein
e1: Cytochrome b559 subunit alpha
f1: Cytochrome b559 subunit beta
h1: Photosystem II reaction center protein H
i1: Photosystem II reaction center protein I
j1: Photosystem II reaction center protein J
k1: Photosystem II reaction center protein K
l1: Photosystem II reaction center protein L
m1: PHOTOSYSTEM II REACTION CENTER PROTEIN M
o1: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
t1: Photosystem II reaction center protein T
u1: Photosystem II 12 kDa extrinsic protein, chloroplastic
v1: Cytochrome c-550
y1: Photosystem II reaction center protein Ycf12
x1: PHOTOSYSTEM II REACTION CENTER PROTEIN X
s1: PEPTIDE CHAIN UNASSIGNED
w1: PEPTIDE CHAIN UNASSIGNED
q1: Extrinsic protein in photosystem II
A2: Photosystem II protein D1
B2: Photosystem II CP47 reaction center protein
C2: Photosystem II CP43 reaction center protein
D2: Photosystem II D2 protein
E2: Cytochrome b559 subunit alpha
F2: Cytochrome b559 subunit beta
H2: Photosystem II reaction center protein H
I2: Photosystem II reaction center protein I
J2: Photosystem II reaction center protein J
K2: Photosystem II reaction center protein K
L2: Photosystem II reaction center protein L
M2: PHOTOSYSTEM II REACTION CENTER PROTEIN M
O2: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
T2: Photosystem II reaction center protein T
U2: Photosystem II 12 kDa extrinsic protein, chloroplastic
V2: Cytochrome c-550
Y2: Photosystem II reaction center protein Ycf12
X2: PHOTOSYSTEM II REACTION CENTER PROTEIN X
S2: PEPTIDE CHAIN UNASSIGNED
W2: PEPTIDE CHAIN UNASSIGNED
Q2: Extrinsic protein in photosystem II
Z2: Photosystem II reaction center protein Z
a2: Photosystem II protein D1
b2: Photosystem II CP47 reaction center protein
c2: Photosystem II CP43 reaction center protein
d2: Photosystem II D2 protein
e2: Cytochrome b559 subunit alpha
f2: Cytochrome b559 subunit beta
h2: Photosystem II reaction center protein H
i2: Photosystem II reaction center protein I
j2: Photosystem II reaction center protein J
k2: Photosystem II reaction center protein K
l2: Photosystem II reaction center protein L
m2: PHOTOSYSTEM II REACTION CENTER PROTEIN M
o2: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
t2: Photosystem II reaction center protein T
u2: Photosystem II 12 kDa extrinsic protein, chloroplastic
v2: Cytochrome c-550
y2: Photosystem II reaction center protein Ycf12
x2: PHOTOSYSTEM II REACTION CENTER PROTEIN X
s2: PEPTIDE CHAIN UNASSIGNED
w2: PEPTIDE CHAIN UNASSIGNED
z2: Photosystem II reaction center protein Z
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,579,524437
ポリマ－1,359,22484
非ポリマー220,300353
水32418
1
A1: Photosystem II protein D1
B1: Photosystem II CP47 reaction center protein
C1: Photosystem II CP43 reaction center protein
D1: Photosystem II D2 protein
E1: Cytochrome b559 subunit alpha
F1: Cytochrome b559 subunit beta
H1: Photosystem II reaction center protein H
I1: Photosystem II reaction center protein I
J1: Photosystem II reaction center protein J
K1: Photosystem II reaction center protein K
L1: Photosystem II reaction center protein L
M1: PHOTOSYSTEM II REACTION CENTER PROTEIN M
O1: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
T1: Photosystem II reaction center protein T
U1: Photosystem II 12 kDa extrinsic protein, chloroplastic
V1: Cytochrome c-550
Y1: Photosystem II reaction center protein Ycf12
X1: PHOTOSYSTEM II REACTION CENTER PROTEIN X
S1: PEPTIDE CHAIN UNASSIGNED
W1: PEPTIDE CHAIN UNASSIGNED
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)381,162103
ポリマ－324,53220
非ポリマー56,62983
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
a1: Photosystem II protein D1
b1: Photosystem II CP47 reaction center protein
c1: Photosystem II CP43 reaction center protein
d1: Photosystem II D2 protein
e1: Cytochrome b559 subunit alpha
f1: Cytochrome b559 subunit beta
h1: Photosystem II reaction center protein H
i1: Photosystem II reaction center protein I
j1: Photosystem II reaction center protein J
k1: Photosystem II reaction center protein K
l1: Photosystem II reaction center protein L
m1: PHOTOSYSTEM II REACTION CENTER PROTEIN M
o1: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
t1: Photosystem II reaction center protein T
u1: Photosystem II 12 kDa extrinsic protein, chloroplastic
v1: Cytochrome c-550
y1: Photosystem II reaction center protein Ycf12
x1: PHOTOSYSTEM II REACTION CENTER PROTEIN X
s1: PEPTIDE CHAIN UNASSIGNED
w1: PEPTIDE CHAIN UNASSIGNED
q1: Extrinsic protein in photosystem II
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)403,739112
ポリマ－348,59621
非ポリマー55,14391
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
A2: Photosystem II protein D1
B2: Photosystem II CP47 reaction center protein
C2: Photosystem II CP43 reaction center protein
D2: Photosystem II D2 protein
E2: Cytochrome b559 subunit alpha
F2: Cytochrome b559 subunit beta
H2: Photosystem II reaction center protein H
I2: Photosystem II reaction center protein I
J2: Photosystem II reaction center protein J
