1ymy
Crystal Structure of the N-Acetylglucosamine-6-phosphate deacetylase from Escherichia coli K12
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 | 1ymy |
| 沉积日期 deposition_date | 2005-01-21 |
| 结构标题 title | Crystal Structure of the N-Acetylglucosamine-6-phosphate deacetylase from Escherichia coli K12 |
| 关键词 keywords | ;NagA, NYSGXRC target T2187, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, 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 | 30.89 Å |
| 回转半径 Rg (电子) rg_electron | 30.44 Å |
| 零角强度 I(0) i0 | 88771900.00 |
| 分子量 molecular_weight | 75620.0 kDa |
| 排除体积 excluded_volume | 95169 ų |
| 包络体积 envelope_volume | 113000 ų |
| 水化壳体积 shell_volume | 31626 ų |
| 包络直径 envelope_diameter | 101.3 Å |
| 壳层 Rg shell_rg | 36.74 Å |
| 包络 Rg envelope_rg | 30.57 Å |
| 形状 Rg shape_rg | 30.43 Å |
| 总 Rg total_rg | 31.02 Å |
| 总原子数 total_atoms | 5306 |
| 残基数 n_residues | 707 |
| 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 | 98.2 Å |
| Rg (实空间) rg_real | 30.98 Å |
| Rg 误差 (实空间) rg_real_error | 0.64 Å |
| I(0) (实空间) i0_real | 8.8770e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.3630e+06 |
| Rg (倒空间) rg_reciprocal | 30.94 Å |
| I(0) (倒空间) i0_reciprocal | 88770000.0000 |
| 解质量估计 total_estimate | 0.8843 |
| 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 | 28.9 Å |
| 偏度 Skewness skewness | 0.331 |
| 峰度 Kurtosis kurtosis | -0.686 |
| 角度范围 angular_range | — – 0.2550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 34580000.0000 |
| 实空间数据点数 n_real_points | 52 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.888; Smooth: 0.891 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (1)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1ymya1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.92 — Composite domain of metallo-dependent hydrolases |
| 超家族 Superfamily superfamily | b.92.1 — Composite domain of metallo-dependent hydrolases |
| 家族 Family family | b.92.1.5 — N-acetylglucosamine-6-phosphate deacetylase, NagA |
| 结构域编号 domain_id | d1ymya2 |
| 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.1.9 — Metallo-dependent hydrolases |
| 家族 Family family | c.1.9.10 — N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain |
| 结构域编号 domain_id | d1ymyb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.92 — Composite domain of metallo-dependent hydrolases |
| 超家族 Superfamily superfamily | b.92.1 — Composite domain of metallo-dependent hydrolases |
| 家族 Family family | b.92.1.5 — N-acetylglucosamine-6-phosphate deacetylase, NagA |
| 结构域编号 domain_id | d1ymyb2 |
| 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.1.9 — Metallo-dependent hydrolases |
| 家族 Family family | c.1.9.10 — N-acetylglucosamine-6-phosphate deacetylase, NagA, catalytic domain |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1ymyA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 40 — Urease, subunit C; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Urease, subunit C, domain 1 |
| 结构域编号 domain_id | 1ymyA02 |
| 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 | 140 — Metal-dependent hydrolases |
| 结构域编号 domain_id | 1ymyB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 40 — Urease, subunit C; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Urease, subunit C, domain 1 |
| 结构域编号 domain_id | 1ymyB02 |
| 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 | 140 — Metal-dependent hydrolases |