2j4l
Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UTP to 2.8 Angstrom resolution
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 | 2j4l |
| 沉积日期 deposition_date | 2006-09-01 |
| 结构标题 title | Crystal structure of uridylate kinase from Sulfolobus solfataricus in complex with UTP to 2.8 Angstrom resolution |
| 关键词 keywords | UMP KINASE, NUCLEOSIDE MONOPHOSPHATE KINASE, PYRIMIDINE NUCLEOTIDE SYNTHESIS, ASPARTOKINASE FOLD, 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 | 47.97 Å |
| 回转半径 Rg (电子) rg_electron | 48.25 Å |
| 零角强度 I(0) i0 | 1060810000.00 |
| 分子量 molecular_weight | 279200.0 kDa |
| 排除体积 excluded_volume | 353460 ų |
| 包络体积 envelope_volume | 456510 ų |
| 水化壳体积 shell_volume | 78733 ų |
| 包络直径 envelope_diameter | 176.2 Å |
| 壳层 Rg shell_rg | 51.92 Å |
| 包络 Rg envelope_rg | 48.19 Å |
| 形状 Rg shape_rg | 48.23 Å |
| 总 Rg total_rg | 48.47 Å |
| 总原子数 total_atoms | 19613 |
| 残基数 n_residues | 2469 |
| 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 | 162.6 Å |
| Rg (实空间) rg_real | 48.28 Å |
| Rg 误差 (实空间) rg_real_error | 1.53 Å |
| I(0) (实空间) i0_real | 1.0610e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.0580e+07 |
| Rg (倒空间) rg_reciprocal | 47.97 Å |
| I(0) (倒空间) i0_reciprocal | 1060000000.0000 |
| 解质量估计 total_estimate | 0.6208 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 49.3 Å |
| 偏度 Skewness skewness | 0.468 |
| 峰度 Kurtosis kurtosis | -0.427 |
| 角度范围 angular_range | — – 0.1650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 157200000.0000 |
| 实空间数据点数 n_real_points | 34 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 0.044; Positv: 1.000; Valcen: 0.976; Smooth: 0.684 |
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) 24 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d2j4la_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
| 结构域编号 domain_id | d2j4lb_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
| 结构域编号 domain_id | d2j4lc_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
| 结构域编号 domain_id | d2j4ld_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
| 结构域编号 domain_id | d2j4le_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
| 结构域编号 domain_id | d2j4lf_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
| 结构域编号 domain_id | d2j4lg_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
| 结构域编号 domain_id | d2j4lh_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
| 结构域编号 domain_id | d2j4li_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
| 结构域编号 domain_id | d2j4lj_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
| 结构域编号 domain_id | d2j4lk_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
| 结构域编号 domain_id | d2j4ll_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.73 — Carbamate kinase-like |
| 超家族 Superfamily superfamily | c.73.1 — Carbamate kinase-like |
| 家族 Family family | c.73.1.0 — automated matches |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 2j4lA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2j4lB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2j4lC00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2j4lD00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2j4lE00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2j4lF00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2j4lG00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2j4lH00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2j4lI00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2j4lJ00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2j4lK00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |
| 结构域编号 domain_id | 2j4lL00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1160 — Carbamate kinase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Acetylglutamate kinase-like |