1sij
Crystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MOP) of Desulfovibrio gigas covalently bound to [AsO3]-
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 | 1sij |
| 沉积日期 deposition_date | 2004-03-01 |
| 结构标题 title | Crystal structure of the Aldehyde Dehydrogenase (a.k.a. AOR or MOP) of Desulfovibrio gigas covalently bound to [AsO3]- |
| 关键词 keywords | Aldehyde Oxidoreductase; Xanthine Oxidase family; Arsenite Inhibition, 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 | 27.77 Å |
| 回转半径 Rg (电子) rg_electron | 26.98 Å |
| 零角强度 I(0) i0 | 160968000.00 |
| 分子量 molecular_weight | 98473.0 kDa |
| 排除体积 excluded_volume | 122220 ų |
| 包络体积 envelope_volume | 140250 ų |
| 水化壳体积 shell_volume | 41051 ų |
| 包络直径 envelope_diameter | 92.0 Å |
| 壳层 Rg shell_rg | 36.18 Å |
| 包络 Rg envelope_rg | 27.59 Å |
| 形状 Rg shape_rg | 27.00 Å |
| 总 Rg total_rg | 27.76 Å |
| 总原子数 total_atoms | 6878 |
| 残基数 n_residues | 907 |
| 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 | 86.8 Å |
| Rg (实空间) rg_real | 27.60 Å |
| Rg 误差 (实空间) rg_real_error | 0.38 Å |
| I(0) (实空间) i0_real | 1.6100e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.2640e+06 |
| Rg (倒空间) rg_reciprocal | 27.66 Å |
| I(0) (倒空间) i0_reciprocal | 161000000.0000 |
| 解质量估计 total_estimate | 0.9009 |
| 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 | 35.0 Å |
| 偏度 Skewness skewness | 0.182 |
| 峰度 Kurtosis kurtosis | -0.450 |
| 角度范围 angular_range | — – 0.2850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 49180000.0000 |
| 实空间数据点数 n_real_points | 58 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.992 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (7)
6. 折叠分类 (SCOP + CATH) 11 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1sija1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.56 — CO dehydrogenase ISP C-domain like |
| 超家族 Superfamily superfamily | a.56.1 — CO dehydrogenase ISP C-domain like |
| 家族 Family family | a.56.1.1 — CO dehydrogenase ISP C-domain like |
| 结构域编号 domain_id | d1sija2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.4 — 2Fe-2S ferredoxin-like |
| 家族 Family family | d.15.4.2 — 2Fe-2S ferredoxin domains from multidomain proteins |
| 结构域编号 domain_id | d1sija3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.41 — alpha/beta-Hammerhead |
| 超家族 Superfamily superfamily | d.41.1 — CO dehydrogenase molybdoprotein N-domain-like |
| 家族 Family family | d.41.1.1 — CO dehydrogenase molybdoprotein N-domain-like |
| 结构域编号 domain_id | d1sija4 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.133 — Molybdenum cofactor-binding domain |
| 超家族 Superfamily superfamily | d.133.1 — Molybdenum cofactor-binding domain |
| 家族 Family family | d.133.1.1 — Molybdenum cofactor-binding domain |
CATH v4.4 (7 domains)
| 结构域编号 domain_id | 1sijA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 30 — Beta-grasp domain |
| 结构域编号 domain_id | 1sijA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 120 — [2Fe-2S]-binding domain |
| 结构域编号 domain_id | 1sijA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1170 — Aldehyde Oxidoreductase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 50 — Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead |
| 结构域编号 domain_id | 1sijA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 365 — Aldehyde Oxidoreductase; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain |
| 结构域编号 domain_id | 1sijA05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 365 — Aldehyde Oxidoreductase; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain |
| 结构域编号 domain_id | 1sijA06 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 365 — Aldehyde Oxidoreductase; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain |
| 结构域编号 domain_id | 1sijA07 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 365 — Aldehyde Oxidoreductase; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain |