2bvf
Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 3 (P1)
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 | 2bvf |
| 沉积日期 deposition_date | 2005-06-28 |
| 结构标题 title | Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans. Crystal Form 3 (P1) |
| 关键词 keywords | AUTOFLAVINYLATION, ENANTIOMERIC SUBSTRATES, FLAVOENZYMES, NICOTINE DEGRADATION, OXIDASE; OXIDASE |
| 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 | 37.33 Å |
| 回转半径 Rg (电子) rg_electron | 37.94 Å |
| 零角强度 I(0) i0 | 153509000.00 |
| 分子量 molecular_weight | 98142.0 kDa |
| 排除体积 excluded_volume | 121800 ų |
| 包络体积 envelope_volume | 153270 ų |
| 水化壳体积 shell_volume | 35457 ų |
| 包络直径 envelope_diameter | 133.9 Å |
| 壳层 Rg shell_rg | 41.37 Å |
| 包络 Rg envelope_rg | 37.97 Å |
| 形状 Rg shape_rg | 37.91 Å |
| 总 Rg total_rg | 38.23 Å |
| 总原子数 total_atoms | 6904 |
| 残基数 n_residues | 906 |
| 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 | 37.84 Å |
| Rg 误差 (实空间) rg_real_error | 1.33 Å |
| I(0) (实空间) i0_real | 1.5350e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.7370e+06 |
| Rg (倒空间) rg_reciprocal | 37.53 Å |
| I(0) (倒空间) i0_reciprocal | 153500000.0000 |
| 解质量估计 total_estimate | 0.7548 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 29.9 Å |
| 偏度 Skewness skewness | 0.534 |
| 峰度 Kurtosis kurtosis | -0.547 |
| 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 | 41280000.0000 |
| 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: 0.560; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.650; Smooth: 0.480 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 10 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2bvfa1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.145 — FAD-binding/transporter-associated domain-like |
| 超家族 Superfamily superfamily | d.145.1 — FAD-binding/transporter-associated domain-like |
| 家族 Family family | d.145.1.1 — FAD-linked oxidases, N-terminal domain |
| 结构域编号 domain_id | d2bvfa2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.32 — FAD-linked oxidases, C-terminal domain |
| 家族 Family family | d.58.32.5 — 6-hydroxy-d-nicotine oxidase |
| 结构域编号 domain_id | d2bvfb1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.145 — FAD-binding/transporter-associated domain-like |
| 超家族 Superfamily superfamily | d.145.1 — FAD-binding/transporter-associated domain-like |
| 家族 Family family | d.145.1.1 — FAD-linked oxidases, N-terminal domain |
| 结构域编号 domain_id | d2bvfb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.32 — FAD-linked oxidases, C-terminal domain |
| 家族 Family family | d.58.32.5 — 6-hydroxy-d-nicotine oxidase |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2bvfA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 |
| 结构域编号 domain_id | 2bvfA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 2bvfA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 462 — Vanillyl-alcohol Oxidase; Chain A, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2bvfB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 |
| 结构域编号 domain_id | 2bvfB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 2bvfB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 462 — Vanillyl-alcohol Oxidase; Chain A, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 20 — |