2c12
Crystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor
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 | 2c12 |
| 沉积日期 deposition_date | 2005-09-10 |
| 结构标题 title | Crystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor |
| 关键词 keywords | OXIDOREDUCTASE, FLAVOENZYME, NITROALKANE, ACYL-COA DEHYDROGENASE, LONG CELL EDGE, FAD, INHIBITOR, FLAVOPROTEIN; 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 | 52.36 Å |
| 回转半径 Rg (电子) rg_electron | 52.84 Å |
| 零角强度 I(0) i0 | 1214290000.00 |
| 分子量 molecular_weight | 290170.0 kDa |
| 排除体积 excluded_volume | 363340 ų |
| 包络体积 envelope_volume | 470520 ų |
| 水化壳体积 shell_volume | 77494 ų |
| 包络直径 envelope_diameter | 186.9 Å |
| 壳层 Rg shell_rg | 52.05 Å |
| 包络 Rg envelope_rg | 53.11 Å |
| 形状 Rg shape_rg | 52.86 Å |
| 总 Rg total_rg | 52.74 Å |
| 总原子数 total_atoms | 20354 |
| 残基数 n_residues | 2580 |
| 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 | 185.2 Å |
| Rg (实空间) rg_real | 52.81 Å |
| Rg 误差 (实空间) rg_real_error | 1.70 Å |
| I(0) (实空间) i0_real | 1.2140e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.3780e+07 |
| Rg (倒空间) rg_reciprocal | 51.97 Å |
| I(0) (倒空间) i0_reciprocal | 1213000000.0000 |
| 解质量估计 total_estimate | 0.7941 |
| 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 | 49.4 Å |
| 偏度 Skewness skewness | 0.585 |
| 峰度 Kurtosis kurtosis | -0.348 |
| 角度范围 angular_range | — – 0.1500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 91030000.0000 |
| 实空间数据点数 n_real_points | 31 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.619; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.555 |
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) 30 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d2c12a1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.29 — Bromodomain-like |
| 超家族 Superfamily superfamily | a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like |
| 家族 Family family | a.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d2c12a2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.6 — Acyl-CoA dehydrogenase NM domain-like |
| 超家族 Superfamily superfamily | e.6.1 — Acyl-CoA dehydrogenase NM domain-like |
| 家族 Family family | e.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains |
| 结构域编号 domain_id | d2c12b1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.29 — Bromodomain-like |
| 超家族 Superfamily superfamily | a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like |
| 家族 Family family | a.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d2c12b2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.6 — Acyl-CoA dehydrogenase NM domain-like |
| 超家族 Superfamily superfamily | e.6.1 — Acyl-CoA dehydrogenase NM domain-like |
| 家族 Family family | e.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains |
| 结构域编号 domain_id | d2c12c1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.29 — Bromodomain-like |
| 超家族 Superfamily superfamily | a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like |
| 家族 Family family | a.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d2c12c2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.6 — Acyl-CoA dehydrogenase NM domain-like |
| 超家族 Superfamily superfamily | e.6.1 — Acyl-CoA dehydrogenase NM domain-like |
| 家族 Family family | e.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains |
| 结构域编号 domain_id | d2c12d1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.29 — Bromodomain-like |
| 超家族 Superfamily superfamily | a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like |
| 家族 Family family | a.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d2c12d2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.6 — Acyl-CoA dehydrogenase NM domain-like |
| 超家族 Superfamily superfamily | e.6.1 — Acyl-CoA dehydrogenase NM domain-like |
| 家族 Family family | e.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains |
| 结构域编号 domain_id | d2c12e1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.29 — Bromodomain-like |
| 超家族 Superfamily superfamily | a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like |
| 家族 Family family | a.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d2c12e2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.6 — Acyl-CoA dehydrogenase NM domain-like |
| 超家族 Superfamily superfamily | e.6.1 — Acyl-CoA dehydrogenase NM domain-like |
| 家族 Family family | e.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains |
| 结构域编号 domain_id | d2c12f1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.29 — Bromodomain-like |
| 超家族 Superfamily superfamily | a.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like |
| 家族 Family family | a.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d2c12f2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.6 — Acyl-CoA dehydrogenase NM domain-like |
| 超家族 Superfamily superfamily | e.6.1 — Acyl-CoA dehydrogenase NM domain-like |
| 家族 Family family | e.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains |
CATH v4.4 (18 domains)
| 结构域编号 domain_id | 2c12A01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain |
| 结构域编号 domain_id | 2c12A02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2 |
| 结构域编号 domain_id | 2c12A03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3 |
| 结构域编号 domain_id | 2c12B01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain |
| 结构域编号 domain_id | 2c12B02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2 |
| 结构域编号 domain_id | 2c12B03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3 |
| 结构域编号 domain_id | 2c12C01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain |
| 结构域编号 domain_id | 2c12C02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2 |
| 结构域编号 domain_id | 2c12C03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3 |
| 结构域编号 domain_id | 2c12D01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain |
| 结构域编号 domain_id | 2c12D02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2 |
| 结构域编号 domain_id | 2c12D03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3 |
| 结构域编号 domain_id | 2c12E01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain |
| 结构域编号 domain_id | 2c12E02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2 |
| 结构域编号 domain_id | 2c12E03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3 |
| 结构域编号 domain_id | 2c12F01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain |
| 结构域编号 domain_id | 2c12F02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2 |
| 结构域编号 domain_id | 2c12F03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3 |