1goi
Crystal structure of the D140N mutant of chitinase B from Serratia marcescens at 1.45 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 | 1goi |
| 沉积日期 deposition_date | 2001-10-21 |
| 结构标题 title | Crystal structure of the D140N mutant of chitinase B from Serratia marcescens at 1.45 A resolution |
| 关键词 keywords | CHITIN DEGRADATION, HYDROLASE, GLYCOSIDASE; 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 | 36.91 Å |
| 回转半径 Rg (电子) rg_electron | 36.35 Å |
| 零角强度 I(0) i0 | 189536000.00 |
| 分子量 molecular_weight | 111640.0 kDa |
| 排除体积 excluded_volume | 139360 ų |
| 包络体积 envelope_volume | 170380 ų |
| 水化壳体积 shell_volume | 39937 ų |
| 包络直径 envelope_diameter | 124.2 Å |
| 壳层 Rg shell_rg | 41.56 Å |
| 包络 Rg envelope_rg | 36.25 Å |
| 形状 Rg shape_rg | 36.32 Å |
| 总 Rg total_rg | 36.76 Å |
| 总原子数 total_atoms | 7885 |
| 残基数 n_residues | 994 |
| 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 | 121.9 Å |
| Rg (实空间) rg_real | 37.16 Å |
| Rg 误差 (实空间) rg_real_error | 1.53 Å |
| I(0) (实空间) i0_real | 1.8950e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.2860e+06 |
| Rg (倒空间) rg_reciprocal | 37.01 Å |
| I(0) (倒空间) i0_reciprocal | 189500000.0000 |
| 解质量估计 total_estimate | 0.8301 |
| 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 | 34.0 Å |
| 偏度 Skewness skewness | 0.415 |
| 峰度 Kurtosis kurtosis | -0.688 |
| 角度范围 angular_range | — – 0.2150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 30470000.0000 |
| 实空间数据点数 n_real_points | 44 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.791; Smooth: 0.854 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1goia1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.72 — WW domain-like |
| 超家族 Superfamily superfamily | b.72.2 — Carbohydrate binding domain |
| 家族 Family family | b.72.2.1 — Carbohydrate binding domain |
| 结构域编号 domain_id | d1goia2 |
| 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.1.8 — (Trans)glycosidases |
| 家族 Family family | c.1.8.5 — Type II chitinase |
| 结构域编号 domain_id | d1goia3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.26 — FKBP-like |
| 超家族 Superfamily superfamily | d.26.3 — Chitinase insertion domain |
| 家族 Family family | d.26.3.1 — Chitinase insertion domain |
| 结构域编号 domain_id | d1goib1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.72 — WW domain-like |
| 超家族 Superfamily superfamily | b.72.2 — Carbohydrate binding domain |
| 家族 Family family | b.72.2.1 — Carbohydrate binding domain |
| 结构域编号 domain_id | d1goib2 |
| 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.1.8 — (Trans)glycosidases |
| 家族 Family family | c.1.8.5 — Type II chitinase |
| 结构域编号 domain_id | d1goib3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.26 — FKBP-like |
| 超家族 Superfamily superfamily | d.26.3 — Chitinase insertion domain |
| 家族 Family family | d.26.3.1 — Chitinase insertion domain |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1goiA01 |
| 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 | 80 — Glycosidases |
| 结构域编号 domain_id | 1goiA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 50 — Chitinase A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1goiA03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 10 — Seminal Fluid Protein PDC-109 (Domain B) |
| 同源超家族 H-superfamily homologous superfamily | 20 — Carbohydrate-binding module superfamily 5/12 |
| 结构域编号 domain_id | 1goiB01 |
| 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 | 80 — Glycosidases |
| 结构域编号 domain_id | 1goiB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 50 — Chitinase A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1goiB03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 10 — Seminal Fluid Protein PDC-109 (Domain B) |
| 同源超家族 H-superfamily homologous superfamily | 20 — Carbohydrate-binding module superfamily 5/12 |