1pby
;Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution ;
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 | 1pby |
| 沉积日期 deposition_date | 2003-05-15 |
| 结构标题 title | ;Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution ; |
| 关键词 keywords | QUINOHEMOPROTEIN, AMINE DEHYDROGENASE, 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 | 31.05 Å |
| 回转半径 Rg (电子) rg_electron | 30.45 Å |
| 零角强度 I(0) i0 | 162571000.00 |
| 分子量 molecular_weight | 99985.0 kDa |
| 排除体积 excluded_volume | 124310 ų |
| 包络体积 envelope_volume | 151180 ų |
| 水化壳体积 shell_volume | 41231 ų |
| 包络直径 envelope_diameter | 108.3 Å |
| 壳层 Rg shell_rg | 37.81 Å |
| 包络 Rg envelope_rg | 30.71 Å |
| 形状 Rg shape_rg | 30.43 Å |
| 总 Rg total_rg | 31.10 Å |
| 总原子数 total_atoms | 7037 |
| 残基数 n_residues | 904 |
| 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 | 101.7 Å |
| Rg (实空间) rg_real | 31.09 Å |
| Rg 误差 (实空间) rg_real_error | 0.74 Å |
| I(0) (实空间) i0_real | 1.6260e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.5050e+06 |
| Rg (倒空间) rg_reciprocal | 31.07 Å |
| I(0) (倒空间) i0_reciprocal | 162600000.0000 |
| 解质量估计 total_estimate | 0.8650 |
| 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 | 35.9 Å |
| 偏度 Skewness skewness | 0.423 |
| 峰度 Kurtosis kurtosis | -0.223 |
| 角度范围 angular_range | — – 0.2550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 38050000.0000 |
| 实空间数据点数 n_real_points | 52 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.861; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.673 |
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) 12 domains
SCOP 2.08 (7 domains)
| 结构域编号 domain_id | d1pbya1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.3 — Cytochrome c |
| 超家族 Superfamily superfamily | a.3.1 — Cytochrome c |
| 家族 Family family | a.3.1.7 — Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 |
| 结构域编号 domain_id | d1pbya2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.3 — Cytochrome c |
| 超家族 Superfamily superfamily | a.3.1 — Cytochrome c |
| 家族 Family family | a.3.1.7 — Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2 |
| 结构域编号 domain_id | d1pbya3 |
| 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.1.18 — E set domains |
| 家族 Family family | b.1.18.14 — Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5 |
| 结构域编号 domain_id | d1pbya4 |
| 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.1.18 — E set domains |
| 家族 Family family | b.1.18.14 — Quinohemoprotein amine dehydrogenase A chain, domains 4 and 5 |
| 结构域编号 domain_id | d1pbya5 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.61 — Streptavidin-like |
| 超家族 Superfamily superfamily | b.61.4 — Quinohemoprotein amine dehydrogenase A chain, domain 3 |
| 家族 Family family | b.61.4.1 — Quinohemoprotein amine dehydrogenase A chain, domain 3 |
| 结构域编号 domain_id | d1pbyb_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.69 — 7-bladed beta-propeller |
| 超家族 Superfamily superfamily | b.69.2 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 家族 Family family | b.69.2.2 — Quinohemoprotein amine dehydrogenase B chain |
| 结构域编号 domain_id | d1pbyc_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.137 — Non-globular all-alpha subunits of globular proteins |
| 超家族 Superfamily superfamily | a.137.9 — Quinohemoprotein amine dehydrogenase C chain |
| 家族 Family family | a.137.9.1 — Quinohemoprotein amine dehydrogenase C chain |
CATH v4.4 (5 domains)
| 结构域编号 domain_id | 1pbyA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 128 — Lipocalin |
| 同源超家族 H-superfamily homologous superfamily | 120 — Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 |
| 结构域编号 domain_id | 1pbyA03 |
| 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 | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1pbyA04 |
| 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 | 10 — Immunoglobulins |
| 结构域编号 domain_id | 1pbyB00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 130 — 7 Propeller |
| 拓扑 Topology topology | 10 — Methylamine Dehydrogenase; Chain H |
| 同源超家族 H-superfamily homologous superfamily | 10 — YVTN repeat-like/Quinoprotein amine dehydrogenase |
| 结构域编号 domain_id | 1pbyC00 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 940 — Quinohemoprotein amine dehydrogenase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Quinohemoprotein amine dehydrogenase, gamma subunit structural domain |