9ldt
DESIGN AND SYNTHESIS OF NEW ENZYMES BASED ON THE LACTATE DEHYDROGENASE FRAMEWORK
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 | 9ldt |
| 沉积日期 deposition_date | 1991-11-26 |
| 结构标题 title | DESIGN AND SYNTHESIS OF NEW ENZYMES BASED ON THE LACTATE DEHYDROGENASE FRAMEWORK |
| 关键词 keywords | OXIDOREDUCTASE(CHOH(D)-NAD+(A)); OXIDOREDUCTASE(CHOH(D)-NAD+(A)) |
| 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 | 27.58 Å |
| 回转半径 Rg (电子) rg_electron | 26.91 Å |
| 零角强度 I(0) i0 | 88648400.00 |
| 分子量 molecular_weight | 74762.0 kDa |
| 排除体积 excluded_volume | 94098 ų |
| 包络体积 envelope_volume | 112980 ų |
| 水化壳体积 shell_volume | 34438 ų |
| 包络直径 envelope_diameter | 91.0 Å |
| 壳层 Rg shell_rg | 34.74 Å |
| 包络 Rg envelope_rg | 27.24 Å |
| 形状 Rg shape_rg | 26.94 Å |
| 总 Rg total_rg | 27.57 Å |
| 总原子数 total_atoms | 5246 |
| 残基数 n_residues | 652 |
| 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 | 89.9 Å |
| Rg (实空间) rg_real | 28.20 Å |
| Rg 误差 (实空间) rg_real_error | 0.21 Å |
| I(0) (实空间) i0_real | 8.7670e+07 |
| I(0) 误差 (实空间) i0_real_error | 9.4950e+05 |
| Rg (倒空间) rg_reciprocal | 27.55 Å |
| I(0) (倒空间) i0_reciprocal | 88650000.0000 |
| 解质量估计 total_estimate | 0.6986 |
| 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 | 31.0 Å |
| 偏度 Skewness skewness | 0.400 |
| 峰度 Kurtosis kurtosis | -0.279 |
| 角度范围 angular_range | — – 0.2900 Å−1 |
| 当前正则化参数 α current_alpha | 4.8480 |
| 最高正则化参数 α highest_alpha | 28620000.0000 |
| 实空间数据点数 n_real_points | 59 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.902; Stabil: 0.918; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.657 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d9ldta1 |
| 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.2.1.5 — LDH N-terminal domain-like |
| 结构域编号 domain_id | d9ldta2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.162 — LDH C-terminal domain-like |
| 超家族 Superfamily superfamily | d.162.1 — LDH C-terminal domain-like |
| 家族 Family family | d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain |
| 结构域编号 domain_id | d9ldtb1 |
| 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.2.1.5 — LDH N-terminal domain-like |
| 结构域编号 domain_id | d9ldtb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.162 — LDH C-terminal domain-like |
| 超家族 Superfamily superfamily | d.162.1 — LDH C-terminal domain-like |
| 家族 Family family | d.162.1.1 — Lactate & malate dehydrogenases, C-terminal domain |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 9ldtA01 |
| 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 | 9ldtA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal |
| 结构域编号 domain_id | 9ldtB01 |
| 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 | 9ldtB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 110 — L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal |