plastoquinol--plastocyanin reductase activity / シトクロムb6f複合体 / シトクロムb6f複合体 / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / 光合成 / respiratory electron transport chain ...plastoquinol--plastocyanin reductase activity / シトクロムb6f複合体 / シトクロムb6f複合体 / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / 光合成 / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / metal ion binding 類似検索 - 分子機能
Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily ...Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily / Cytochrome B6-F complex subunit 5 / ペンスリット / PetM family of cytochrome b6f complex subunit 7 / Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Single helix bin / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / : / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Rudiment single hybrid motif / Rieske iron-sulphur protein / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Βバレル / サンドイッチ / Orthogonal Bundle / Mainly Beta / Mainly Alpha 類似検索 - ドメイン・相同性
温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: 15-20 MG/ML B6F DIMER MIXED WITH EQUAL VOLUME OF CRYSTALLIZATION BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
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データ収集
回折
ID
平均測定温度 (K)
Crystal-ID
1
100
1
2
100
1
放射光源
由来
サイト
ビームライン
ID
波長 (Å)
シンクロトロン
APS
23-ID-B
1
1.0332
シンクロトロン
APS
23-ID-B
2
1.0332
検出器
タイプ
ID
検出器
MARMOSAIC 300 mm CCD
1
CCD
MAR scanner 300 mm plate
2
IMAGE PLATE
放射
ID
プロトコル
単色(M)・ラウエ(L)
散乱光タイプ
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
1
放射波長
波長: 1.0332 Å / 相対比: 1
反射
解像度: 2.8→48.52 Å / Num. all: 67115 / Num. obs: 67054 / % possible obs: 99.2 %
反射 シェル
解像度: 2.8→2.85 Å / % possible all: 94.7
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解析
ソフトウェア
名称
バージョン
分類
PHENIX
1.8.2_1309
精密化
REFMAC
精密化
HKL-2000
データ削減
HKL-2000
データスケーリング
REFMAC
位相決定
JBluIce-EPICS
データ収集
精密化
解像度: 2.803→48.517 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.897 / SU ML: 0.43 / σ(F): 1.45 / 位相誤差: 26.09 / 立体化学のターゲット値: ML / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
反射数
%反射
Rfree
0.2718
3405
5.08 %
Rwork
0.2484
-
-
obs
0.2496
67054
99.21 %
all
-
67115
-
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: 82.647 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.57 Å2
0.57 Å2
0 Å2
2-
-
0.57 Å2
0 Å2
3-
-
-
-1.84 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.803→48.517 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
6386
0
560
13
6959
拘束条件
Refine-ID
タイプ
Dev ideal
数
X-RAY DIFFRACTION
f_bond_d
0.005
7158
X-RAY DIFFRACTION
f_angle_d
1.058
9782
X-RAY DIFFRACTION
f_dihedral_angle_d
15.071
2608
X-RAY DIFFRACTION
f_chiral_restr
0.187
1077
X-RAY DIFFRACTION
f_plane_restr
0.004
1158
LS精密化 シェル
解像度 (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.8026-2.8427
0.3766
124
0.3735
2474
X-RAY DIFFRACTION
94
2.8427-2.8851
0.37
129
0.3634
2547
X-RAY DIFFRACTION
97
2.8851-2.9302
0.3702
160
0.3431
2549
X-RAY DIFFRACTION
99
2.9302-2.9782
0.3733
150
0.3489
2598
X-RAY DIFFRACTION
99
2.9782-3.0296
0.3435
122
0.3341
2602
X-RAY DIFFRACTION
99
3.0296-3.0846
0.3365
165
0.3119
2579
X-RAY DIFFRACTION
99
3.0846-3.144
0.318
142
0.3022
2640
X-RAY DIFFRACTION
99
3.144-3.2081
0.2789
151
0.2997
2606
X-RAY DIFFRACTION
100
3.2081-3.2779
0.2779
148
0.2771
2606
X-RAY DIFFRACTION
99
3.2779-3.3541
0.2615
145
0.2636
2632
X-RAY DIFFRACTION
100
3.3541-3.4379
0.2563
132
0.2549
2628
X-RAY DIFFRACTION
100
3.4379-3.5309
0.276
125
0.2481
2662
X-RAY DIFFRACTION
100
3.5309-3.6347
0.2705
140
0.2354
2671
X-RAY DIFFRACTION
100
3.6347-3.752
0.2457
125
0.2152
2628
X-RAY DIFFRACTION
100
3.752-3.8861
0.2216
161
0.2017
2656
X-RAY DIFFRACTION
100
3.8861-4.0416
0.2351
138
0.2046
2643
X-RAY DIFFRACTION
100
4.0416-4.2254
0.2444
141
0.2076
2673
X-RAY DIFFRACTION
100
4.2254-4.448
0.2268
138
0.1993
2686
X-RAY DIFFRACTION
100
4.448-4.7265
0.2258
119
0.1913
2704
X-RAY DIFFRACTION
100
4.7265-5.0911
0.2205
140
0.1973
2697
X-RAY DIFFRACTION
100
5.0911-5.6028
0.2589
141
0.2202
2716
X-RAY DIFFRACTION
100
5.6028-6.4119
0.2778
169
0.2502
2738
X-RAY DIFFRACTION
100
6.4119-8.0723
0.2379
171
0.2309
2762
X-RAY DIFFRACTION
100
8.0723-48.5243
0.3244
129
0.2877
2952
X-RAY DIFFRACTION
98
精密化 TLS
手法: refined / Origin x: -48.0265 Å / Origin y: 67.0967 Å / Origin z: 4.4455 Å