1nvf
Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+, ADP and carbaphosphonate
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 | 1nvf |
| 沉积日期 deposition_date | 2003-02-03 |
| 结构标题 title | Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+, ADP and carbaphosphonate |
| 关键词 keywords | SHIKIMATE PATHWAY, AROMATIC AMINO ACID BIOSYNTHESIS, DHQS, CLOSED FORM, FORM H, DOMAIN MOVEMENT, CYCLASE, 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 | 85.66 Å |
| 回转半径 Rg (电子) rg_electron | 87.99 Å |
| 零角强度 I(0) i0 | 228749000.00 |
| 分子量 molecular_weight | 129310.0 kDa |
| 排除体积 excluded_volume | 162510 ų |
| 包络体积 envelope_volume | 289450 ų |
| 水化壳体积 shell_volume | 28937 ų |
| 包络直径 envelope_diameter | 251.5 Å |
| 壳层 Rg shell_rg | 74.19 Å |
| 包络 Rg envelope_rg | 85.28 Å |
| 形状 Rg shape_rg | 87.97 Å |
| 总 Rg total_rg | 87.86 Å |
| 总原子数 total_atoms | 9058 |
| 残基数 n_residues | 1164 |
| 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 | 366.1 Å |
| Rg (实空间) rg_real | 87.70 Å |
| Rg 误差 (实空间) rg_real_error | 9.94 Å |
| I(0) (实空间) i0_real | 2.2870e+08 |
| I(0) 误差 (实空间) i0_real_error | 6.4290e+06 |
| Rg (倒空间) rg_reciprocal | 76.04 Å |
| I(0) (倒空间) i0_reciprocal | 222600000.0000 |
| 解质量估计 total_estimate | 0.5388 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 4 |
| 主峰位置 r_peak_primary | 20.3 Å |
| 偏度 Skewness skewness | 0.307 |
| 峰度 Kurtosis kurtosis | -1.645 |
| 角度范围 angular_range | — – 0.0900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0004 |
| 最高正则化参数 α highest_alpha | 3839000.0000 |
| 实空间数据点数 n_real_points | 19 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.000; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.000 |
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) 9 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1nvfa_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.22 — Dehydroquinate synthase-like |
| 超家族 Superfamily superfamily | e.22.1 — Dehydroquinate synthase-like |
| 家族 Family family | e.22.1.1 — Dehydroquinate synthase, DHQS |
| 结构域编号 domain_id | d1nvfb_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.22 — Dehydroquinate synthase-like |
| 超家族 Superfamily superfamily | e.22.1 — Dehydroquinate synthase-like |
| 家族 Family family | e.22.1.1 — Dehydroquinate synthase, DHQS |
| 结构域编号 domain_id | d1nvfc_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.22 — Dehydroquinate synthase-like |
| 超家族 Superfamily superfamily | e.22.1 — Dehydroquinate synthase-like |
| 家族 Family family | e.22.1.1 — Dehydroquinate synthase, DHQS |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1nvfA01 |
| 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 | 1970 — |
| 结构域编号 domain_id | 1nvfA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1090 — Dehydroquinate synthase-like, alpha domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dehydroquinate synthase-like - alpha domain |
| 结构域编号 domain_id | 1nvfB01 |
| 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 | 1970 — |
| 结构域编号 domain_id | 1nvfB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1090 — Dehydroquinate synthase-like, alpha domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dehydroquinate synthase-like - alpha domain |
| 结构域编号 domain_id | 1nvfC01 |
| 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 | 1970 — |
| 结构域编号 domain_id | 1nvfC02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1090 — Dehydroquinate synthase-like, alpha domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dehydroquinate synthase-like - alpha domain |