K2: Photosystem II reaction center protein K
L2: Photosystem II reaction center protein L
M2: PHOTOSYSTEM II REACTION CENTER PROTEIN M
O2: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
T2: Photosystem II reaction center protein T
U2: Photosystem II 12 kDa extrinsic protein, chloroplastic
V2: Cytochrome c-550
Y2: Photosystem II reaction center protein Ycf12
X2: PHOTOSYSTEM II REACTION CENTER PROTEIN X
S2: PEPTIDE CHAIN UNASSIGNED
W2: PEPTIDE CHAIN UNASSIGNED
Q2: Extrinsic protein in photosystem II
Z2: Photosystem II reaction center protein Z
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)407,319108
ポリマ－355,08022
非ポリマー52,23986
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
a2: Photosystem II protein D1
b2: Photosystem II CP47 reaction center protein
c2: Photosystem II CP43 reaction center protein
d2: Photosystem II D2 protein
e2: Cytochrome b559 subunit alpha
f2: Cytochrome b559 subunit beta
h2: Photosystem II reaction center protein H
i2: Photosystem II reaction center protein I
j2: Photosystem II reaction center protein J
k2: Photosystem II reaction center protein K
l2: Photosystem II reaction center protein L
m2: PHOTOSYSTEM II REACTION CENTER PROTEIN M
o2: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
t2: Photosystem II reaction center protein T
u2: Photosystem II 12 kDa extrinsic protein, chloroplastic
v2: Cytochrome c-550
y2: Photosystem II reaction center protein Ycf12
x2: PHOTOSYSTEM II REACTION CENTER PROTEIN X
s2: PEPTIDE CHAIN UNASSIGNED
w2: PEPTIDE CHAIN UNASSIGNED
z2: Photosystem II reaction center protein Z
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)387,305114
ポリマ－331,01621
非ポリマー56,28893
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)210.445, 240.31, 300.063
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A1 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
21chain A2 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
31chain a1 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
41chain a2 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
12chain B1 and (resseq 2:481)
22chain B2 and (resseq 2:481)
32chain b1 and (resseq 2:481)
42chain b2 and (resseq 2:481)
13chain C1 and (resseq 26:146 or resseq 155:472)
23chain C2 and (resseq 26:146 or resseq 155:472)
33chain c1 and (resseq 26:146 or resseq 155:472)
43chain c2 and (resseq 26:146 or resseq 155:472)
14chain D1 and (resseq 14:235 or resseq 239:352)
24chain D2 and (resseq 14:235 or resseq 239:352)
34chain d1 and (resseq 14:235 or resseq 239:352)
44chain d2 and (resseq 14:235 or resseq 239:352)
15chain E1 and (resseq 23:78 )
25chain E2 and (resseq 23:78)
35chain e1 and (resseq 23:78 )
45chain e2 and (resseq 23:78)
16chain F1 and (resseq 18:44 )
26chain F2 and (resseq 18:44)
36chain f1 and (resseq 18:44 )
46chain f2 and (resseq 18:44)
17chain H1 and (resseq 2:55 or resseq 58:63)
27chain H2 and (resseq 2:55 or resseq 58:63)
37chain h1 and (resseq 2:55 or resseq 58:63)
47chain h2 and (resseq 2:55 or resseq 58:63)
18chain I1 and (resseq 1:32)
28chain I2 and (resseq 1:32)
38chain i1 and (resseq 1:32)
48chain i2 and (resseq 1:32)
19chain J1 and (resseq 9:39)
29chain J2 and (resseq 9:39)
39chain j1 and (resseq 9:39)
49chain j2 and (resseq 9:39)
110chain K1 and (resseq 10:44)
210chain K2 and (resseq 10:44)
310chain k1 and (resseq 10:44)
410chain k2 and (resseq 10:44)
111chain L1 and (resseq 2:38)
211chain L2 and (resseq 2:38)
311chain l1 and (resseq 2:38)
411chain l2 and (resseq 2:38)
112chain M1 and (resseq 1:40 )
212chain M2 and (resseq 1:40)
312chain m1 and (resseq 1:40 )
412chain m2 and (resseq 1:40)
113chain O1 and (resseq -2:22 or resseq 39:54 or resseq...
213chain O2 and (resseq -2:22 or resseq 39:54 or resseq...
313chain o1 and (resseq -2:22 or resseq 39:54 or resseq...
413chain o2 and (resseq -2:22 or resseq 39:54 or resseq...
114chain T1 and (resseq 1:29)
214chain T2 and (resseq 1:29)
314chain t1 and (resseq 1:29)
414chain t2 and (resseq 1:29)
115chain U1 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
215chain U2 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
315chain u1 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
415chain u2 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
116chain V1 and (resseq 9:137)
216chain V2 and (resseq 9:137)
316chain v1 and (resseq 9:137)
416chain v2 and (resseq 9:137)
117chain Y1 and (resseq 16:40)
217chain Y2 and (resseq 16:40)
317chain y1 and (resseq 16:40)
417chain y2 and (resseq 16:40)
118chain X1 and (resseq 5:31)
218chain X2 and (resseq 5:31)
318chain x1 and (resseq 5:31)
418chain x2 and (resseq 5:31)
119chain S1 and (resseq 8:31)
219chain S2 and (resseq 8:31)
319chain s1 and (resseq 8:31)
419chain s2 and (resseq 8:31)
120chain W1 and (resseq 4:21)
220chain W2 and (resseq 4:21)
320chain w1 and (resseq 4:21)
420chain w2 and (resseq 4:21)
121chain q1 and (resseq 109:217)
221chain Q2 and (resseq 109:217 )
122chain Z2 and (resseq 2:58)
222chain z2 and (resseq 2:58)

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection details
111chain A1 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
211chain A2 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
311chain a1 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
411chain a2 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
112chain B1 and (resseq 2:481)
212chain B2 and (resseq 2:481)
312chain b1 and (resseq 2:481)
412chain b2 and (resseq 2:481)
113chain C1 and (resseq 26:146 or resseq 155:472)
213chain C2 and (resseq 26:146 or resseq 155:472)
313chain c1 and (resseq 26:146 or resseq 155:472)
413chain c2 and (resseq 26:146 or resseq 155:472)
114chain D1 and (resseq 14:235 or resseq 239:352)
214chain D2 and (resseq 14:235 or resseq 239:352)
314chain d1 and (resseq 14:235 or resseq 239:352)
414chain d2 and (resseq 14:235 or resseq 239:352)
115chain E1 and (resseq 23:78 )
215chain E2 and (resseq 23:78)
315chain e1 and (resseq 23:78 )
415chain e2 and (resseq 23:78)
116chain F1 and (resseq 18:44 )
216chain F2 and (resseq 18:44)
316chain f1 and (resseq 18:44 )
416chain f2 and (resseq 18:44)
117chain H1 and (resseq 2:55 or resseq 58:63)
217chain H2 and (resseq 2:55 or resseq 58:63)
317chain h1 and (resseq 2:55 or resseq 58:63)
417chain h2 and (resseq 2:55 or resseq 58:63)
118chain I1 and (resseq 1:32)
218chain I2 and (resseq 1:32)
318chain i1 and (resseq 1:32)
418chain i2 and (resseq 1:32)
119chain J1 and (resseq 9:39)
219chain J2 and (resseq 9:39)
319chain j1 and (resseq 9:39)
419chain j2 and (resseq 9:39)
1110chain K1 and (resseq 10:44)
2110chain K2 and (resseq 10:44)
3110chain k1 and (resseq 10:44)
4110chain k2 and (resseq 10:44)
1111chain L1 and (resseq 2:38)
2111chain L2 and (resseq 2:38)
3111chain l1 and (resseq 2:38)
4111chain l2 and (resseq 2:38)
1112chain M1 and (resseq 1:40 )
2112chain M2 and (resseq 1:40)
3112chain m1 and (resseq 1:40 )
4112chain m2 and (resseq 1:40)
1113chain O1 and (resseq -2:22 or resseq 39:54 or resseq...
2113chain O2 and (resseq -2:22 or resseq 39:54 or resseq...
3113chain o1 and (resseq -2:22 or resseq 39:54 or resseq...
4113chain o2 and (resseq -2:22 or resseq 39:54 or resseq...
1114chain T1 and (resseq 1:29)
2114chain T2 and (resseq 1:29)
3114chain t1 and (resseq 1:29)
4114chain t2 and (resseq 1:29)
1115chain U1 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
2115chain U2 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
3115chain u1 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
4115chain u2 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
1116chain V1 and (resseq 9:137)
2116chain V2 and (resseq 9:137)
3116chain v1 and (resseq 9:137)
4116chain v2 and (resseq 9:137)
1117chain Y1 and (resseq 16:40)
2117chain Y2 and (resseq 16:40)
3117chain y1 and (resseq 16:40)
4117chain y2 and (resseq 16:40)
1118chain X1 and (resseq 5:31)
2118chain X2 and (resseq 5:31)
3118chain x1 and (resseq 5:31)
4118chain x2 and (resseq 5:31)
1119chain S1 and (resseq 8:31)
2119chain S2 and (resseq 8:31)
3119chain s1 and (resseq 8:31)
4119chain s2 and (resseq 8:31)
1120chain W1 and (resseq 4:21)
2120chain W2 and (resseq 4:21)
3120chain w1 and (resseq 4:21)
4120chain w2 and (resseq 4:21)
1121chain q1 and (resseq 109:217)
2121chain Q2 and (resseq 109:217 )
1122chain Z2 and (resseq 2:58)
2122chain z2 and (resseq 2:58)

