1vzi
Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray induced photoreduction
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 | 1vzi |
| 沉积日期 deposition_date | 2004-05-19 |
| 结构标题 title | Structure of superoxide reductase bound to ferrocyanide and active site expansion upon X-ray induced photoreduction |
| 关键词 keywords | FERROCYANIDE, MICROSPECTROPHOTOMETRY, REDOX STATES, PHOTOREDUCTION, DINUCLEAR IRON CLUSTER, OXIDOREDUCTASE, ELECTRON TRANSPORT; 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 | 18.90 Å |
| 回转半径 Rg (电子) rg_electron | 17.87 Å |
| 零角强度 I(0) i0 | 14503800.00 |
| 分子量 molecular_weight | 28374.0 kDa |
| 排除体积 excluded_volume | 35352 ų |
| 包络体积 envelope_volume | 39965 ų |
| 水化壳体积 shell_volume | 18491 ų |
| 包络直径 envelope_diameter | 57.8 Å |
| 壳层 Rg shell_rg | 24.24 Å |
| 包络 Rg envelope_rg | 18.16 Å |
| 形状 Rg shape_rg | 17.82 Å |
| 总 Rg total_rg | 18.94 Å |
| 总原子数 total_atoms | 1966 |
| 残基数 n_residues | 250 |
| 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 | 58.0 Å |
| Rg (实空间) rg_real | 18.79 Å |
| Rg 误差 (实空间) rg_real_error | 0.24 Å |
| I(0) (实空间) i0_real | 1.4500e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.6880e+05 |
| Rg (倒空间) rg_reciprocal | 18.81 Å |
| I(0) (倒空间) i0_reciprocal | 14500000.0000 |
| 解质量估计 total_estimate | 0.7640 |
| 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 | 57.2 Å |
| 偏度 Skewness skewness | 0.138 |
| 峰度 Kurtosis kurtosis | -0.518 |
| 角度范围 angular_range | — – 0.4200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 3143000.0000 |
| 实空间数据点数 n_real_points | 73 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 0.374; Positv: 1.000; Valcen: 0.995; Smooth: 0.983 |
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) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1vzia1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.13 — Superoxide reductase-like |
| 家族 Family family | b.1.13.1 — Superoxide reductase-like |
| 结构域编号 domain_id | d1vzia2 |
| 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.41.5.2 — Desulforedoxin |
| 结构域编号 domain_id | d1vzib1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.13 — Superoxide reductase-like |
| 家族 Family family | b.1.13.1 — Superoxide reductase-like |
| 结构域编号 domain_id | d1vzib2 |
| 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.41.5.2 — Desulforedoxin |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1vziA01 |
| 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 | 100 — Desulphoferrodoxin, N-terminal domain |
| 结构域编号 domain_id | 1vziA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 730 — SOR catalytic domain |
| 结构域编号 domain_id | 1vziB01 |
| 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 | 100 — Desulphoferrodoxin, N-terminal domain |
| 结构域编号 domain_id | 1vziB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 730 — SOR catalytic domain |