8syb
;X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N variant in the presence of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and UDP-N-acetylglucosamine at pH 9 ;
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 | 8syb |
| 沉积日期 deposition_date | 2023-05-25 |
| 结构标题 title | ;X-ray crystal structure of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid-2-epimerase from Thermus thermophilus strain HB27, D98N variant in the presence of UDP-2,3-diacetamido-2,3-dideoxy-glucuronic acid and UDP-N-acetylglucosamine at pH 9 ; |
| 关键词 keywords | lipopolysaccharide, O-antigen, 2-epimerase, ISOMERASE; ISOMERASE |
| 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 | 28.78 Å |
| 回转半径 Rg (电子) rg_electron | 28.46 Å |
| 零角强度 I(0) i0 | 111490000.00 |
| 分子量 molecular_weight | 82965.0 kDa |
| 排除体积 excluded_volume | 103570 ų |
| 包络体积 envelope_volume | 119800 ų |
| 水化壳体积 shell_volume | 35338 ų |
| 包络直径 envelope_diameter | 102.5 Å |
| 壳层 Rg shell_rg | 35.74 Å |
| 包络 Rg envelope_rg | 28.83 Å |
| 形状 Rg shape_rg | 28.46 Å |
| 总 Rg total_rg | 29.09 Å |
| 总原子数 total_atoms | 5833 |
| 残基数 n_residues | 722 |
| 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 | 96.5 Å |
| Rg (实空间) rg_real | 28.89 Å |
| Rg 误差 (实空间) rg_real_error | 0.55 Å |
| I(0) (实空间) i0_real | 1.1150e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.5930e+06 |
| Rg (倒空间) rg_reciprocal | 28.84 Å |
| I(0) (倒空间) i0_reciprocal | 111500000.0000 |
| 解质量估计 total_estimate | 0.8598 |
| 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 | 29.8 Å |
| 偏度 Skewness skewness | 0.502 |
| 峰度 Kurtosis kurtosis | -0.235 |
| 角度范围 angular_range | — – 0.2750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 70070000.0000 |
| 实空间数据点数 n_real_points | 56 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; Smooth: 0.904 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 4 domains
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 8sybA01 |
| 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 | 2000 — Glycogen Phosphorylase B; |
| 结构域编号 domain_id | 8sybA02 |
| 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 | 2000 — Glycogen Phosphorylase B; |
| 结构域编号 domain_id | 8sybB01 |
| 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 | 2000 — Glycogen Phosphorylase B; |
| 结构域编号 domain_id | 8sybB02 |
| 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 | 2000 — Glycogen Phosphorylase B; |