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22

NCS oper:
IDCodeMatrixベクター
1given(-0.994688217729, -0.101094938656, -0.0193691220559), (-0.0866947037877, 0.924242778818, -0.371832373708), (0.0554921422026, -0.368178080799, -0.928097798173)433.120859872, 47.0809240207, 135.025280081
2given(-0.0861082173904, -0.144006686415, -0.985823234239), (-0.148360252587, -0.976612344918, 0.155619931908), (-0.985177451199, 0.159657138965, 0.0627294797315)297.039492026, 285.997598022, 233.44479834
3given(0.0462949424116, 0.214399564113, 0.97564829996), (0.242276162477, -0.949943576186, 0.197254817832), (0.969102182127, 0.22724442561, -0.0959214867839)122.244648675, 197.87423474, -177.849810215
4given(-0.99511539619, -0.0960614193251, -0.0227497688494), (-0.0811593959149, 0.927289004356, -0.365442546585), (0.0562005402124, -0.361811147033, -0.930555851716)432.495343171, 45.3075450849, 134.186589846
5given(-0.0888791646716, -0.147684105777, -0.985032943098), (-0.148228629518, -0.97597338248, 0.159700438577), (-0.984951149793, 0.160204124764, 0.0648526863757)297.862583106, 285.625213502, 233.188675125
6given(0.045584286663, 0.216906868873, 0.975127418877), (0.24733465169, -0.948199958182, 0.199354983326), (0.967857243029, 0.232095345794, -0.0968716035696)122.187176474, 196.225389507, -178.189790032
7given(-0.994875114783, -0.0993255838258, -0.018919153888), (-0.0852498218619, 0.924605162241, -0.371265082966), (0.0543688684698, -0.367749537532, -0.928334155241)433.030837872, 46.9130273562, 135.259178975
8given(-0.0817664181085, -0.142766251961, -0.986373179973), (-0.145738949628, -0.977336076679, 0.153539414431), (-0.985938340583, 0.156307359147, 0.0591066666752)296.202587607, 285.874408822, 234.306620338
9given(0.0464773443275, 0.214611694311, 0.975592987433), (0.239868898215, -0.950470557124, 0.197657865284), (0.969692099655, 0.224827802338, -0.0956540180152)122.118997349, 198.648341474, -177.617850767
10given(-0.994994824437, -0.0978284927247, -0.0203687347392), (-0.0834360691764, 0.925521998083, -0.369387944342), (0.0549883779, -0.365839605669, -0.929052022881)432.798429673, 46.139573157, 134.910835703
11given(-0.0877814784142, -0.148367745888, -0.985028641222), (-0.147165050057, -0.976063600916, 0.160132117357), (-0.985209043853, 0.159018423296, 0.0638457591642)297.874736427, 285.415512164, 233.481810323
12given(0.0461342899598, 0.21279757064, 0.976006568226), (0.241248555903, -0.950499161352, 0.195832782097), (0.969366164855, 0.226425568783, -0.0951877105329)122.520826276, 198.256492365, -177.86500981
13given(-0.993681686101, -0.112233964083, -0.00049397814865), (-0.104658516429, 0.928182955191, -0.3571036217), (0.0405376571497, -0.354795629904, -0.934064644098)434.969452945, 50.6076417004, 136.310811595
14given(-0.102256877186, -0.165513387095, -0.980891864458), (-0.15822989713, -0.970800238959, 0.180305839318), (-0.982093086587, 0.173643930876, 0.0730818345933)301.68807023, 284.856006245, 230.838305638
15given(0.0421528222667, 0.20891687859, 0.977024501952), (0.250522432498, -0.94886313853, 0.19208658244), (0.967192664566, 0.23666956327, -0.0923356238483)124.048082421, 195.441331685, -178.650382784
16given(-0.991360751479, -0.130609618425, 0.0120410964108), (-0.124861245463, 0.911627605193, -0.391592618458), (0.0401687665898, -0.389713018803, -0.920059907379)436.722037925, 55.4545239229, 140.884214806
17given(-0.108002962146, -0.186115690701, -0.976573760575), (-0.165566197286, -0.96523398559, 0.202265141281), (-0.980266899617, 0.183532838305, 0.0734336624435)304.990091218, 284.467860872, 229.27244508
18given(0.0411398303761, 0.209516604269, 0.976939254454), (0.249195632692, -0.949020010334, 0.193035117618), (0.967578963705, 0.235507563619, -0.0912531450089)124.248869462, 195.948436818, -178.699766945
19given(-0.994791522452, -0.098850470402, -0.0248678780692), (-0.0831338961891, 0.927995980253, -0.363197213561), (0.0589795062949, -0.359238145435, -0.931380358769)432.902663296, 45.5133040734, 133.102652489
20given(-0.0900195954688, -0.148778699132, -0.984764627267), (-0.147272410351, -0.975920292574, 0.16090500207), (-0.984991020051, 0.159513263481, 0.0659409523174)298.163301597, 285.256515643, 233.256195273
21given(0.0443246621877, 0.213692675301, 0.975894853375), (0.240249008663, -0.950467019249, 0.197212725647), (0.969698787335, 0.225716383639, -0.0934685829484)122.807138076, 198.33388471, -178.13203079
22given(-0.994981896228, -0.0977002039087, -0.0215799985024), (-0.0832816903506, 0.928227787117, -0.362570455603), (0.0554543616995, -0.358953820679, -0.931706481886)433.092716715, 45.777667289, 134.198513206
23given(-0.0826279580462, -0.143439491014, -0.986203697502), (-0.150067860639, -0.97651291149, 0.154603269357), (-0.985216858236, 0.160772031492, 0.0591616103346)296.556716825, 286.347046123, 233.415933203
24given(0.0495438851498, 0.216384330723, 0.975050370423), (0.239312541956, -0.950382997007, 0.198750261036), (0.969677735491, 0.223494922575, -0.098869150277)121.234571824, 198.589537337, -177.279204537
25given(-0.996380597315, -0.0835178726258, -0.0158262517877), (-0.0721871763766, 0.929662753884, -0.361270225188), (0.0448855974713, -0.358820190336, -0.932326849419)431.628589293, 43.932309601, 136.142401096
26given(-0.0857481117677, -0.131034577298, -0.987662493406), (-0.148716049158, -0.978524724117, 0.14273367162), (-0.985155215208, 0.159120406748, 0.0644197027723)295.274730598, 286.725286328, 233.548367416
27given(0.0539346215476, 0.223494077448, 0.973211926532), (0.240811562435, -0.94877527477, 0.204536718909), (0.969072158302, 0.223329074082, -0.104991793364)118.682982232, 197.647325619, -176.64229757
28given(-0.994276018151, -0.105466634091, -0.0170876804323), (-0.0911840323755, 0.920994052803, -0.378755101538), (0.0556836777582, -0.375028990606, -0.925339172539)433.449280555, 48.1633132464, 135.688387074
29given(-0.0813506823574, -0.134166402877, -0.987614015098), (-0.144834436866, -0.978788870649, 0.144897662479), (-0.986106004635, 0.154828043432, 0.060193227104)294.802043198, 286.234374787, 234.503956686
30given(0.0539170868628, 0.214846838969, 0.975158337671), (0.238193368702, -0.951154806022, 0.196388528401), (0.969719994045, 0.221687552123, -0.102458588625)120.030461539, 199.39782297, -176.753479995
31given(-0.994210362084, -0.105884307838, -0.0182830325316), (-0.0916584392649, 0.924515913332, -0.369958182107), (0.0560757205609, -0.366140463962, -0.928868491345)433.556686803, 48.0705136935, 134.718529303
