1jde
K22A mutant of pyruvate, phosphate dikinase
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 | 1jde |
| 沉积日期 deposition_date | 2001-06-13 |
| 结构标题 title | K22A mutant of pyruvate, phosphate dikinase |
| 关键词 keywords | TRANSFERASE, PHOSPHOTRANSFERASE, KINASE, nucleotide binding site mutant; TRANSFERASE |
| 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 | 32.16 Å |
| 回转半径 Rg (电子) rg_electron | 32.06 Å |
| 零角强度 I(0) i0 | 148770000.00 |
| 分子量 molecular_weight | 96045.0 kDa |
| 排除体积 excluded_volume | 119570 ų |
| 包络体积 envelope_volume | 147600 ų |
| 水化壳体积 shell_volume | 39355 ų |
| 包络直径 envelope_diameter | 110.0 Å |
| 壳层 Rg shell_rg | 38.20 Å |
| 包络 Rg envelope_rg | 31.73 Å |
| 形状 Rg shape_rg | 32.07 Å |
| 总 Rg total_rg | 32.51 Å |
| 总原子数 total_atoms | 6727 |
| 残基数 n_residues | 868 |
| 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 | 107.8 Å |
| Rg (实空间) rg_real | 32.30 Å |
| Rg 误差 (实空间) rg_real_error | 0.73 Å |
| I(0) (实空间) i0_real | 1.4880e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.1030e+06 |
| Rg (倒空间) rg_reciprocal | 32.24 Å |
| I(0) (倒空间) i0_reciprocal | 148800000.0000 |
| 解质量估计 total_estimate | 0.8709 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 35.2 Å |
| 偏度 Skewness skewness | 0.458 |
| 峰度 Kurtosis kurtosis | -0.344 |
| 角度范围 angular_range | — – 0.2450 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 22350000.0000 |
| 实空间数据点数 n_real_points | 50 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.892 |
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) 9 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1jdea1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.2 — Pyruvate phosphate dikinase, C-terminal domain |
| 结构域编号 domain_id | d1jdea2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.8 — The 'swivelling' beta/beta/alpha domain |
| 超家族 Superfamily superfamily | c.8.1 — Phosphohistidine domain |
| 家族 Family family | c.8.1.1 — Pyruvate phosphate dikinase, central domain |
| 结构域编号 domain_id | d1jdea3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.142 — ATP-grasp |
| 超家族 Superfamily superfamily | d.142.1 — Glutathione synthetase ATP-binding domain-like |
| 家族 Family family | d.142.1.5 — Pyruvate phosphate dikinase, N-terminal domain |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1jdeA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP-grasp fold, A domain |
| 结构域编号 domain_id | 1jdeA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 189 — Pyruvate Phosphate di-kinase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Pyruvate Phosphate Dikinase, domain 2 |
| 结构域编号 domain_id | 1jdeA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 30 — Glucose Oxidase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Phosphohistidine domain |
| 结构域编号 domain_id | 1jdeA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 1jdeA05 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 80 — Acyl-CoA Binding Protein |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 1jdeA06 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 470 — D-amino Acid Aminotransferase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP-grasp fold, B domain |