1frv
CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE
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 | 1frv |
| 沉积日期 deposition_date | 1996-03-28 |
| 结构标题 title | CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE |
| 关键词 keywords | NI-FE HYDROGENASE, OXIDOREDUCTASE; OXIDOREDUCTASE |
| 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 | 38.04 Å |
| 回转半径 Rg (电子) rg_electron | 38.10 Å |
| 零角强度 I(0) i0 | 472207000.00 |
| 分子量 molecular_weight | 175700.0 kDa |
| 排除体积 excluded_volume | 218510 ų |
| 包络体积 envelope_volume | 258290 ų |
| 水化壳体积 shell_volume | 55713 ų |
| 包络直径 envelope_diameter | 127.6 Å |
| 壳层 Rg shell_rg | 44.65 Å |
| 包络 Rg envelope_rg | 37.84 Å |
| 形状 Rg shape_rg | 38.21 Å |
| 总 Rg total_rg | 38.08 Å |
| 总原子数 total_atoms | 12268 |
| 残基数 n_residues | 1584 |
| 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 | 125.7 Å |
| Rg (实空间) rg_real | 38.18 Å |
| Rg 误差 (实空间) rg_real_error | 0.91 Å |
| I(0) (实空间) i0_real | 4.7220e+08 |
| I(0) 误差 (实空间) i0_real_error | 7.6310e+06 |
| Rg (倒空间) rg_reciprocal | 38.10 Å |
| I(0) (倒空间) i0_reciprocal | 472200000.0000 |
| 解质量估计 total_estimate | 0.8682 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 35.9 Å |
| 偏度 Skewness skewness | 0.390 |
| 峰度 Kurtosis kurtosis | -0.568 |
| 角度范围 angular_range | — – 0.2100 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 173300000.0000 |
| 实空间数据点数 n_real_points | 43 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.819; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.849 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 10 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1frva_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.19 — HydA/Nqo6-like |
| 超家族 Superfamily superfamily | e.19.1 — HydA/Nqo6-like |
| 家族 Family family | e.19.1.1 — Nickel-iron hydrogenase, small subunit |
| 结构域编号 domain_id | d1frvb_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.18 — HydB/Nqo4-like |
| 超家族 Superfamily superfamily | e.18.1 — HydB/Nqo4-like |
| 家族 Family family | e.18.1.1 — Nickel-iron hydrogenase, large subunit |
| 结构域编号 domain_id | d1frvc_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.19 — HydA/Nqo6-like |
| 超家族 Superfamily superfamily | e.19.1 — HydA/Nqo6-like |
| 家族 Family family | e.19.1.1 — Nickel-iron hydrogenase, small subunit |
| 结构域编号 domain_id | d1frvd_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.18 — HydB/Nqo4-like |
| 超家族 Superfamily superfamily | e.18.1 — HydB/Nqo4-like |
| 家族 Family family | e.18.1.1 — Nickel-iron hydrogenase, large subunit |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1frvA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit |
| 结构域编号 domain_id | 1frvA02 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome-c3 hydrogenase, C-terminal domain |
| 结构域编号 domain_id | 1frvB00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 645 — Cytochrome-c3 Hydrogenase; chain B |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome-c3 Hydrogenase, chain B |
| 结构域编号 domain_id | 1frvC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 700 — NADH:ubiquinone oxidoreductase-like, 20kDa subunit |
| 结构域编号 domain_id | 1frvC02 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 480 — Cytochrome-c3 Hydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome-c3 hydrogenase, C-terminal domain |
| 结构域编号 domain_id | 1frvD00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 645 — Cytochrome-c3 Hydrogenase; chain B |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cytochrome-c3 Hydrogenase, chain B |