32given(-0.0894508324748, -0.140278570416, -0.986063117276), (-0.155149910898, -0.975983735371, 0.152919107503), (-0.9838328383, 0.166666346252, 0.06553834991)297.126293269, 287.299091056, 232.007532403
33given(0.048299628765, 0.218078798676, 0.974735237605), (0.248710833272, -0.947763017532, 0.199720264401), (0.967372765419, 0.232780798537, -0.100015161642)121.369115974, 195.890494843, -178.117128846
34given(-0.994375388868, -0.104984960034, -0.013990860598), (-0.0921494394209, 0.922692129294, -0.374363079581), (0.0522117499038, -0.370968182875, -0.927176650087)433.39872118, 48.5326708682, 136.124614248
35given(-0.0863855400729, -0.142455513077, -0.986024322854), (-0.15951766953, -0.974977075417, 0.154834800736), (-0.983408181568, 0.170663789965, 0.0614997497609)296.975578231, 287.855453757, 231.604085779
36given(0.0477869785461, 0.217062277331, 0.974987370401), (0.241980675524, -0.94954213054, 0.199537202053), (0.96910358443, 0.226392822523, -0.09790062592)121.695641982, 197.764921612, -177.793529402
37given(-0.995440236131, -0.0950926451487, -0.00749167069322), (-0.0854738869113, 0.924095165172, -0.372481328877), (0.0423432514981, -0.370142559758, -0.928009447424)432.784805281, 46.9933101494, 138.384813685
38given(-0.0765342294589, -0.150759479856, -0.985603414642), (-0.145261140303, -0.976269990424, 0.160611664942), (-0.98642876724, 0.155462165916, 0.0528185775056)296.630410407, 285.2439603, 235.03988298
39given(0.0373162324461, 0.208790064724, 0.977248283533), (0.244012480677, -0.950230595268, 0.193700090581), (0.969053872636, 0.231232620297, -0.0864064074045)125.456935812, 197.493272556, -178.538510571
40given(-0.995674515425, -0.0916542963121, -0.01522331437), (-0.0801978707902, 0.930557396903, -0.357255136548), (0.0469101359365, -0.354488957566, -0.93388276465)432.192364995, 44.4968786355, 135.527192025
41given(-0.0840541298632, -0.154111145098, -0.98447176608), (-0.139562310623, -0.976409192332, 0.164764834183), (-0.98663937926, 0.151244319186, 0.0605631175492)298.082289788, 283.790209629, 235.077925276
42given(0.0477002972203, 0.217226598394, 0.974955017729), (0.239320578279, -0.950121978493, 0.199984716409), (0.969768190063, 0.223787468227, -0.0973078959149)121.659267462, 198.462178265, -177.51018097
43given(-0.994134811123, -0.107558599792, -0.0112749688866), (-0.0960028049691, 0.925684862313, -0.365911187481), (0.0497939629952, -0.362682620615, -0.930581473033)433.796814147, 49.4673391561, 135.723051226
44given(-0.0890135934054, -0.152265767032, -0.984322973611), (-0.14709900338, -0.975399542379, 0.164187745987), (-0.985108351093, 0.159407869686, 0.0644256756937)298.503388512, 285.068197966, 233.305204242
45given(0.0443419800112, 0.208652275693, 0.976984143503), (0.241717982365, -0.95112934946, 0.192159771015), (0.969332866362, 0.227633891245, -0.0926099656984)123.513216997, 198.390792481, -178.053081209
46given(-0.994742426285, -0.101344504743, -0.0147240180324), (-0.0884760221118, 0.922882843507, -0.374778935737), (0.0515703292601, -0.37150578531, -0.926997277569)433.259447053, 47.6889621078, 136.280110871
47given(-0.0875251571543, -0.155302054795, -0.983982021503), (-0.143637632111, -0.975482924588, 0.166737201843), (-0.985752290135, 0.155930547403, 0.0630720768632)298.828683184, 284.47104027, 234.214095945
48given(0.0386178150388, 0.212533884124, 0.976390297197), (0.235092504672, -0.951624389873, 0.197844724081), (0.97120552851, 0.221901709544, -0.0867147778208)124.727899869, 200.31521905, -177.824386223
49given(-0.994447848264, -0.100574626792, -0.0309551535121), (-0.080992031864, 0.919334180335, -0.385051886949), (0.0671845805066, -0.380406899667, -0.922375640847)432.605478233, 46.2883935595, 134.595329682
50given(-0.0841938014331, -0.142847306695, -0.986157214023), (-0.138149049552, -0.978440191924, 0.153524040256), (-0.986826349419, 0.149162454387, 0.062644379582)296.29325265, 285.083441673, 235.541140406
51given(0.0545452606973, 0.181299452687, 0.98191411182), (0.224907504635, -0.96033861858, 0.164822183042), (0.972852213285, 0.211849583713, -0.0931575278038)124.573607609, 207.117044031, -176.383809185
52given(-0.992475243553, -0.121535146278, -0.0149029914068), (-0.105579732643, 0.911051536313, -0.398544876063), (0.0620146030275, -0.393972469089, -0.917027743643)436.241410137, 51.9721190182, 137.604770477
53given(-0.0636856731943, -0.176634530988, -0.982214018171), (-0.10489600335, -0.977575294433, 0.182601676323), (-0.992441919465, 0.114659435623, 0.0437292843699)297.06779619, 277.997181907, 239.49722595
54given(0.0250790080371, 0.20031157961, 0.979411208038), (0.234433673365, -0.953577668931, 0.189025083281), (0.971808569703, 0.224866405652, -0.0708745614485)129.455669218, 200.714354066, -180.386289942
55given(-0.996308479749, -0.0827042158853, -0.0230092558654), (-0.0696334033152, 0.935340437998, -0.34682770101), (0.0502056005185, -0.343945166734, -0.93764658585)432.304243215, 41.9920839088, 134.498982997
56given(-0.0789616528541, -0.14085187209, -0.986876794492), (-0.1594128514, -0.97544407043, 0.151975025159), (-0.984049084237, 0.169321042969, 0.0545690775131)295.530496095, 287.910742441, 231.864658474
57given(0.0500116831004, 0.214068670286, 0.975537511301), (0.241935847214, -0.950265226327, 0.196119977224), (0.969002516708, 0.226209204135, -0.099315248468)121.589848604, 198.065163512, -177.436827952
58given(-0.995673708128, -0.0901073088022, -0.0226834706815), (-0.076270565704, 0.931988709632, -0.354372467787), (0.0530722879563, -0.35110926792, -0.934829189869)431.575705529, 43.2010994534, 133.157182324
59given(-0.0866895303462, -0.130348697329, -0.987671069959), (-0.152064722984, -0.978054701938, 0.142426542611), (-0.984561448236, 0.162536817741, 0.0649656642133)296.059910416, 287.971740564, 233.015626247
60given(0.038520317682, 0.236423085523, 0.970886352648), (0.254808539174, -0.94181172194, 0.219233411641), (0.966223987225, 0.23894519256, -0.0965215077751)122.173859214, 193.11674007, -178.492577139
61given(0.017352437443, 0.188449468902, 0.981929575166), (0.232790629046, -0.955849932138, 0.179330505656), (0.972372056336, 0.225472182101, -0.0604555965614)129.607396846, 198.361114733, -177.773245793
62given(-0.0162193681033, -0.12365664378, -0.992192504783), (-0.157908400935, -0.97955303253, 0.124662718467), (-0.987320550284, 0.158697482369, -0.00363869167306)280.434926007, 290.908808746, 235.879207237

