1v1j
Crystal structure of type II Dehydroquintae Dehydratase from Streptomyces coelicolor in complex with 3-fluoro
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 | 1v1j |
| 沉积日期 deposition_date | 2004-04-16 |
| 结构标题 title | Crystal structure of type II Dehydroquintae Dehydratase from Streptomyces coelicolor in complex with 3-fluoro |
| 关键词 keywords | DHQ, SHIKIMATE, DEHYDROQUINASE, AROMATIC AMINO ACID BIOSYNTHESIS, 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 | 36.26 Å |
| 回转半径 Rg (电子) rg_electron | 35.36 Å |
| 零角强度 I(0) i0 | 615738000.00 |
| 分子量 molecular_weight | 194270.0 kDa |
| 排除体积 excluded_volume | 239910 ų |
| 包络体积 envelope_volume | 295470 ų |
| 水化壳体积 shell_volume | 65351 ų |
| 包络直径 envelope_diameter | 105.6 Å |
| 壳层 Rg shell_rg | 45.06 Å |
| 包络 Rg envelope_rg | 34.69 Å |
| 形状 Rg shape_rg | 35.32 Å |
| 总 Rg total_rg | 36.07 Å |
| 总原子数 total_atoms | 13676 |
| 残基数 n_residues | 1800 |
| 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 | 105.1 Å |
| Rg (实空间) rg_real | 35.92 Å |
| Rg 误差 (实空间) rg_real_error | 0.54 Å |
| I(0) (实空间) i0_real | 6.1570e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.0310e+07 |
| Rg (倒空间) rg_reciprocal | 36.13 Å |
| I(0) (倒空间) i0_reciprocal | 615900000.0000 |
| 解质量估计 total_estimate | 0.8930 |
| 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 | 52.5 Å |
| 偏度 Skewness skewness | -0.075 |
| 峰度 Kurtosis kurtosis | -0.559 |
| 角度范围 angular_range | — – 0.2200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 271300000.0000 |
| 实空间数据点数 n_real_points | 45 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.893 |
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) 24 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1v1ja_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
| 结构域编号 domain_id | d1v1jb_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
| 结构域编号 domain_id | d1v1jc_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
| 结构域编号 domain_id | d1v1jd_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
| 结构域编号 domain_id | d1v1je_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
| 结构域编号 domain_id | d1v1jf_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
| 结构域编号 domain_id | d1v1jg_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
| 结构域编号 domain_id | d1v1jh_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
| 结构域编号 domain_id | d1v1ji_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
| 结构域编号 domain_id | d1v1jj_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
| 结构域编号 domain_id | d1v1jk_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
| 结构域编号 domain_id | d1v1jl_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.13 — Type II 3-dehydroquinate dehydratase |
| 家族 Family family | c.23.13.1 — Type II 3-dehydroquinate dehydratase |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 1v1jA00 |
| 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 | 9100 — Dehydroquinase, class II |
| 结构域编号 domain_id | 1v1jB00 |
| 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 | 9100 — Dehydroquinase, class II |
| 结构域编号 domain_id | 1v1jC00 |
| 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 | 9100 — Dehydroquinase, class II |
| 结构域编号 domain_id | 1v1jD00 |
| 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 | 9100 — Dehydroquinase, class II |
| 结构域编号 domain_id | 1v1jE00 |
| 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 | 9100 — Dehydroquinase, class II |
| 结构域编号 domain_id | 1v1jF00 |
| 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 | 9100 — Dehydroquinase, class II |
| 结构域编号 domain_id | 1v1jG00 |
| 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 | 9100 — Dehydroquinase, class II |
| 结构域编号 domain_id | 1v1jH00 |
| 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 | 9100 — Dehydroquinase, class II |
| 结构域编号 domain_id | 1v1jI00 |
| 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 | 9100 — Dehydroquinase, class II |
| 结构域编号 domain_id | 1v1jJ00 |
| 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 | 9100 — Dehydroquinase, class II |
| 结构域编号 domain_id | 1v1jK00 |
| 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 | 9100 — Dehydroquinase, class II |
| 结构域编号 domain_id | 1v1jL00 |
| 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 | 9100 — Dehydroquinase, class II |