1v7v
Crystal structure of Vibrio proteolyticus chitobiose phosphorylase
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 | 1v7v |
| 沉积日期 deposition_date | 2003-12-24 |
| 结构标题 title | Crystal structure of Vibrio proteolyticus chitobiose phosphorylase |
| 关键词 keywords | beta-sandwich, (alpha/alpha)6 barrel, 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 | 28.59 Å |
| 回转半径 Rg (电子) rg_electron | 27.51 Å |
| 零角强度 I(0) i0 | 129647000.00 |
| 分子量 molecular_weight | 88094.0 kDa |
| 排除体积 excluded_volume | 108990 ų |
| 包络体积 envelope_volume | 125970 ų |
| 水化壳体积 shell_volume | 37473 ų |
| 包络直径 envelope_diameter | 92.4 Å |
| 壳层 Rg shell_rg | 35.74 Å |
| 包络 Rg envelope_rg | 27.66 Å |
| 形状 Rg shape_rg | 27.48 Å |
| 总 Rg total_rg | 28.32 Å |
| 总原子数 total_atoms | 6225 |
| 残基数 n_residues | 779 |
| 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 | 88.7 Å |
| Rg (实空间) rg_real | 28.53 Å |
| Rg 误差 (实空间) rg_real_error | 0.55 Å |
| I(0) (实空间) i0_real | 1.2960e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.8470e+06 |
| Rg (倒空间) rg_reciprocal | 28.56 Å |
| I(0) (倒空间) i0_reciprocal | 129600000.0000 |
| 解质量估计 total_estimate | 0.9026 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 32.2 Å |
| 偏度 Skewness skewness | 0.290 |
| 峰度 Kurtosis kurtosis | -0.445 |
| 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 | 28770000.0000 |
| 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: 0.934; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.930 |
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) 5 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1v7va1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.102 — alpha/alpha toroid |
| 超家族 Superfamily superfamily | a.102.1 — Six-hairpin glycosidases |
| 家族 Family family | a.102.1.4 — Glycosyltransferase family 36 C-terminal domain |
| 结构域编号 domain_id | d1v7va2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.30 — Supersandwich |
| 超家族 Superfamily superfamily | b.30.5 — Galactose mutarotase-like |
| 家族 Family family | b.30.5.3 — Glycosyltransferase family 36 N-terminal domain |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1v7vA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 98 — Beta-galactosidase; Chain A, domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 40 — Glycoside hydrolase, family 65, N-terminal domain |
| 结构域编号 domain_id | 1v7vA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 420 — Maltose phosphorylase, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Maltose phosphorylase, domain 3 |
| 结构域编号 domain_id | 1v7vA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 50 — Alpha/alpha barrel |
| 拓扑 Topology topology | 10 — Glycosyltransferase |
| 同源超家族 H-superfamily homologous superfamily | 10 — |