1i4y
THE CRYSTAL STRUCTURE OF PHASCOLOPSIS GOULDII WILD TYPE METHEMERYTHRIN
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 | 1i4y |
| 沉积日期 deposition_date | 2001-02-23 |
| 结构标题 title | THE CRYSTAL STRUCTURE OF PHASCOLOPSIS GOULDII WILD TYPE METHEMERYTHRIN |
| 关键词 keywords | hemerythrin, oxygen binding, diiron, four-helix bundle, OXYGEN STORAGE-TRANSPORT COMPLEX; OXYGEN STORAGE/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 | 30.00 Å |
| 回转半径 Rg (电子) rg_electron | 29.18 Å |
| 零角强度 I(0) i0 | 183067000.00 |
| 分子量 molecular_weight | 107760.0 kDa |
| 排除体积 excluded_volume | 134220 ų |
| 包络体积 envelope_volume | 162780 ų |
| 水化壳体积 shell_volume | 44521 ų |
| 包络直径 envelope_diameter | 92.8 Å |
| 壳层 Rg shell_rg | 38.17 Å |
| 包络 Rg envelope_rg | 28.58 Å |
| 形状 Rg shape_rg | 29.24 Å |
| 总 Rg total_rg | 29.77 Å |
| 总原子数 total_atoms | 7608 |
| 残基数 n_residues | 904 |
| 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 | 87.8 Å |
| Rg (实空间) rg_real | 29.76 Å |
| Rg 误差 (实空间) rg_real_error | 0.38 Å |
| I(0) (实空间) i0_real | 1.8310e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.4250e+06 |
| Rg (倒空间) rg_reciprocal | 29.87 Å |
| I(0) (倒空间) i0_reciprocal | 183100000.0000 |
| 解质量估计 total_estimate | 0.9012 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 43.1 Å |
| 偏度 Skewness skewness | -0.019 |
| 峰度 Kurtosis kurtosis | -0.545 |
| 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 | 50130000.0000 |
| 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: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.931 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 16 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d1i4ya_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.4 — Hemerythrin-like |
| 家族 Family family | a.24.4.1 — Hemerythrin-like |
| 结构域编号 domain_id | d1i4yb_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.4 — Hemerythrin-like |
| 家族 Family family | a.24.4.1 — Hemerythrin-like |
| 结构域编号 domain_id | d1i4yc_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.4 — Hemerythrin-like |
| 家族 Family family | a.24.4.1 — Hemerythrin-like |
| 结构域编号 domain_id | d1i4yd_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.4 — Hemerythrin-like |
| 家族 Family family | a.24.4.1 — Hemerythrin-like |
| 结构域编号 domain_id | d1i4ye_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.4 — Hemerythrin-like |
| 家族 Family family | a.24.4.1 — Hemerythrin-like |
| 结构域编号 domain_id | d1i4yf_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.4 — Hemerythrin-like |
| 家族 Family family | a.24.4.1 — Hemerythrin-like |
| 结构域编号 domain_id | d1i4yg_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.4 — Hemerythrin-like |
| 家族 Family family | a.24.4.1 — Hemerythrin-like |
| 结构域编号 domain_id | d1i4yh_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.24 — Four-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.24.4 — Hemerythrin-like |
| 家族 Family family | a.24.4.1 — Hemerythrin-like |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1i4yA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hemerythrin-like |
| 结构域编号 domain_id | 1i4yB00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hemerythrin-like |
| 结构域编号 domain_id | 1i4yC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hemerythrin-like |
| 结构域编号 domain_id | 1i4yD00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hemerythrin-like |
| 结构域编号 domain_id | 1i4yE00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hemerythrin-like |
| 结构域编号 domain_id | 1i4yF00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hemerythrin-like |
| 结构域编号 domain_id | 1i4yG00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hemerythrin-like |
| 结构域编号 domain_id | 1i4yH00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 50 — Hemerythrin-like |