2gb5
Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 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 | 2gb5 |
| 沉积日期 deposition_date | 2006-03-09 |
| 结构标题 title | Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 A resolution |
| 关键词 keywords | ;1790429, NADH pyrophosphatase (EC 3.6.1.22), Structural Genomics, PSI, Protein Structure Initiative, Joint Center for Structural Genomics, JCSG, 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 | 25.58 Å |
| 回转半径 Rg (电子) rg_electron | 24.41 Å |
| 零角强度 I(0) i0 | 62891700.00 |
| 分子量 molecular_weight | 60036.0 kDa |
| 排除体积 excluded_volume | 73982 ų |
| 包络体积 envelope_volume | 90834 ų |
| 水化壳体积 shell_volume | 30667 ų |
| 包络直径 envelope_diameter | 79.2 Å |
| 壳层 Rg shell_rg | 31.96 Å |
| 包络 Rg envelope_rg | 24.39 Å |
| 形状 Rg shape_rg | 24.45 Å |
| 总 Rg total_rg | 25.12 Å |
| 总原子数 total_atoms | 4173 |
| 残基数 n_residues | 510 |
| 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 | 77.0 Å |
| Rg (实空间) rg_real | 25.41 Å |
| Rg 误差 (实空间) rg_real_error | 0.36 Å |
| I(0) (实空间) i0_real | 6.2890e+07 |
| I(0) 误差 (实空间) i0_real_error | 7.9450e+05 |
| Rg (倒空间) rg_reciprocal | 25.46 Å |
| I(0) (倒空间) i0_reciprocal | 62890000.0000 |
| 解质量估计 total_estimate | 0.7524 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 34.8 Å |
| 偏度 Skewness skewness | 0.047 |
| 峰度 Kurtosis kurtosis | -0.583 |
| 角度范围 angular_range | — – 0.3100 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 8756000.0000 |
| 实空间数据点数 n_real_points | 63 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 0.315; Positv: 1.000; Valcen: 0.985; Smooth: 0.988 |
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) 12 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d2gb5a1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.113 — Nudix |
| 超家族 Superfamily superfamily | d.113.1 — Nudix |
| 家族 Family family | d.113.1.4 — NADH pyrophosphatase |
| 结构域编号 domain_id | d2gb5a2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.41 — Rubredoxin-like |
| 超家族 Superfamily superfamily | g.41.14 — NADH pyrophosphatase intervening domain |
| 家族 Family family | g.41.14.1 — NADH pyrophosphatase intervening domain |
| 结构域编号 domain_id | d2gb5a3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.113 — Nudix |
| 超家族 Superfamily superfamily | d.113.1 — Nudix |
| 家族 Family family | d.113.1.4 — NADH pyrophosphatase |
| 结构域编号 domain_id | d2gb5a4 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d2gb5b1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.113 — Nudix |
| 超家族 Superfamily superfamily | d.113.1 — Nudix |
| 家族 Family family | d.113.1.4 — NADH pyrophosphatase |
| 结构域编号 domain_id | d2gb5b2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.41 — Rubredoxin-like |
| 超家族 Superfamily superfamily | g.41.14 — NADH pyrophosphatase intervening domain |
| 家族 Family family | g.41.14.1 — NADH pyrophosphatase intervening domain |
| 结构域编号 domain_id | d2gb5b3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.113 — Nudix |
| 超家族 Superfamily superfamily | d.113.1 — Nudix |
| 家族 Family family | d.113.1.4 — NADH pyrophosphatase |
| 结构域编号 domain_id | d2gb5b4 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2gb5A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 79 — Nucleoside Triphosphate Pyrophosphohydrolase |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2gb5A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 79 — Nucleoside Triphosphate Pyrophosphohydrolase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Nucleoside Triphosphate Pyrophosphohydrolase |
| 结构域编号 domain_id | 2gb5B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 79 — Nucleoside Triphosphate Pyrophosphohydrolase |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2gb5B02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 79 — Nucleoside Triphosphate Pyrophosphohydrolase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Nucleoside Triphosphate Pyrophosphohydrolase |