1l1f
Structure of human glutamate dehydrogenase-apo form
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 | 1l1f |
| 沉积日期 deposition_date | 2002-02-15 |
| 结构标题 title | Structure of human glutamate dehydrogenase-apo form |
| 关键词 keywords | Allostery, negative cooperativity, 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 | 43.78 Å |
| 回转半径 Rg (电子) rg_electron | 43.41 Å |
| 零角强度 I(0) i0 | 1597000000.00 |
| 分子量 molecular_weight | 330220.0 kDa |
| 排除体积 excluded_volume | 412880 ų |
| 包络体积 envelope_volume | 520320 ų |
| 水化壳体积 shell_volume | 94716 ų |
| 包络直径 envelope_diameter | 149.8 Å |
| 壳层 Rg shell_rg | 51.39 Å |
| 包络 Rg envelope_rg | 43.30 Å |
| 形状 Rg shape_rg | 43.40 Å |
| 总 Rg total_rg | 43.78 Å |
| 总原子数 total_atoms | 23244 |
| 残基数 n_residues | 2976 |
| 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 | 137.2 Å |
| Rg (实空间) rg_real | 43.99 Å |
| Rg 误差 (实空间) rg_real_error | 0.38 Å |
| I(0) (实空间) i0_real | 1.5570e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.3910e+07 |
| Rg (倒空间) rg_reciprocal | 43.77 Å |
| I(0) (倒空间) i0_reciprocal | 1597000000.0000 |
| 解质量估计 total_estimate | 0.7066 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 53.4 Å |
| 偏度 Skewness skewness | 0.288 |
| 峰度 Kurtosis kurtosis | -0.251 |
| 角度范围 angular_range | — – 0.1800 Å−1 |
| 当前正则化参数 α current_alpha | 2.2080 |
| 最高正则化参数 α highest_alpha | 303400000.0000 |
| 实空间数据点数 n_real_points | 37 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.894; Stabil: 0.926; Sysdev: 0.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.757 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (1)
6. 折叠分类 (SCOP + CATH) 30 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1l1fa1 |
| 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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d1l1fa2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.58 — Aminoacid dehydrogenase-like, N-terminal domain |
| 超家族 Superfamily superfamily | c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain |
| 家族 Family family | c.58.1.1 — Aminoacid dehydrogenases |
| 结构域编号 domain_id | d1l1fb1 |
| 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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d1l1fb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.58 — Aminoacid dehydrogenase-like, N-terminal domain |
| 超家族 Superfamily superfamily | c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain |
| 家族 Family family | c.58.1.1 — Aminoacid dehydrogenases |
| 结构域编号 domain_id | d1l1fc1 |
| 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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d1l1fc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.58 — Aminoacid dehydrogenase-like, N-terminal domain |
| 超家族 Superfamily superfamily | c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain |
| 家族 Family family | c.58.1.1 — Aminoacid dehydrogenases |
| 结构域编号 domain_id | d1l1fd1 |
| 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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d1l1fd2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.58 — Aminoacid dehydrogenase-like, N-terminal domain |
| 超家族 Superfamily superfamily | c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain |
| 家族 Family family | c.58.1.1 — Aminoacid dehydrogenases |
| 结构域编号 domain_id | d1l1fe1 |
| 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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d1l1fe2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.58 — Aminoacid dehydrogenase-like, N-terminal domain |
| 超家族 Superfamily superfamily | c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain |
| 家族 Family family | c.58.1.1 — Aminoacid dehydrogenases |
| 结构域编号 domain_id | d1l1ff1 |
| 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.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain |
| 结构域编号 domain_id | d1l1ff2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.58 — Aminoacid dehydrogenase-like, N-terminal domain |
| 超家族 Superfamily superfamily | c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain |
| 家族 Family family | c.58.1.1 — Aminoacid dehydrogenases |
CATH v4.4 (18 domains)
| 结构域编号 domain_id | 1l1fA01 |
| 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 | 10860 — Leucine Dehydrogenase, chain A, domain 1 |
| 结构域编号 domain_id | 1l1fA02 |
| 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 | 1l1fA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 140 — |
| 结构域编号 domain_id | 1l1fB01 |
| 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 | 10860 — Leucine Dehydrogenase, chain A, domain 1 |
| 结构域编号 domain_id | 1l1fB02 |
| 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 | 1l1fB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 140 — |
| 结构域编号 domain_id | 1l1fC01 |
| 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 | 10860 — Leucine Dehydrogenase, chain A, domain 1 |
| 结构域编号 domain_id | 1l1fC02 |
| 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 | 1l1fC03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 140 — |
| 结构域编号 domain_id | 1l1fD01 |
| 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 | 10860 — Leucine Dehydrogenase, chain A, domain 1 |
| 结构域编号 domain_id | 1l1fD02 |
| 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 | 1l1fD03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 140 — |
| 结构域编号 domain_id | 1l1fE01 |
| 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 | 10860 — Leucine Dehydrogenase, chain A, domain 1 |
| 结构域编号 domain_id | 1l1fE02 |
| 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 | 1l1fE03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 140 — |
| 结构域编号 domain_id | 1l1fF01 |
| 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 | 10860 — Leucine Dehydrogenase, chain A, domain 1 |
| 结构域编号 domain_id | 1l1fF02 |
| 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 | 1l1fF03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 140 — |