-
要素

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Photosystem II ... , 6種, 24分子 A1a1A2a2B1b1B2b2C1c1C2c2D1d1D2d2O1o1O2o2U1u1U2u2

#1: タンパク質
Photosystem II protein D1 / PSII D1 protein / Photosystem II Q(B) protein


分子量: 38073.512 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: O19895, photosystem II
#2: タンパク質
Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


分子量: 56618.441 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: O19928
#3: タンパク質
Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


分子量: 50515.613 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: Q9TM46
#4: タンパク質
Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


分子量: 39341.867 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: Q9TM47, photosystem II
#13: タンパク質
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO


分子量: 35495.527 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物)
#15: タンパク質
Photosystem II 12 kDa extrinsic protein, chloroplastic / PS II complex 12 kDa extrinsic protein / PSII-U


分子量: 16870.379 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: Q9ZQS5

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Cytochrome b559 subunit ... , 2種, 8分子 E1e1E2e2F1f1F2f2

#5: タンパク質
Cytochrome b559 subunit alpha / PSII reaction center subunit V


分子量: 9534.586 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: Q9TM20
#6: タンパク質・ペプチド
Cytochrome b559 subunit beta / PSII reaction center subunit VI


分子量: 4958.928 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: Q9TM21

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PHOTOSYSTEM II REACTION CENTER PROTEIN ... , 10種, 38分子 H1h1H2h2I1i1I2i2J1j1J2j2K1k1K2k2L1l1L2l2M1m1M2m2T1t1T2t2Y1y1...

#7: タンパク質
Photosystem II reaction center protein H / PSII-H


分子量: 7498.996 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: O19925
#8: タンパク質・ペプチド
Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


分子量: 4472.214 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: O19882
#9: タンパク質・ペプチド
Photosystem II reaction center protein J / PSII-J


分子量: 4089.821 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: Q9TM23
#10: タンパク質・ペプチド
Photosystem II reaction center protein K / PSII-K


分子量: 4703.714 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: Q9TLR0
#11: タンパク質・ペプチド
Photosystem II reaction center protein L / PSII-L / PSII 5 kDa protein


分子量: 4379.130 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: Q9TM22
#12: タンパク質
PHOTOSYSTEM II REACTION CENTER PROTEIN M


分子量: 11755.917 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物)
#14: タンパク質・ペプチド
Photosystem II reaction center protein T / PSII-T


分子量: 3732.606 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: O19927
#17: タンパク質・ペプチド
Photosystem II reaction center protein Ycf12


分子量: 4042.914 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: Q9TLX0
#18: タンパク質・ペプチド
PHOTOSYSTEM II REACTION CENTER PROTEIN X


分子量: 4594.444 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物)
#22: タンパク質 Photosystem II reaction center protein Z


分子量: 6483.804 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物)

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タンパク質 , 2種, 6分子 V1v1V2v2q1Q2

#16: タンパク質
Cytochrome c-550 / Cytochrome c550


分子量: 17240.738 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: Q76FB0
#21: タンパク質 Extrinsic protein in photosystem II


分子量: 24063.545 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物) / 参照: UniProt: Q76B86

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PEPTIDE CHAIN ... , 2種, 8分子 S1s1S2s2W1w1W2w2

#19: タンパク質・ペプチド
PEPTIDE CHAIN UNASSIGNED


分子量: 4302.190 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物)
#20: タンパク質・ペプチド
PEPTIDE CHAIN UNASSIGNED


分子量: 2310.772 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Cyanidium caldarium (真核生物)

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糖 , 2種, 28分子

#34: 糖
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


タイプ: saccharide / 分子量: 949.299 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C51H96O15
#35: 糖
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE / ドデシルβ-D-マルトシド


タイプ: D-saccharide / 分子量: 510.615 Da / 分子数: 14 / 由来タイプ: 合成 / 式: C24H46O11 / コメント: 可溶化剤*YM

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非ポリマー , 16種, 343分子

#23: 化合物...
ChemComp-BCR / BETA-CAROTENE / 9,13-cis-β-カロテン


分子量: 536.873 Da / 分子数: 38 / 由来タイプ: 合成 / 式: C40H56
#24: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Cl
#25: 化合物...
ChemComp-CLA / CHLOROPHYLL A


分子量: 893.489 Da / 分子数: 140 / 由来タイプ: 合成 / 式: C55H72MgN4O5
#26: 化合物
ChemComp-OEX / CA-MN4-O5 CLUSTER


分子量: 339.827 Da / 分子数: 4 / 由来タイプ: 合成 / 式: CaMn4O5
#27: 化合物
ChemComp-PHO / PHEOPHYTIN A / 132α-(メトキシカルボニル)-31,32-ジデヒ(以下略)


分子量: 871.200 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C55H74N4O5
#28: 化合物...
ChemComp-UNL / UNKNOWN LIGAND


分子数: 52 / 由来タイプ: 合成
#29: 化合物...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


分子量: 787.158 Da / 分子数: 25 / 由来タイプ: 合成 / 式: C45H86O10
#30: 化合物
ChemComp-FE / FE (III) ION


分子量: 55.845 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Fe
#31: 化合物
ChemComp-BCT / BICARBONATE ION / オキシラトぎ酸


分子量: 61.017 Da / 分子数: 4 / 由来タイプ: 合成 / 式: CHO3 / コメント: pH緩衝剤*YM
#32: 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: 9 / 由来タイプ: 合成 / 式: C3H8O3
#33: 化合物
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / ジパルミトイルホスファチジルグリセロ-ル


