1o4u
Crystal structure of a nicotinate nucleotide pyrophosphorylase (tm1645) from thermotoga maritima at 2.50 A 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 | 1o4u |
| 沉积日期 deposition_date | 2003-07-09 |
| 结构标题 title | Crystal structure of a nicotinate nucleotide pyrophosphorylase (tm1645) from thermotoga maritima at 2.50 A resolution |
| 关键词 keywords | Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, 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 | 26.66 Å |
| 回转半径 Rg (电子) rg_electron | 25.59 Å |
| 零角强度 I(0) i0 | 53789700.00 |
| 分子量 molecular_weight | 58063.0 kDa |
| 排除体积 excluded_volume | 73378 ų |
| 包络体积 envelope_volume | 91384 ų |
| 水化壳体积 shell_volume | 30084 ų |
| 包络直径 envelope_diameter | 86.3 Å |
| 壳层 Rg shell_rg | 32.68 Å |
| 包络 Rg envelope_rg | 25.46 Å |
| 形状 Rg shape_rg | 25.61 Å |
| 总 Rg total_rg | 26.36 Å |
| 总原子数 total_atoms | 4074 |
| 残基数 n_residues | 531 |
| 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 | 85.2 Å |
| Rg (实空间) rg_real | 26.63 Å |
| Rg 误差 (实空间) rg_real_error | 0.50 Å |
| I(0) (实空间) i0_real | 5.3790e+07 |
| I(0) 误差 (实空间) i0_real_error | 6.9760e+05 |
| Rg (倒空间) rg_reciprocal | 26.64 Å |
| I(0) (倒空间) i0_reciprocal | 53790000.0000 |
| 解质量估计 total_estimate | 0.8955 |
| 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 | 83.8 Å |
| 偏度 Skewness skewness | 0.334 |
| 峰度 Kurtosis kurtosis | -0.307 |
| 角度范围 angular_range | — – 0.3000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 27550000.0000 |
| 实空间数据点数 n_real_points | 61 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.933 |
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) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1o4ua1 |
| 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.1.17 — Nicotinate/Quinolinate PRTase C-terminal domain-like |
| 家族 Family family | c.1.17.1 — NadC C-terminal domain-like |
| 结构域编号 domain_id | d1o4ua2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.41 — alpha/beta-Hammerhead |
| 超家族 Superfamily superfamily | d.41.2 — Nicotinate/Quinolinate PRTase N-terminal domain-like |
| 家族 Family family | d.41.2.1 — NadC N-terminal domain-like |
| 结构域编号 domain_id | d1o4ub1 |
| 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.1.17 — Nicotinate/Quinolinate PRTase C-terminal domain-like |
| 家族 Family family | c.1.17.1 — NadC C-terminal domain-like |
| 结构域编号 domain_id | d1o4ub2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.41 — alpha/beta-Hammerhead |
| 超家族 Superfamily superfamily | d.41.2 — Nicotinate/Quinolinate PRTase N-terminal domain-like |
| 家族 Family family | d.41.2.1 — NadC N-terminal domain-like |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1o4uA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1170 — Aldehyde Oxidoreductase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Quinolinate phosphoribosyl transferase, N-terminal domain |
| 结构域编号 domain_id | 1o4uA02 |
| 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 | 70 — Aldolase class I |
| 结构域编号 domain_id | 1o4uB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1170 — Aldehyde Oxidoreductase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Quinolinate phosphoribosyl transferase, N-terminal domain |
| 结构域编号 domain_id | 1o4uB02 |
| 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 | 70 — Aldolase class I |