1qyb
;X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures ;
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 | 1qyb |
| 沉积日期 deposition_date | 2003-09-10 |
| 结构标题 title | ;X-ray crystal structure of Desulfovibrio vulgaris rubrerythrin with zinc substituted into the [Fe(SCys)4] site and alternative diiron site structures ; |
| 关键词 keywords | Rubrerythrin, zinc-substituted, diiron four-helix bundle, rubredoxin-like, ELECTRON TRANSPORT; ELECTRON TRANSPORT |
| 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 | 20.05 Å |
| 回转半径 Rg (电子) rg_electron | 19.69 Å |
| 零角强度 I(0) i0 | 9168140.00 |
| 分子量 molecular_weight | 21683.0 kDa |
| 排除体积 excluded_volume | 26739 ų |
| 包络体积 envelope_volume | 32235 ų |
| 水化壳体积 shell_volume | 14905 ų |
| 包络直径 envelope_diameter | 66.3 Å |
| 壳层 Rg shell_rg | 24.17 Å |
| 包络 Rg envelope_rg | 19.93 Å |
| 形状 Rg shape_rg | 19.64 Å |
| 总 Rg total_rg | 20.50 Å |
| 总原子数 total_atoms | 1522 |
| 残基数 n_residues | 190 |
| 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 | 66.9 Å |
| Rg (实空间) rg_real | 20.21 Å |
| Rg 误差 (实空间) rg_real_error | 0.52 Å |
| I(0) (实空间) i0_real | 9.1680e+06 |
| I(0) 误差 (实空间) i0_real_error | 1.2130e+05 |
| Rg (倒空间) rg_reciprocal | 20.18 Å |
| I(0) (倒空间) i0_reciprocal | 9168000.0000 |
| 解质量估计 total_estimate | 0.8610 |
| 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 | 20.1 Å |
| 偏度 Skewness skewness | 0.539 |
| 峰度 Kurtosis kurtosis | -0.266 |
| 角度范围 angular_range | — – 0.3950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 1224000.0000 |
| 实空间数据点数 n_real_points | 71 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.868; Smooth: 0.921 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1qyba1 |
| 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.25.1.1 — Ferritin |
| 结构域编号 domain_id | d1qyba2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.41 — Rubredoxin-like |
| 超家族 Superfamily superfamily | g.41.5 — Rubredoxin-like |
| 家族 Family family | g.41.5.1 — Rubredoxin |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1qybA01 |
| 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 | 1qybA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 20 — Single Sheet |
| 拓扑 Topology topology | 28 — Rubrerythrin, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |