1l9j
;X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals ;
SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
1. 结构基本信息 1. Structure Basics
| 条目编号 entry_id | 1l9j |
| 沉积日期 deposition_date | 2002-03-24 |
| 结构标题 title | ;X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals ; |
| 关键词 keywords | ;bacterial photosynthesis, electron transfer proteins, protein-protein interactions, membrane proteins, protein complexes, PHOTOSYNTHESIS ;; PHOTOSYNTHESIS |
| 实验方法 method | X-RAY DIFFRACTION |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 71.04 Å |
| 回转半径 Rg (电子) rg_electron | 70.84 Å |
| 零角强度 I(0) i0 | 523449000.00 |
| 分子量 molecular_weight | 216490.0 kDa |
| 排除体积 excluded_volume | 278800 ų |
| 包络体积 envelope_volume | 445780 ų |
| 水化壳体积 shell_volume | 50881 ų |
| 包络直径 envelope_diameter | 207.9 Å |
| 壳层 Rg shell_rg | 80.13 Å |
| 包络 Rg envelope_rg | 65.79 Å |
| 形状 Rg shape_rg | 70.83 Å |
| 总 Rg total_rg | 71.02 Å |
| 总原子数 total_atoms | 15368 |
| 残基数 n_residues | 1836 |
| 球谐函数阶数 n_harmonics | 20 |
| q 范围 q_range | — – 0.5000 Å−1 |
| 数据点数 n_points | 101 |
| 壳层类型 shell_type | directional |
| 溶剂电子密度 solvent_density | 0.3340 e/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| CRYSOL 版本 crysol_version | 4.1.3 |
3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)
| 最大尺寸 Dmax dmax | 240.4 Å |
| Rg (实空间) rg_real | 71.32 Å |
| Rg 误差 (实空间) rg_real_error | 3.14 Å |
| I(0) (实空间) i0_real | 5.2340e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.2830e+07 |
| Rg (倒空间) rg_reciprocal | 69.51 Å |
| I(0) (倒空间) i0_reciprocal | 521400000.0000 |
| 解质量估计 total_estimate | 0.5783 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 32.8 Å |
| 偏度 Skewness skewness | 0.054 |
| 峰度 Kurtosis kurtosis | -1.477 |
| 角度范围 angular_range | — – 0.1100 Å−1 |
| 当前正则化参数 α current_alpha | 0.0007 |
| 最高正则化参数 α highest_alpha | 13030000.0000 |
| 实空间数据点数 n_real_points | 23 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.002; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.509; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (12)
6. 折叠分类 (SCOP + CATH) 24 domains
SCOP 2.08 (10 domains)
| 结构域编号 domain_id | d1l9jc_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.3 — Cytochrome c |
| 超家族 Superfamily superfamily | a.3.1 — Cytochrome c |
| 家族 Family family | a.3.1.1 — monodomain cytochrome c |
| 结构域编号 domain_id | d1l9jd_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.3 — Cytochrome c |
| 超家族 Superfamily superfamily | a.3.1 — Cytochrome c |
| 家族 Family family | a.3.1.1 — monodomain cytochrome c |
| 结构域编号 domain_id | d1l9jh1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.41 — PRC-barrel domain |
| 超家族 Superfamily superfamily | b.41.1 — PRC-barrel domain |
| 家族 Family family | b.41.1.1 — Photosynthetic reaction centre, H-chain, cytoplasmic domain |
| 结构域编号 domain_id | d1l9jh2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.23 — Single transmembrane helix |
| 超家族 Superfamily superfamily | f.23.10 — Photosystem II reaction centre subunit H, transmembrane region |
| 家族 Family family | f.23.10.1 — Photosystem II reaction centre subunit H, transmembrane region |
| 结构域编号 domain_id | d1l9jl_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.26 — Bacterial photosystem II reaction centre, L and M subunits |
| 超家族 Superfamily superfamily | f.26.1 — Bacterial photosystem II reaction centre, L and M subunits |
| 家族 Family family | f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits |
| 结构域编号 domain_id | d1l9jm_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.26 — Bacterial photosystem II reaction centre, L and M subunits |
| 超家族 Superfamily superfamily | f.26.1 — Bacterial photosystem II reaction centre, L and M subunits |
| 家族 Family family | f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits |
| 结构域编号 domain_id | d1l9jr_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.26 — Bacterial photosystem II reaction centre, L and M subunits |
| 超家族 Superfamily superfamily | f.26.1 — Bacterial photosystem II reaction centre, L and M subunits |
| 家族 Family family | f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits |
| 结构域编号 domain_id | d1l9js_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.26 — Bacterial photosystem II reaction centre, L and M subunits |
| 超家族 Superfamily superfamily | f.26.1 — Bacterial photosystem II reaction centre, L and M subunits |
| 家族 Family family | f.26.1.1 — Bacterial photosystem II reaction centre, L and M subunits |
| 结构域编号 domain_id | d1l9jt1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.41 — PRC-barrel domain |
| 超家族 Superfamily superfamily | b.41.1 — PRC-barrel domain |
| 家族 Family family | b.41.1.1 — Photosynthetic reaction centre, H-chain, cytoplasmic domain |
| 结构域编号 domain_id | d1l9jt2 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.23 — Single transmembrane helix |
| 超家族 Superfamily superfamily | f.23.10 — Photosystem II reaction centre subunit H, transmembrane region |
| 家族 Family family | f.23.10.1 — Photosystem II reaction centre subunit H, transmembrane region |
CATH v4.4 (14 domains)
| 结构域编号 domain_id | 1l9jC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 760 — Cytochrome Bc1 Complex; Chain D, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome c-like domain |
| 结构域编号 domain_id | 1l9jD00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 760 — Cytochrome Bc1 Complex; Chain D, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome c-like domain |
| 结构域编号 domain_id | 1l9jH01 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 540 — Photosynthetic Reaction Center; Chain H, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosynthetic reaction centre, H subunit, N-terminal domain |
| 结构域编号 domain_id | 1l9jH02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 50 — Photosynthetic Reaction Center; Chain H, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosynthetic Reaction Center, subunit H, domain 2 |
| 结构域编号 domain_id | 1l9jL01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 85 — Photosynthetic Reaction Center, subunit M; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosystem II protein D1-like |
| 结构域编号 domain_id | 1l9jL02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 85 — Photosynthetic Reaction Center, subunit M; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosystem II protein D1-like |
| 结构域编号 domain_id | 1l9jM01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 85 — Photosynthetic Reaction Center, subunit M; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosystem II protein D1-like |
| 结构域编号 domain_id | 1l9jM02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 85 — Photosynthetic Reaction Center, subunit M; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosystem II protein D1-like |
| 结构域编号 domain_id | 1l9jR01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 85 — Photosynthetic Reaction Center, subunit M; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosystem II protein D1-like |
| 结构域编号 domain_id | 1l9jR02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 85 — Photosynthetic Reaction Center, subunit M; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosystem II protein D1-like |
| 结构域编号 domain_id | 1l9jS01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 85 — Photosynthetic Reaction Center, subunit M; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosystem II protein D1-like |
| 结构域编号 domain_id | 1l9jS02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 85 — Photosynthetic Reaction Center, subunit M; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosystem II protein D1-like |
| 结构域编号 domain_id | 1l9jT01 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 540 — Photosynthetic Reaction Center; Chain H, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosynthetic reaction centre, H subunit, N-terminal domain |
| 结构域编号 domain_id | 1l9jT02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 50 — Photosynthetic Reaction Center; Chain H, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Photosynthetic Reaction Center, subunit H, domain 2 |