1nkz
Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution
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 | 1nkz |
| 沉积日期 deposition_date | 2003-01-06 |
| 结构标题 title | Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution |
| 关键词 keywords | LIGHT HARVESTING COMPLEX II, TRANS-MEMBRANE HELICES, RHODOPIN GLUCOSIDE, BACTERIOCHLOROPHYLL A, PHOTOSYNTHESIS, MEMBRANE PROTEIN; MEMBRANE PROTEIN |
| 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 | 24.63 Å |
| 回转半径 Rg (电子) rg_electron | 22.70 Å |
| 零角强度 I(0) i0 | 18268300.00 |
| 分子量 molecular_weight | 45266.0 kDa |
| 排除体积 excluded_volume | 61975 ų |
| 包络体积 envelope_volume | 69855 ų |
| 水化壳体积 shell_volume | 25482 ų |
| 包络直径 envelope_diameter | 90.9 Å |
| 壳层 Rg shell_rg | 30.02 Å |
| 包络 Rg envelope_rg | 23.72 Å |
| 形状 Rg shape_rg | 22.65 Å |
| 总 Rg total_rg | 24.15 Å |
| 总原子数 total_atoms | 3231 |
| 残基数 n_residues | 279 |
| 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 | 88.0 Å |
| Rg (实空间) rg_real | 24.64 Å |
| Rg 误差 (实空间) rg_real_error | 0.86 Å |
| I(0) (实空间) i0_real | 1.8270e+07 |
| I(0) 误差 (实空间) i0_real_error | 2.8420e+05 |
| Rg (倒空间) rg_reciprocal | 24.64 Å |
| I(0) (倒空间) i0_reciprocal | 18270000.0000 |
| 解质量估计 total_estimate | 0.7714 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 25.1 Å |
| 偏度 Skewness skewness | 0.334 |
| 峰度 Kurtosis kurtosis | -0.223 |
| 角度范围 angular_range | — – 0.3200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 2804000.0000 |
| 实空间数据点数 n_real_points | 64 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.874; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (7)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1nkza_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.3 — Light-harvesting complex subunits |
| 超家族 Superfamily superfamily | f.3.1 — Light-harvesting complex subunits |
| 家族 Family family | f.3.1.1 — Light-harvesting complex subunits |
| 结构域编号 domain_id | d1nkzb_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.3 — Light-harvesting complex subunits |
| 超家族 Superfamily superfamily | f.3.1 — Light-harvesting complex subunits |
| 家族 Family family | f.3.1.1 — Light-harvesting complex subunits |
| 结构域编号 domain_id | d1nkzc_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.3 — Light-harvesting complex subunits |
| 超家族 Superfamily superfamily | f.3.1 — Light-harvesting complex subunits |
| 家族 Family family | f.3.1.1 — Light-harvesting complex subunits |
| 结构域编号 domain_id | d1nkzd_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.3 — Light-harvesting complex subunits |
| 超家族 Superfamily superfamily | f.3.1 — Light-harvesting complex subunits |
| 家族 Family family | f.3.1.1 — Light-harvesting complex subunits |
| 结构域编号 domain_id | d1nkze_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.3 — Light-harvesting complex subunits |
| 超家族 Superfamily superfamily | f.3.1 — Light-harvesting complex subunits |
| 家族 Family family | f.3.1.1 — Light-harvesting complex subunits |
| 结构域编号 domain_id | d1nkzf_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.3 — Light-harvesting complex subunits |
| 超家族 Superfamily superfamily | f.3.1 — Light-harvesting complex subunits |
| 家族 Family family | f.3.1.1 — Light-harvesting complex subunits |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1nkzA00 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 220 — Light-harvesting Protein |
| 同源超家族 H-superfamily homologous superfamily | 20 — Light-harvesting complex |
| 结构域编号 domain_id | 1nkzB00 |
| 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 | 250 — |
| 结构域编号 domain_id | 1nkzC00 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 220 — Light-harvesting Protein |
| 同源超家族 H-superfamily homologous superfamily | 20 — Light-harvesting complex |
| 结构域编号 domain_id | 1nkzD00 |
| 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 | 250 — |
| 结构域编号 domain_id | 1nkzE00 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 220 — Light-harvesting Protein |
| 同源超家族 H-superfamily homologous superfamily | 20 — Light-harvesting complex |
| 结构域编号 domain_id | 1nkzF00 |
| 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 | 250 — |