2ger
Crystal Structure and Oxidative Mechanism of Human Pyrroline-5-carboxylate Reductase
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 | 2ger |
| 沉积日期 deposition_date | 2006-03-20 |
| 结构标题 title | Crystal Structure and Oxidative Mechanism of Human Pyrroline-5-carboxylate Reductase |
| 关键词 keywords | Oxidative Mechanism of Human Pyrroline-5-carboxylate, 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 | 40.06 Å |
| 回转半径 Rg (电子) rg_electron | 39.30 Å |
| 零角强度 I(0) i0 | 324518000.00 |
| 分子量 molecular_weight | 145190.0 kDa |
| 排除体积 excluded_volume | 181920 ų |
| 包络体积 envelope_volume | 283450 ų |
| 水化壳体积 shell_volume | 59594 ų |
| 包络直径 envelope_diameter | 117.3 Å |
| 壳层 Rg shell_rg | 46.59 Å |
| 包络 Rg envelope_rg | 36.95 Å |
| 形状 Rg shape_rg | 39.30 Å |
| 总 Rg total_rg | 39.80 Å |
| 总原子数 total_atoms | 10171 |
| 残基数 n_residues | 1383 |
| 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 | 116.1 Å |
| Rg (实空间) rg_real | 39.82 Å |
| Rg 误差 (实空间) rg_real_error | 0.63 Å |
| I(0) (实空间) i0_real | 3.2450e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.3340e+06 |
| Rg (倒空间) rg_reciprocal | 40.06 Å |
| I(0) (倒空间) i0_reciprocal | 324600000.0000 |
| 解质量估计 total_estimate | 0.6906 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 53.6 Å |
| 偏度 Skewness skewness | -0.018 |
| 峰度 Kurtosis kurtosis | -0.637 |
| 角度范围 angular_range | — – 0.1950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 22400000.0000 |
| 实空间数据点数 n_real_points | 40 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 0.107; Positv: 1.000; Valcen: 0.975; Smooth: 0.739 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 25 domains
SCOP 2.08 (15 domains)
| 结构域编号 domain_id | d2gera1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.0 — automated matches |
| 结构域编号 domain_id | d2gera2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 超家族 Superfamily superfamily | a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 家族 Family family | a.100.1.0 — automated matches |
| 结构域编号 domain_id | d2gera3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2gerb1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.0 — automated matches |
| 结构域编号 domain_id | d2gerb2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 超家族 Superfamily superfamily | a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 家族 Family family | a.100.1.0 — automated matches |
| 结构域编号 domain_id | d2gerb3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2gerc1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.0 — automated matches |
| 结构域编号 domain_id | d2gerc2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 超家族 Superfamily superfamily | a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 家族 Family family | a.100.1.0 — automated matches |
| 结构域编号 domain_id | d2gerc3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2gerd1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.0 — automated matches |
| 结构域编号 domain_id | d2gerd2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 超家族 Superfamily superfamily | a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 家族 Family family | a.100.1.0 — automated matches |
| 结构域编号 domain_id | d2gerd3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2gere1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.0 — automated matches |
| 结构域编号 domain_id | d2gere2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 超家族 Superfamily superfamily | a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like |
| 家族 Family family | a.100.1.0 — automated matches |
| 结构域编号 domain_id | d2gere3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (10 domains)
| 结构域编号 domain_id | 2gerA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 2gerA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3730 — ProC C-terminal domain-like fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — ProC C-terminal domain-like |
| 结构域编号 domain_id | 2gerB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 2gerB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3730 — ProC C-terminal domain-like fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — ProC C-terminal domain-like |
| 结构域编号 domain_id | 2gerC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 2gerC02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3730 — ProC C-terminal domain-like fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — ProC C-terminal domain-like |
| 结构域编号 domain_id | 2gerD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 2gerD02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3730 — ProC C-terminal domain-like fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — ProC C-terminal domain-like |
| 结构域编号 domain_id | 2gerE01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 2gerE02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3730 — ProC C-terminal domain-like fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — ProC C-terminal domain-like |