1mmf
Crystal structure of substrate free form of glycerol dehydratase
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 | 1mmf |
| 沉积日期 deposition_date | 2002-09-03 |
| 结构标题 title | Crystal structure of substrate free form of glycerol dehydratase |
| 关键词 keywords | Glycerol dehydratase, Diol dehydratase, Coenzyme B12, TIM barrel, Lyase; LYASE |
| 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 | 37.72 Å |
| 回转半径 Rg (电子) rg_electron | 37.26 Å |
| 零角强度 I(0) i0 | 576740000.00 |
| 分子量 molecular_weight | 193520.0 kDa |
| 排除体积 excluded_volume | 240920 ų |
| 包络体积 envelope_volume | 283270 ų |
| 水化壳体积 shell_volume | 61133 ų |
| 包络直径 envelope_diameter | 123.1 Å |
| 壳层 Rg shell_rg | 45.07 Å |
| 包络 Rg envelope_rg | 37.71 Å |
| 形状 Rg shape_rg | 37.30 Å |
| 总 Rg total_rg | 37.53 Å |
| 总原子数 total_atoms | 13575 |
| 残基数 n_residues | 1735 |
| 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 | 124.8 Å |
| Rg (实空间) rg_real | 37.73 Å |
| Rg 误差 (实空间) rg_real_error | 0.71 Å |
| I(0) (实空间) i0_real | 5.7670e+08 |
| I(0) 误差 (实空间) i0_real_error | 8.6550e+06 |
| Rg (倒空间) rg_reciprocal | 37.72 Å |
| I(0) (倒空间) i0_reciprocal | 576700000.0000 |
| 解质量估计 total_estimate | 0.8847 |
| 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 | 41.6 Å |
| 偏度 Skewness skewness | 0.355 |
| 峰度 Kurtosis kurtosis | -0.481 |
| 角度范围 angular_range | — – 0.2100 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 173600000.0000 |
| 实空间数据点数 n_real_points | 43 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.953 |
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) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1mmfa_ |
| 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.1.19 — Cobalamin (vitamin B12)-dependent enzymes |
| 家族 Family family | c.1.19.3 — Diol dehydratase, alpha subunit |
| 结构域编号 domain_id | d1mmfb_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.51 — Anticodon-binding domain-like |
| 超家族 Superfamily superfamily | c.51.3 — B12-dependent dehydatase associated subunit |
| 家族 Family family | c.51.3.1 — Diol dehydratase, beta subunit |
| 结构域编号 domain_id | d1mmfe_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.51 — Anticodon-binding domain-like |
| 超家族 Superfamily superfamily | c.51.3 — B12-dependent dehydatase associated subunit |
| 家族 Family family | c.51.3.1 — Diol dehydratase, beta subunit |
| 结构域编号 domain_id | d1mmfg_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.23 — Open three-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.23.2 — Diol dehydratase, gamma subunit |
| 家族 Family family | a.23.2.1 — Diol dehydratase, gamma subunit |
| 结构域编号 domain_id | d1mmfl_ |
| 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.1.19 — Cobalamin (vitamin B12)-dependent enzymes |
| 家族 Family family | c.1.19.3 — Diol dehydratase, alpha subunit |
| 结构域编号 domain_id | d1mmfm_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.23 — Open three-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.23.2 — Diol dehydratase, gamma subunit |
| 家族 Family family | a.23.2.1 — Diol dehydratase, gamma subunit |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1mmfA00 |
| 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 | 350 — Diol/glycerol dehydratase, large subunit |
| 结构域编号 domain_id | 1mmfB00 |
| 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 | 10150 — B12-dependent dehydatase associated subunit |
| 结构域编号 domain_id | 1mmfE00 |
| 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 | 10150 — B12-dependent dehydatase associated subunit |
| 结构域编号 domain_id | 1mmfG02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1510 — Hypothetical Protein Yqey; Chain: A; domain1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Propanediol/glycerol dehydratase, small subunit |
| 结构域编号 domain_id | 1mmfL00 |
| 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 | 350 — Diol/glycerol dehydratase, large subunit |
| 结构域编号 domain_id | 1mmfM02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1510 — Hypothetical Protein Yqey; Chain: A; domain1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Propanediol/glycerol dehydratase, small subunit |