2glp
Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori complexed with compound 1
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 | 2glp |
| 沉积日期 deposition_date | 2006-04-05 |
| 结构标题 title | Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) from Helicobacter pylori complexed with compound 1 |
| 关键词 keywords | FabZ complex, 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 | 28.77 Å |
| 回转半径 Rg (电子) rg_electron | 27.61 Å |
| 零角强度 I(0) i0 | 155797000.00 |
| 分子量 molecular_weight | 105360.0 kDa |
| 排除体积 excluded_volume | 134540 ų |
| 包络体积 envelope_volume | 156000 ų |
| 水化壳体积 shell_volume | 44255 ų |
| 包络直径 envelope_diameter | 88.2 Å |
| 壳层 Rg shell_rg | 37.03 Å |
| 包络 Rg envelope_rg | 27.63 Å |
| 形状 Rg shape_rg | 27.57 Å |
| 总 Rg total_rg | 28.70 Å |
| 总原子数 total_atoms | 7428 |
| 残基数 n_residues | 905 |
| 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 | 83.4 Å |
| Rg (实空间) rg_real | 28.57 Å |
| Rg 误差 (实空间) rg_real_error | 0.33 Å |
| I(0) (实空间) i0_real | 1.5580e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.0420e+06 |
| Rg (倒空间) rg_reciprocal | 28.66 Å |
| I(0) (倒空间) i0_reciprocal | 155800000.0000 |
| 解质量估计 total_estimate | 0.7136 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 37.9 Å |
| 偏度 Skewness skewness | 0.038 |
| 峰度 Kurtosis kurtosis | -0.578 |
| 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 | 61350000.0000 |
| 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: 0.965; Stabil: 1.000; Sysdev: 0.156; Positv: 1.000; Valcen: 0.972; Smooth: 0.937 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d2glpa_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.38 — Thioesterase/thiol ester dehydrase-isomerase |
| 超家族 Superfamily superfamily | d.38.1 — Thioesterase/thiol ester dehydrase-isomerase |
| 家族 Family family | d.38.1.6 — FabZ-like |
| 结构域编号 domain_id | d2glpb_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.38 — Thioesterase/thiol ester dehydrase-isomerase |
| 超家族 Superfamily superfamily | d.38.1 — Thioesterase/thiol ester dehydrase-isomerase |
| 家族 Family family | d.38.1.6 — FabZ-like |
| 结构域编号 domain_id | d2glpc_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.38 — Thioesterase/thiol ester dehydrase-isomerase |
| 超家族 Superfamily superfamily | d.38.1 — Thioesterase/thiol ester dehydrase-isomerase |
| 家族 Family family | d.38.1.6 — FabZ-like |
| 结构域编号 domain_id | d2glpd_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.38 — Thioesterase/thiol ester dehydrase-isomerase |
| 超家族 Superfamily superfamily | d.38.1 — Thioesterase/thiol ester dehydrase-isomerase |
| 家族 Family family | d.38.1.6 — FabZ-like |
| 结构域编号 domain_id | d2glpe_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.38 — Thioesterase/thiol ester dehydrase-isomerase |
| 超家族 Superfamily superfamily | d.38.1 — Thioesterase/thiol ester dehydrase-isomerase |
| 家族 Family family | d.38.1.6 — FabZ-like |
| 结构域编号 domain_id | d2glpf_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.38 — Thioesterase/thiol ester dehydrase-isomerase |
| 超家族 Superfamily superfamily | d.38.1 — Thioesterase/thiol ester dehydrase-isomerase |
| 家族 Family family | d.38.1.6 — FabZ-like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2glpA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 129 — Thiol Ester Dehydrase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hotdog Thioesterase |
| 结构域编号 domain_id | 2glpB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 129 — Thiol Ester Dehydrase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hotdog Thioesterase |
| 结构域编号 domain_id | 2glpC00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 129 — Thiol Ester Dehydrase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hotdog Thioesterase |
| 结构域编号 domain_id | 2glpD00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 129 — Thiol Ester Dehydrase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hotdog Thioesterase |
| 结构域编号 domain_id | 2glpE00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 129 — Thiol Ester Dehydrase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hotdog Thioesterase |
| 结构域编号 domain_id | 2glpF00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 129 — Thiol Ester Dehydrase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hotdog Thioesterase |