分子量: 722.970 Da / 分子数: 19 / 由来タイプ: 合成 / 式: C38H75O10P / コメント: リン脂質*YM
#36: 化合物
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


分子量: 749.201 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C53H80O2
#37: 化合物
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL / (2S)-1-O,2-O-ジパルミトイル-3-O-(6-スルホ-6-デオキシ-α-D-グルコピラノシル)グリセロ-ル


分子量: 795.116 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C41H78O12S
#38: 化合物
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


分子量: 616.487 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C34H32FeN4O4
#39: 化合物 ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Ca
#40: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 18 / 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

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試料調製

結晶マシュー密度: 2.79 Å3/Da / 溶媒含有率: 55.93 %
結晶化温度: 277 K / 手法: batch mode / pH: 6.1 / 詳細: PEG1450, glycerol, MES-NaOH, CaCl2, beta-DDM

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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: SPring-8 / ビームライン: BL41XU / 波長: 0.9 Å
検出器タイプ: RAYONIX MX225HE / 検出器: CCD / 日付: 2011年1月21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: 0.9 Å / 相対比: 1
反射解像度: 2.767→29.775 Å / Num. obs: 382176 / % possible obs: 99.4 % / 冗長度: 7.5 % / Biso Wilson estimate: 67.7883864741 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 17.43
反射 シェル解像度: 2.76→2.93 Å / 冗長度: 7.15 % / Rmerge(I) obs: 1.162 / Mean I/σ(I) obs: 2.04 / % possible all: 97.7

