1wkl
Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with ATP and ADP
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 | 1wkl |
| 沉积日期 deposition_date | 2004-06-01 |
| 结构标题 title | Crystal Structure of Nucleoside Diphosphate Kinase from Thermus thermophilus HB8 in Complex with ATP and ADP |
| 关键词 keywords | ;nucleotide diphosphate kinase, complex with ATP and ADP, reaction intermediate, Thermus thermophilus HB8, kinase, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, 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 | 20.62 Å |
| 回转半径 Rg (电子) rg_electron | 19.44 Å |
| 零角强度 I(0) i0 | 18283900.00 |
| 分子量 molecular_weight | 31728.0 kDa |
| 排除体积 excluded_volume | 39549 ų |
| 包络体积 envelope_volume | 45214 ų |
| 水化壳体积 shell_volume | 19713 ų |
| 包络直径 envelope_diameter | 70.9 Å |
| 壳层 Rg shell_rg | 25.66 Å |
| 包络 Rg envelope_rg | 19.76 Å |
| 形状 Rg shape_rg | 19.46 Å |
| 总 Rg total_rg | 20.23 Å |
| 总原子数 total_atoms | 2221 |
| 残基数 n_residues | 274 |
| 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 | 69.4 Å |
| Rg (实空间) rg_real | 20.60 Å |
| Rg 误差 (实空间) rg_real_error | 0.54 Å |
| I(0) (实空间) i0_real | 1.8280e+07 |
| I(0) 误差 (实空间) i0_real_error | 2.1930e+05 |
| Rg (倒空间) rg_reciprocal | 20.60 Å |
| I(0) (倒空间) i0_reciprocal | 18280000.0000 |
| 解质量估计 total_estimate | 0.8028 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 25.1 Å |
| 偏度 Skewness skewness | 0.330 |
| 峰度 Kurtosis kurtosis | -0.301 |
| 角度范围 angular_range | — – 0.3850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 4754000.0000 |
| 实空间数据点数 n_real_points | 70 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1wkla_ |
| 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 | d1wklb_ |
| 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 |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1wklA00 |
| 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 | 1wklB00 |
| 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 |