1pku
Crystal Structure of Nucleoside Diphosphate Kinase from Rice
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 | 1pku |
| 沉积日期 deposition_date | 2003-06-06 |
| 结构标题 title | Crystal Structure of Nucleoside Diphosphate Kinase from Rice |
| 关键词 keywords | nucleoside diphosphate kinase, rice, TRANSFERASE; 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 | 43.91 Å |
| 回转半径 Rg (电子) rg_electron | 43.90 Å |
| 零角强度 I(0) i0 | 575916000.00 |
| 分子量 molecular_weight | 202960.0 kDa |
| 排除体积 excluded_volume | 255760 ų |
| 包络体积 envelope_volume | 326870 ų |
| 水化壳体积 shell_volume | 62738 ų |
| 包络直径 envelope_diameter | 147.5 Å |
| 壳层 Rg shell_rg | 47.64 Å |
| 包络 Rg envelope_rg | 43.86 Å |
| 形状 Rg shape_rg | 43.91 Å |
| 总 Rg total_rg | 44.05 Å |
| 总原子数 total_atoms | 14352 |
| 残基数 n_residues | 1788 |
| 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 | 145.1 Å |
| Rg (实空间) rg_real | 44.16 Å |
| Rg 误差 (实空间) rg_real_error | 1.35 Å |
| I(0) (实空间) i0_real | 5.7590e+08 |
| I(0) 误差 (实空间) i0_real_error | 9.8850e+06 |
| Rg (倒空间) rg_reciprocal | 43.92 Å |
| I(0) (倒空间) i0_reciprocal | 575800000.0000 |
| 解质量估计 total_estimate | 0.8331 |
| 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 | 40.3 Å |
| 偏度 Skewness skewness | 0.444 |
| 峰度 Kurtosis kurtosis | -0.595 |
| 角度范围 angular_range | — – 0.1800 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 186400000.0000 |
| 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: 0.739; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.682 |
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) 36 domains
SCOP 2.08 (24 domains)
| 结构域编号 domain_id | d1pkua1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkua2 |
| 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 | d1pkub2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkub3 |
| 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 | d1pkuc2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkuc3 |
| 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 | d1pkud2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkud3 |
| 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 | d1pkue2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkue3 |
| 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 | d1pkuf2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkuf3 |
| 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 | d1pkug2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkug3 |
| 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 | d1pkuh2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkuh3 |
| 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 | d1pkui2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkui3 |
| 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 | d1pkuj2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkuj3 |
| 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 | d1pkuk2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkuk3 |
| 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 | d1pkul2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.6 — Nucleoside diphosphate kinase, NDK |
| 家族 Family family | d.58.6.1 — Nucleoside diphosphate kinase, NDK |
| 结构域编号 domain_id | d1pkul3 |
| 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 (12 domains)
| 结构域编号 domain_id | 1pkuA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |
| 结构域编号 domain_id | 1pkuB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |
| 结构域编号 domain_id | 1pkuC00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |
| 结构域编号 domain_id | 1pkuD00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |
| 结构域编号 domain_id | 1pkuE00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |
| 结构域编号 domain_id | 1pkuF00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |
| 结构域编号 domain_id | 1pkuG00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |
| 结构域编号 domain_id | 1pkuH00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |
| 结构域编号 domain_id | 1pkuI00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |
| 结构域编号 domain_id | 1pkuJ00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |
| 结构域编号 domain_id | 1pkuK00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |
| 结构域编号 domain_id | 1pkuL00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 141 — Nucleoside diphosphate kinase-like domain |