1n4r
Protein Geranylgeranyltransferase type-I Complexed with a Geranylgeranylated KKKSKTKCVIL Peptide Product
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 | 1n4r |
| 沉积日期 deposition_date | 2002-11-01 |
| 结构标题 title | Protein Geranylgeranyltransferase type-I Complexed with a Geranylgeranylated KKKSKTKCVIL Peptide Product |
| 关键词 keywords | protein geranylgeranyltransferase type-I, GGTase, geranylgeranyl, protein prenylation, CaaX, lipid modification, rap2b, 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 | 65.44 Å |
| 回转半径 Rg (电子) rg_electron | 65.47 Å |
| 零角强度 I(0) i0 | 3012220000.00 |
| 分子量 molecular_weight | 462360.0 kDa |
| 排除体积 excluded_volume | 577150 ų |
| 包络体积 envelope_volume | 816870 ų |
| 水化壳体积 shell_volume | 103810 ų |
| 包络直径 envelope_diameter | 220.4 Å |
| 壳层 Rg shell_rg | 65.74 Å |
| 包络 Rg envelope_rg | 63.82 Å |
| 形状 Rg shape_rg | 65.48 Å |
| 总 Rg total_rg | 65.47 Å |
| 总原子数 total_atoms | 32539 |
| 残基数 n_residues | 3996 |
| 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 | 233.7 Å |
| Rg (实空间) rg_real | 65.49 Å |
| Rg 误差 (实空间) rg_real_error | 2.22 Å |
| I(0) (实空间) i0_real | 3.0120e+09 |
| I(0) 误差 (实空间) i0_real_error | 6.4190e+07 |
| Rg (倒空间) rg_reciprocal | 65.34 Å |
| I(0) (倒空间) i0_reciprocal | 3011000000.0000 |
| 解质量估计 total_estimate | 0.8552 |
| 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 | 97.4 Å |
| 偏度 Skewness skewness | 0.224 |
| 峰度 Kurtosis kurtosis | -0.512 |
| 角度范围 angular_range | — – 0.1200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0016 |
| 最高正则化参数 α highest_alpha | 137400000.0000 |
| 实空间数据点数 n_real_points | 25 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.801 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (9)
6. 折叠分类 (SCOP + CATH) 24 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1n4ra_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.118 — alpha-alpha superhelix |
| 超家族 Superfamily superfamily | a.118.6 — Protein prenylyltransferase |
| 家族 Family family | a.118.6.1 — Protein prenylyltransferase |
| 结构域编号 domain_id | d1n4rb_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.102 — alpha/alpha toroid |
| 超家族 Superfamily superfamily | a.102.4 — Terpenoid cyclases/Protein prenyltransferases |
| 家族 Family family | a.102.4.3 — Protein prenyltransferases |
| 结构域编号 domain_id | d1n4rc_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.118 — alpha-alpha superhelix |
| 超家族 Superfamily superfamily | a.118.6 — Protein prenylyltransferase |
| 家族 Family family | a.118.6.1 — Protein prenylyltransferase |
| 结构域编号 domain_id | d1n4rd_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.102 — alpha/alpha toroid |
| 超家族 Superfamily superfamily | a.102.4 — Terpenoid cyclases/Protein prenyltransferases |
| 家族 Family family | a.102.4.3 — Protein prenyltransferases |
| 结构域编号 domain_id | d1n4re_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.118 — alpha-alpha superhelix |
| 超家族 Superfamily superfamily | a.118.6 — Protein prenylyltransferase |
| 家族 Family family | a.118.6.1 — Protein prenylyltransferase |
| 结构域编号 domain_id | d1n4rf_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.102 — alpha/alpha toroid |
| 超家族 Superfamily superfamily | a.102.4 — Terpenoid cyclases/Protein prenyltransferases |
| 家族 Family family | a.102.4.3 — Protein prenyltransferases |
| 结构域编号 domain_id | d1n4rg_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.118 — alpha-alpha superhelix |
| 超家族 Superfamily superfamily | a.118.6 — Protein prenylyltransferase |
| 家族 Family family | a.118.6.1 — Protein prenylyltransferase |
| 结构域编号 domain_id | d1n4rh_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.102 — alpha/alpha toroid |
| 超家族 Superfamily superfamily | a.102.4 — Terpenoid cyclases/Protein prenyltransferases |
| 家族 Family family | a.102.4.3 — Protein prenyltransferases |
