- PDB-1rg5: Structure of the photosynthetic reaction centre from Rhodobacter ... -
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基本情報
登録情報
データベース: PDB / ID: 1rg5
タイトル
Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides carotenoidless strain R-26.1
要素
(Reaction center protein ...) x 3
キーワード
PHOTOSYNTHESIS / PHOTOSYNTHETIC REACTION CENTER / CAROTENOIDLESS MUTANT / CAROTENOID BINDING SITE / MEMBRANE PROTEIN
機能・相同性
機能・相同性情報
: / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / membrane => GO:0016020 / metal ion binding 類似検索 - 分子機能
Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal ...Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta 類似検索 - ドメイン・相同性
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / HEPTANE-1,2,3-TRIOL / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain / Reaction center protein L chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / HEPTANE-1,2,3-TRIOL / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Reaction center protein H chain 類似検索 - 構成要素
ReactioncenterproteinLchain / Photosynthetic reaction center L subunit
分子量: 31346.389 Da / 分子数: 1 / 由来タイプ: 天然 詳細: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26.1 ...詳細: Strain R-26.1 of Rhodobacter sphaeroides bacteria is a partial revertant of the R-26 chemical mutant of the wild-type strain 2.4.1. While R-26 has no LH2 antenna and no carotenoid, the R-26.1 has altered LH2 antenna and no carotenoid. Reaction center from R-26.1 strain is therefore identical with the wild-type strain 2.4.1 except for the missing carotenoid. 由来: (天然) Rhodobacter sphaeroides (バクテリア) / 株: R-26.1 / 参照: UniProt: P02954, UniProt: P0C0Y8*PLUS
#2: タンパク質
ReactioncenterproteinMchain / Photosynthetic reaction center M subunit
解像度: 2.5→2.54 Å / 冗長度: 4.8 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3889 / % possible all: 99
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.1.9999
精密化
DENZO
データ削減
SCALEPACK
データスケーリング
AMoRE
位相決定
精密化
構造決定の手法: 分子置換 / 解像度: 2.5→23.34 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 9.905 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL Isotropic thermal model: TLS thermal mode followed by the restrained refinement of atomic coordinates and isotropic B-factors 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.161 / ESU R Free: 0.146 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the limited electron density quality some atoms at the end of the carbohydrate tails of ligands U10 and CDL were not modelled.
Rfactor
反射数
%反射
Selection details
Rfree
0.18188
3918
5 %
RANDOM
Rwork
0.15541
-
-
-
all
0.15672
78682
-
-
obs
0.15672
74764
99.12 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータ
Biso mean: 52.933 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.87 Å2
0.44 Å2
0 Å2
2-
-
0.87 Å2
0 Å2
3-
-
-
-1.31 Å2
精密化ステップ
サイクル: LAST / 解像度: 2.5→23.34 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
6474
0
688
243
7405
拘束条件
Refine-ID
タイプ
Dev ideal
Dev ideal target
数
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
7473
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
7003
X-RAY DIFFRACTION
r_angle_refined_deg
1.686
2.025
10213
X-RAY DIFFRACTION
r_angle_other_deg
1.322
3
16165
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.699
5
818
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.024
22.699
289
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.258
15
985
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.303
15
32
X-RAY DIFFRACTION
r_chiral_restr
0.106
0.2
1023
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
7978
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1569
X-RAY DIFFRACTION
r_nbd_refined
0.2
0.2
1214
X-RAY DIFFRACTION
r_nbd_other
0.172
0.2
5894
X-RAY DIFFRACTION
r_nbtor_other
0.09
0.2
3594
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.12
0.2
173
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.078
0.2
2
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.295
0.2
10
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.054
0.2
2
X-RAY DIFFRACTION
r_mcbond_it
0.907
1.5
5237
X-RAY DIFFRACTION
r_mcbond_other
0.146
1.5
1697
X-RAY DIFFRACTION
r_mcangle_it
1.107
2
6525
X-RAY DIFFRACTION
r_scbond_it
1.714
3
4309
X-RAY DIFFRACTION
r_scangle_it
2.51
4.5
3677
LS精密化 シェル
解像度: 2.5→2.564 Å / Total num. of bins used: 20 /
Rfactor
反射数
Rfree
0.268
295
Rwork
0.232
5435
obs
-
5435
精密化 TLS
手法: refined / Origin x: 11.3247 Å / Origin y: 105.5932 Å / Origin z: 34.8431 Å