2g07
;X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, phospho-enzyme intermediate analog with Beryllium fluoride ;
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 | 2g07 |
| 沉积日期 deposition_date | 2006-02-11 |
| 结构标题 title | ;X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, phospho-enzyme intermediate analog with Beryllium fluoride ; |
| 关键词 keywords | ;UniProt Q9D020, UMPH-1, Cytosolic 5'-nucleotidase III, Pyrimidine 5'-nucleotidase 1, P5n-1, NT5C3 PROTEIN, AAH38029, BC038029, MM.158936, Lead Poisoning, STRUCTURAL GENOMICS FUNCTIONAL FOLLOW-UP STUDY, PROTEIN STRUCTURE INITIATIVE, PSI, CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS, CESG, HYDROLASE ;; HYDROLASE |
| 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 | 27.65 Å |
| 回转半径 Rg (电子) rg_electron | 26.67 Å |
| 零角强度 I(0) i0 | 72850100.00 |
| 分子量 molecular_weight | 67132.0 kDa |
| 排除体积 excluded_volume | 84014 ų |
| 包络体积 envelope_volume | 103580 ų |
| 水化壳体积 shell_volume | 32276 ų |
| 包络直径 envelope_diameter | 92.2 Å |
| 壳层 Rg shell_rg | 34.35 Å |
| 包络 Rg envelope_rg | 26.68 Å |
| 形状 Rg shape_rg | 26.62 Å |
| 总 Rg total_rg | 27.66 Å |
| 总原子数 total_atoms | 4662 |
| 残基数 n_residues | 564 |
| 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 | 87.1 Å |
| Rg (实空间) rg_real | 27.61 Å |
| Rg 误差 (实空间) rg_real_error | 0.40 Å |
| I(0) (实空间) i0_real | 7.2850e+07 |
| I(0) 误差 (实空间) i0_real_error | 9.4090e+05 |
| Rg (倒空间) rg_reciprocal | 27.62 Å |
| I(0) (倒空间) i0_reciprocal | 72850000.0000 |
| 解质量估计 total_estimate | 0.9051 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 85.5 Å |
| 偏度 Skewness skewness | 0.287 |
| 峰度 Kurtosis kurtosis | -0.497 |
| 角度范围 angular_range | — – 0.2850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 23900000.0000 |
| 实空间数据点数 n_real_points | 58 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.974 |
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) 6 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d2g07a_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.108 — HAD-like |
| 超家族 Superfamily superfamily | c.108.1 — HAD-like |
| 家族 Family family | c.108.1.21 — Pyrimidine 5'-nucleotidase (UMPH-1) |
| 结构域编号 domain_id | d2g07b_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.108 — HAD-like |
| 超家族 Superfamily superfamily | c.108.1 — HAD-like |
| 家族 Family family | c.108.1.21 — Pyrimidine 5'-nucleotidase (UMPH-1) |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2g07A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 1000 — HAD superfamily/HAD-like |
| 结构域编号 domain_id | 2g07A02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 340 — Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain |
| 结构域编号 domain_id | 2g07B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 1000 — HAD superfamily/HAD-like |
| 结构域编号 domain_id | 2g07B02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 340 — Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain |