2d2c
Crystal Structure Of Cytochrome B6F Complex with DBMIB From M. Laminosus
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 | 2d2c |
| 沉积日期 deposition_date | 2005-09-07 |
| 结构标题 title | Crystal Structure Of Cytochrome B6F Complex with DBMIB From M. Laminosus |
| 关键词 keywords | 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 | 42.46 Å |
| 回转半径 Rg (电子) rg_electron | 41.41 Å |
| 零角强度 I(0) i0 | 545164000.00 |
| 分子量 molecular_weight | 212690.0 kDa |
| 排除体积 excluded_volume | 274630 ų |
| 包络体积 envelope_volume | 378500 ų |
| 水化壳体积 shell_volume | 73952 ų |
| 包络直径 envelope_diameter | 148.5 Å |
| 壳层 Rg shell_rg | 48.08 Å |
| 包络 Rg envelope_rg | 41.70 Å |
| 形状 Rg shape_rg | 41.43 Å |
| 总 Rg total_rg | 41.74 Å |
| 总原子数 total_atoms | 14982 |
| 残基数 n_residues | 1828 |
| 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 | 138.0 Å |
| Rg (实空间) rg_real | 42.37 Å |
| Rg 误差 (实空间) rg_real_error | 1.39 Å |
| I(0) (实空间) i0_real | 5.4520e+08 |
| I(0) 误差 (实空间) i0_real_error | 9.9070e+06 |
| Rg (倒空间) rg_reciprocal | 42.46 Å |
| I(0) (倒空间) i0_reciprocal | 545200000.0000 |
| 解质量估计 total_estimate | 0.8915 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 52.2 Å |
| 偏度 Skewness skewness | 0.252 |
| 峰度 Kurtosis kurtosis | -0.426 |
| 角度范围 angular_range | — – 0.1850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 70850000.0000 |
| 实空间数据点数 n_real_points | 38 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.904; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.883 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (15)
6. 折叠分类 (SCOP + CATH) 32 domains
SCOP 2.08 (16 domains)
| 结构域编号 domain_id | d2d2ca1 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.21 — Heme-binding four-helical bundle |
| 超家族 Superfamily superfamily | f.21.1 — Transmembrane di-heme cytochromes |
| 家族 Family family | f.21.1.2 — Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 结构域编号 domain_id | d2d2cb1 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.32 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 超家族 Superfamily superfamily | f.32.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 家族 Family family | f.32.1.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 结构域编号 domain_id | d2d2cd1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.33 — ISP domain |
| 超家族 Superfamily superfamily | b.33.1 — ISP domain |
| 家族 Family family | b.33.1.1 — Rieske iron-sulfur protein (ISP) |
| 结构域编号 domain_id | d2d2cd2 |
| 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.23.12 — ISP transmembrane anchor |
| 家族 Family family | f.23.12.1 — ISP transmembrane anchor |
| 结构域编号 domain_id | d2d2ce1 |
| 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.23.24 — PetL subunit of the cytochrome b6f complex |
| 家族 Family family | f.23.24.1 — PetL subunit of the cytochrome b6f complex |
| 结构域编号 domain_id | d2d2cf1 |
| 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.23.25 — PetM subunit of the cytochrome b6f complex |
| 家族 Family family | f.23.25.1 — PetM subunit of the cytochrome b6f complex |
| 结构域编号 domain_id | d2d2cg1 |
| 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.23.26 — PetG subunit of the cytochrome b6f complex |
| 家族 Family family | f.23.26.1 — PetG subunit of the cytochrome b6f complex |
| 结构域编号 domain_id | d2d2ch1 |
| 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.23.27 — PetN subunit of the cytochrome b6f complex |
| 家族 Family family | f.23.27.1 — PetN subunit of the cytochrome b6f complex |
| 结构域编号 domain_id | d2d2cn1 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.21 — Heme-binding four-helical bundle |
| 超家族 Superfamily superfamily | f.21.1 — Transmembrane di-heme cytochromes |
| 家族 Family family | f.21.1.2 — Cytochrome b of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 结构域编号 domain_id | d2d2co1 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.32 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 超家族 Superfamily superfamily | f.32.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 家族 Family family | f.32.1.1 — a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 结构域编号 domain_id | d2d2cq1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.33 — ISP domain |
| 超家族 Superfamily superfamily | b.33.1 — ISP domain |
| 家族 Family family | b.33.1.1 — Rieske iron-sulfur protein (ISP) |
| 结构域编号 domain_id | d2d2cq2 |
| 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.23.12 — ISP transmembrane anchor |
| 家族 Family family | f.23.12.1 — ISP transmembrane anchor |
| 结构域编号 domain_id | d2d2cr1 |
| 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.23.24 — PetL subunit of the cytochrome b6f complex |
| 家族 Family family | f.23.24.1 — PetL subunit of the cytochrome b6f complex |
| 结构域编号 domain_id | d2d2cs1 |
| 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.23.25 — PetM subunit of the cytochrome b6f complex |
| 家族 Family family | f.23.25.1 — PetM subunit of the cytochrome b6f complex |
| 结构域编号 domain_id | d2d2ct1 |
| 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.23.26 — PetG subunit of the cytochrome b6f complex |
| 家族 Family family | f.23.26.1 — PetG subunit of the cytochrome b6f complex |
| 结构域编号 domain_id | d2d2cu1 |
| 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.23.27 — PetN subunit of the cytochrome b6f complex |
| 家族 Family family | f.23.27.1 — PetN subunit of the cytochrome b6f complex |
CATH v4.4 (16 domains)
| 结构域编号 domain_id | 2d2cA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 810 — Cytochrome Bc1 Complex; Chain C |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome Bc1 Complex; Chain C |
| 结构域编号 domain_id | 2d2cB01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 510 — Single helix bin |
| 结构域编号 domain_id | 2d2cB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 980 — plastocyanin oxidoreductase |
| 结构域编号 domain_id | 2d2cC01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 830 — Cytochrome f large domain |
| 结构域编号 domain_id | 2d2cC02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain |
| 结构域编号 domain_id | 2d2cC03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 700 — Single helix bin |
| 结构域编号 domain_id | 2d2cD01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 700 — Single helix bin |
| 结构域编号 domain_id | 2d2cD02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 102 — 3-layer Sandwich |
| 拓扑 Topology topology | 10 — Rieske Iron-sulfur Protein |
| 同源超家族 H-superfamily homologous superfamily | 10 — Rieske [2Fe-2S] iron-sulphur domain |
| 结构域编号 domain_id | 2d2cN00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 810 — Cytochrome Bc1 Complex; Chain C |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome Bc1 Complex; Chain C |
| 结构域编号 domain_id | 2d2cO01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 510 — Single helix bin |
| 结构域编号 domain_id | 2d2cO02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 980 — plastocyanin oxidoreductase |
| 结构域编号 domain_id | 2d2cP01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 830 — Cytochrome f large domain |
| 结构域编号 domain_id | 2d2cP02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain |
| 结构域编号 domain_id | 2d2cP03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 700 — Single helix bin |
| 结构域编号 domain_id | 2d2cQ01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 700 — Single helix bin |
| 结构域编号 domain_id | 2d2cQ02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 102 — 3-layer Sandwich |
| 拓扑 Topology topology | 10 — Rieske Iron-sulfur Protein |
| 同源超家族 H-superfamily homologous superfamily | 10 — Rieske [2Fe-2S] iron-sulphur domain |