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692精密化
XDSデータ削減
XDSデータスケーリング
SHARP位相決定
SOLVE位相決定
精密化解像度: 2.77000368116→9.99956834485 Å / SU ML: 0.393299385627 / 交差検証法: THROUGHOUT / σ(F): 1.33646382975 / 位相誤差: 32.5479940329
Rfactor反射数%反射
Rfree0.277700681274 18739 5.01470505592 %
Rwork0.249195678604 354942 -
obs0.250629430593 373681 99.7464171411 %
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: 68.5703747251 Å2
精密化ステップサイクル: LAST / 解像度: 2.77000368116→9.99956834485 Å
タンパク質核酸リガンド溶媒全体
原子数77709 0 15016 18 92743
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.006149511692496131
X-RAY DIFFRACTIONf_angle_d1.18202202501132656
X-RAY DIFFRACTIONf_chiral_restr0.039276736384113466
X-RAY DIFFRACTIONf_plane_restr0.0049586553672716811
X-RAY DIFFRACTIONf_dihedral_angle_d15.429647774732055
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A12447X-RAY DIFFRACTIONPOSITIONAL0.011
12A22447X-RAY DIFFRACTIONPOSITIONAL0.011
13a12517X-RAY DIFFRACTIONPOSITIONAL0.011
14a22486X-RAY DIFFRACTIONPOSITIONAL0.01
21B13591X-RAY DIFFRACTIONPOSITIONAL0.009
22B23591X-RAY DIFFRACTIONPOSITIONAL0.009
23b13658X-RAY DIFFRACTIONPOSITIONAL0.011
24b23628X-RAY DIFFRACTIONPOSITIONAL0.009
31C13065X-RAY DIFFRACTIONPOSITIONAL0.011
32C23065X-RAY DIFFRACTIONPOSITIONAL0.011
33c13279X-RAY DIFFRACTIONPOSITIONAL0.01
34c23249X-RAY DIFFRACTIONPOSITIONAL0.009
41D12526X-RAY DIFFRACTIONPOSITIONAL0.009
42D22526X-RAY DIFFRACTIONPOSITIONAL0.009
43d12600X-RAY DIFFRACTIONPOSITIONAL0.01
44d22594X-RAY DIFFRACTIONPOSITIONAL0.008
51E1362X-RAY DIFFRACTIONPOSITIONAL0.011
52E2362X-RAY DIFFRACTIONPOSITIONAL0.011
53e1378X-RAY DIFFRACTIONPOSITIONAL0.01
54e2374X-RAY DIFFRACTIONPOSITIONAL0.006
61F1183X-RAY DIFFRACTIONPOSITIONAL0.01
62F2183X-RAY DIFFRACTIONPOSITIONAL0.01
63f1199X-RAY DIFFRACTIONPOSITIONAL0.008
64f2197X-RAY DIFFRACTIONPOSITIONAL0.008
71H1407X-RAY DIFFRACTIONPOSITIONAL0.007
72H2407X-RAY DIFFRACTIONPOSITIONAL0.007
73h1423X-RAY DIFFRACTIONPOSITIONAL0.009
74h2420X-RAY DIFFRACTIONPOSITIONAL0.006
81I1244X-RAY DIFFRACTIONPOSITIONAL0.007
82I2244X-RAY DIFFRACTIONPOSITIONAL0.007
83i1258X-RAY DIFFRACTIONPOSITIONAL0.008
84i2253X-RAY DIFFRACTIONPOSITIONAL0.008
91J1205X-RAY DIFFRACTIONPOSITIONAL0.008
92J2205X-RAY DIFFRACTIONPOSITIONAL0.008
93j1209X-RAY DIFFRACTIONPOSITIONAL0.009
94j2209X-RAY DIFFRACTIONPOSITIONAL0.008
101K1231X-RAY DIFFRACTIONPOSITIONAL0.015
102K2231X-RAY DIFFRACTIONPOSITIONAL0.015
103k1259X-RAY DIFFRACTIONPOSITIONAL0.008
104k2244X-RAY DIFFRACTIONPOSITIONAL0.014
111L1286X-RAY DIFFRACTIONPOSITIONAL0.01
112L2286X-RAY DIFFRACTIONPOSITIONAL0.01
113l1286X-RAY DIFFRACTIONPOSITIONAL0.01
114l2286X-RAY DIFFRACTIONPOSITIONAL0.01
121M1281X-RAY DIFFRACTIONPOSITIONAL0.01
122M2281X-RAY DIFFRACTIONPOSITIONAL0.01
123m1285X-RAY DIFFRACTIONPOSITIONAL0.01
124m2284X-RAY DIFFRACTIONPOSITIONAL0.012
131O11174X-RAY DIFFRACTIONPOSITIONAL0.067
132O21174X-RAY DIFFRACTIONPOSITIONAL0.067
133o11242X-RAY DIFFRACTIONPOSITIONAL0.019
134o21255X-RAY DIFFRACTIONPOSITIONAL0.03
141T1230X-RAY DIFFRACTIONPOSITIONAL0.008
142T2230X-RAY DIFFRACTIONPOSITIONAL0.008
143t1236X-RAY DIFFRACTIONPOSITIONAL0.009
144t2230X-RAY DIFFRACTIONPOSITIONAL0.008
151U1562X-RAY DIFFRACTIONPOSITIONAL0.055
152U2562X-RAY DIFFRACTIONPOSITIONAL0.055
153u1649X-RAY DIFFRACTIONPOSITIONAL0.009
154u2658X-RAY DIFFRACTIONPOSITIONAL0.014
161V1825X-RAY DIFFRACTIONPOSITIONAL0.017
162V2825X-RAY DIFFRACTIONPOSITIONAL0.017
163v1881X-RAY DIFFRACTIONPOSITIONAL0.009
164v2909X-RAY DIFFRACTIONPOSITIONAL0.01
171Y1147X-RAY DIFFRACTIONPOSITIONAL0.009
172Y2147X-RAY DIFFRACTIONPOSITIONAL0.009
173y1158X-RAY DIFFRACTIONPOSITIONAL0.014
174y2152X-RAY DIFFRACTIONPOSITIONAL0.015
181X1179X-RAY DIFFRACTIONPOSITIONAL0.009
182X2179X-RAY DIFFRACTIONPOSITIONAL0.009
183x1181X-RAY DIFFRACTIONPOSITIONAL0.015
184x2175X-RAY DIFFRACTIONPOSITIONAL0.018
191S1150X-RAY DIFFRACTIONPOSITIONAL0.008
192S2150X-RAY DIFFRACTIONPOSITIONAL0.008
193s1159X-RAY DIFFRACTIONPOSITIONAL0.006
194s2159X-RAY DIFFRACTIONPOSITIONAL0.006
201W1114X-RAY DIFFRACTIONPOSITIONAL0.007
202W2114X-RAY DIFFRACTIONPOSITIONAL0.007
203w1117X-RAY DIFFRACTIONPOSITIONAL0.007
204w2117X-RAY DIFFRACTIONPOSITIONAL0.005
211q1590X-RAY DIFFRACTIONPOSITIONAL0.013
212Q2590X-RAY DIFFRACTIONPOSITIONAL0.013
221Z2328X-RAY DIFFRACTIONPOSITIONAL0.007
222z2328X-RAY DIFFRACTIONPOSITIONAL0.007
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.80080.4025518948685960.37742469830111225X-RAY DIFFRACTION95.2461526066
2.8008-2.8330.3948788762116200.34030821142811763X-RAY DIFFRACTION99.8951274605
2.833-2.86680.3805361186956370.33424365443311785X-RAY DIFFRACTION99.9356395817
2.8668-2.90220.3743710414586330.32655416573911762X-RAY DIFFRACTION99.9032804062
2.9022-2.93940.3902938742255650.33265312122211823X-RAY DIFFRACTION99.9354630526
2.9394-2.97860.3656045343536180.31801586754111815X-RAY DIFFRACTION99.967837903
2.9786-3.020.3575024118126160.31029657840311769X-RAY DIFFRACTION99.9193223074
3.02-3.06380.3631901736486880.30778677298911739X-RAY DIFFRACTION99.9356654604
3.0638-3.11030.3434294367186430.29534743267411768X-RAY DIFFRACTION99.9436302142
3.1103-3.15970.3397944943626480.29911227117211794X-RAY DIFFRACTION99.943770584
3.1597-3.21240.3243135660796040.28179783823211806X-RAY DIFFRACTION99.9194847021
3.2124-3.26880.3208336141725910.27766750114111826X-RAY DIFFRACTION99.9597488327
3.2688-3.32940.3141407752446150.27485203129211839X-RAY DIFFRACTION99.9117529081
3.3294-3.39480.2972607674175970.25867402481211873X-RAY DIFFRACTION99.9198717949
3.3948-3.46560.3085210911876470.26266016090911727X-RAY DIFFRACTION99.9434617559
3.4656-3.54270.3014021689936090.26335317947511855X-RAY DIFFRACTION99.9759364723
3.5427-3.62720.2954728587356220.25664569500511856X-RAY DIFFRACTION99.9119224918
3.6272-3.72030.309747667446180.25547948485911813X-RAY DIFFRACTION99.9437208554
3.7203-3.82390.2868349142166280.24824335803611853X-RAY DIFFRACTION99.8559884791
3.8239-3.940.2665384022975970.24202180090811869X-RAY DIFFRACTION99.8158379374
3.94-4.07160.2725194233456180.23704265594211860X-RAY DIFFRACTION99.824
4.0716-4.22280.2642629328776190.23706988607511871X-RAY DIFFRACTION99.7603833866
4.2228-4.39930.2471630858826830.22905164614911766X-RAY DIFFRACTION99.7675909601
4.3993-4.60950.2497989688356010.22219919569911897X-RAY DIFFRACTION99.7207372537
4.6095-4.86680.2356992838956210.21997840278711900X-RAY DIFFRACTION99.7927791504
4.8668-5.19320.2535872899636400.22716348008211904X-RAY DIFFRACTION99.8885172798
5.1932-5.62950.2543484257566560.23850039588811936X-RAY DIFFRACTION99.9206475163
5.6295-6.26320.253245493226230.24466348417112024X-RAY DIFFRACTION99.976284585
6.2632-7.33390.2622985571896090.23023950370112077X-RAY DIFFRACTION99.976357475
7.3339-9.99960.2112190077866770.20582587372512147X-RAY DIFFRACTION99.9610258009

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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

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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。

-
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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