2d5k
Crystal structure of Dps from Staphylococcus aureus
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 | 2d5k |
| 沉积日期 deposition_date | 2005-11-02 |
| 结构标题 title | Crystal structure of Dps from Staphylococcus aureus |
| 关键词 keywords | FOUR HELIX BUNDLE, METAL BINDING PROTEIN; METAL BINDING 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 | 29.69 Å |
| 回转半径 Rg (电子) rg_electron | 28.82 Å |
| 零角强度 I(0) i0 | 73994300.00 |
| 分子量 molecular_weight | 67005.0 kDa |
| 排除体积 excluded_volume | 83262 ų |
| 包络体积 envelope_volume | 103960 ų |
| 水化壳体积 shell_volume | 29860 ų |
| 包络直径 envelope_diameter | 99.0 Å |
| 壳层 Rg shell_rg | 36.37 Å |
| 包络 Rg envelope_rg | 28.64 Å |
| 形状 Rg shape_rg | 28.79 Å |
| 总 Rg total_rg | 29.62 Å |
| 总原子数 total_atoms | 4725 |
| 残基数 n_residues | 591 |
| 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 | 94.4 Å |
| Rg (实空间) rg_real | 29.70 Å |
| Rg 误差 (实空间) rg_real_error | 0.70 Å |
| I(0) (实空间) i0_real | 7.3990e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.0510e+06 |
| Rg (倒空间) rg_reciprocal | 29.70 Å |
| I(0) (倒空间) i0_reciprocal | 73990000.0000 |
| 解质量估计 total_estimate | 0.9025 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 30.3 Å |
| 偏度 Skewness skewness | 0.250 |
| 峰度 Kurtosis kurtosis | -0.687 |
| 角度范围 angular_range | — – 0.2650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 19430000.0000 |
| 实空间数据点数 n_real_points | 54 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.938 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 13 domains
SCOP 2.08 (9 domains)
| 结构域编号 domain_id | d2d5ka1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.25 — Ferritin-like |
| 超家族 Superfamily superfamily | a.25.1 — Ferritin-like |
| 家族 Family family | a.25.1.0 — automated matches |
| 结构域编号 domain_id | d2d5ka2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2d5kb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.25 — Ferritin-like |
| 超家族 Superfamily superfamily | a.25.1 — Ferritin-like |
| 家族 Family family | a.25.1.0 — automated matches |
| 结构域编号 domain_id | d2d5kb2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2d5kb3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2d5kc1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.25 — Ferritin-like |
| 超家族 Superfamily superfamily | a.25.1 — Ferritin-like |
| 家族 Family family | a.25.1.0 — automated matches |
| 结构域编号 domain_id | d2d5kc2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2d5kd1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.25 — Ferritin-like |
| 超家族 Superfamily superfamily | a.25.1 — Ferritin-like |
| 家族 Family family | a.25.1.0 — automated matches |
| 结构域编号 domain_id | d2d5kd2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2d5kA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1260 — Ferritin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ferritin, core subunit, four-helix bundle |
| 结构域编号 domain_id | 2d5kB00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1260 — Ferritin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ferritin, core subunit, four-helix bundle |
| 结构域编号 domain_id | 2d5kC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1260 — Ferritin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ferritin, core subunit, four-helix bundle |
| 结构域编号 domain_id | 2d5kD00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1260 — Ferritin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ferritin, core subunit, four-helix bundle |