| 结构域编号 domain_id | d1n4ri_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.118 — alpha-alpha superhelix |
| 超家族 Superfamily superfamily | a.118.6 — Protein prenylyltransferase |
| 家族 Family family | a.118.6.1 — Protein prenylyltransferase |
| 结构域编号 domain_id | d1n4rj_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.102 — alpha/alpha toroid |
| 超家族 Superfamily superfamily | a.102.4 — Terpenoid cyclases/Protein prenyltransferases |
| 家族 Family family | a.102.4.3 — Protein prenyltransferases |
| 结构域编号 domain_id | d1n4rk_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.118 — alpha-alpha superhelix |
| 超家族 Superfamily superfamily | a.118.6 — Protein prenylyltransferase |
| 家族 Family family | a.118.6.1 — Protein prenylyltransferase |
| 结构域编号 domain_id | d1n4rl_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.102 — alpha/alpha toroid |
| 超家族 Superfamily superfamily | a.102.4 — Terpenoid cyclases/Protein prenyltransferases |
| 家族 Family family | a.102.4.3 — Protein prenyltransferases |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 1n4rA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 25 — Alpha Horseshoe |
| 拓扑 Topology topology | 40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat |
| 同源超家族 H-superfamily homologous superfamily | 120 — Protein prenylyltransferase |
| 结构域编号 domain_id | 1n4rB00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 50 — Alpha/alpha barrel |
| 拓扑 Topology topology | 10 — Glycosyltransferase |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1n4rC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 25 — Alpha Horseshoe |
| 拓扑 Topology topology | 40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat |
| 同源超家族 H-superfamily homologous superfamily | 120 — Protein prenylyltransferase |
| 结构域编号 domain_id | 1n4rD00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 50 — Alpha/alpha barrel |
| 拓扑 Topology topology | 10 — Glycosyltransferase |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1n4rE00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 25 — Alpha Horseshoe |
| 拓扑 Topology topology | 40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat |
| 同源超家族 H-superfamily homologous superfamily | 120 — Protein prenylyltransferase |
| 结构域编号 domain_id | 1n4rF00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 50 — Alpha/alpha barrel |
| 拓扑 Topology topology | 10 — Glycosyltransferase |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1n4rG00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 25 — Alpha Horseshoe |
| 拓扑 Topology topology | 40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat |
| 同源超家族 H-superfamily homologous superfamily | 120 — Protein prenylyltransferase |
| 结构域编号 domain_id | 1n4rH00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 50 — Alpha/alpha barrel |
| 拓扑 Topology topology | 10 — Glycosyltransferase |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1n4rI00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 25 — Alpha Horseshoe |
| 拓扑 Topology topology | 40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat |
| 同源超家族 H-superfamily homologous superfamily | 120 — Protein prenylyltransferase |
| 结构域编号 domain_id | 1n4rJ00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 50 — Alpha/alpha barrel |
| 拓扑 Topology topology | 10 — Glycosyltransferase |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1n4rK00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 25 — Alpha Horseshoe |
| 拓扑 Topology topology | 40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat |
| 同源超家族 H-superfamily homologous superfamily | 120 — Protein prenylyltransferase |
| 结构域编号 domain_id | 1n4rL00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 50 — Alpha/alpha barrel |
| 拓扑 Topology topology | 10 — Glycosyltransferase |
| 同源超家族 H-superfamily homologous superfamily | 20 — |