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High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24
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 | 1xf6 |
| 沉积日期 deposition_date | 2004-09-14 |
| 结构标题 title | High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24 |
| 关键词 keywords | phycoerythrin, light-harvesting protein, cryptophyte, 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 | 24.17 Å |
| 回转半径 Rg (电子) rg_electron | 23.07 Å |
| 零角强度 I(0) i0 | 53404800.00 |
| 分子量 molecular_weight | 56517.0 kDa |
| 排除体积 excluded_volume | 70572 ų |
| 包络体积 envelope_volume | 81056 ų |
| 水化壳体积 shell_volume | 28782 ų |
| 包络直径 envelope_diameter | 78.9 Å |
| 壳层 Rg shell_rg | 30.77 Å |
| 包络 Rg envelope_rg | 23.17 Å |
| 形状 Rg shape_rg | 23.08 Å |
| 总 Rg total_rg | 23.85 Å |
| 总原子数 total_atoms | 3952 |
| 残基数 n_residues | 490 |
| 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 | 84.7 Å |
| Rg (实空间) rg_real | 24.96 Å |
| Rg 误差 (实空间) rg_real_error | 0.25 Å |
| I(0) (实空间) i0_real | 5.3260e+07 |
| I(0) 误差 (实空间) i0_real_error | 6.5740e+05 |
| Rg (倒空间) rg_reciprocal | 24.09 Å |
| I(0) (倒空间) i0_reciprocal | 53410000.0000 |
| 解质量估计 total_estimate | 0.6660 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 29.1 Å |
| 偏度 Skewness skewness | 0.465 |
| 峰度 Kurtosis kurtosis | 0.094 |
| 角度范围 angular_range | — – 0.3300 Å−1 |
| 当前正则化参数 α current_alpha | 4.4000 |
| 最高正则化参数 α highest_alpha | 16270000.0000 |
| 实空间数据点数 n_real_points | 65 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.779; Stabil: 0.904; Sysdev: 0.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.669 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (8)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1xf6a_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.184 — Non-globular alpha+beta subunits of globular proteins |
| 超家族 Superfamily superfamily | d.184.1 — Non-globular alpha+beta subunits of globular proteins |
| 家族 Family family | d.184.1.1 — Phycoerythrin 545 alpha-subunits |
| 结构域编号 domain_id | d1xf6b_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.184 — Non-globular alpha+beta subunits of globular proteins |
| 超家族 Superfamily superfamily | d.184.1 — Non-globular alpha+beta subunits of globular proteins |
| 家族 Family family | d.184.1.1 — Phycoerythrin 545 alpha-subunits |
| 结构域编号 domain_id | d1xf6c_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.1 — Globin-like |
| 超家族 Superfamily superfamily | a.1.1 — Globin-like |
| 家族 Family family | a.1.1.3 — Phycocyanin-like phycobilisome proteins |
| 结构域编号 domain_id | d1xf6d_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.1 — Globin-like |
| 超家族 Superfamily superfamily | a.1.1 — Globin-like |
| 家族 Family family | a.1.1.3 — Phycocyanin-like phycobilisome proteins |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1xf6A00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 510 — Cryptophytan Phycoerythrin (Alpha-1 Chain); Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Phycoerythrin alpha chain |
| 结构域编号 domain_id | 1xf6B00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 510 — Cryptophytan Phycoerythrin (Alpha-1 Chain); Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Phycoerythrin alpha chain |
| 结构域编号 domain_id | 1xf6C00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 490 — Globin-like |
| 同源超家族 H-superfamily homologous superfamily | 20 — Phycocyanins |
| 结构域编号 domain_id | 1xf6D00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 490 — Globin-like |
| 同源超家族 H-superfamily homologous superfamily | 20 — Phycocyanins |