1ghd
Crystal structure of the glutaryl-7-aminocephalosporanic acid acylase by mad phasing
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 | 1ghd |
| 沉积日期 deposition_date | 2000-12-07 |
| 结构标题 title | Crystal structure of the glutaryl-7-aminocephalosporanic acid acylase by mad phasing |
| 关键词 keywords | cephalosporin acylase, HYDROLASE; 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 | 26.58 Å |
| 回转半径 Rg (电子) rg_electron | 25.63 Å |
| 零角强度 I(0) i0 | 96660400.00 |
| 分子量 molecular_weight | 75494.0 kDa |
| 排除体积 excluded_volume | 93203 ų |
| 包络体积 envelope_volume | 107310 ų |
| 水化壳体积 shell_volume | 33914 ų |
| 包络直径 envelope_diameter | 85.4 Å |
| 壳层 Rg shell_rg | 33.86 Å |
| 包络 Rg envelope_rg | 25.78 Å |
| 形状 Rg shape_rg | 25.65 Å |
| 总 Rg total_rg | 26.32 Å |
| 总原子数 total_atoms | 5306 |
| 残基数 n_residues | 661 |
| 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 | 81.2 Å |
| Rg (实空间) rg_real | 26.42 Å |
| Rg 误差 (实空间) rg_real_error | 0.40 Å |
| I(0) (实空间) i0_real | 9.6660e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.3890e+06 |
| Rg (倒空间) rg_reciprocal | 26.47 Å |
| I(0) (倒空间) i0_reciprocal | 96660000.0000 |
| 解质量估计 total_estimate | 0.9112 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 33.8 Å |
| 偏度 Skewness skewness | 0.130 |
| 峰度 Kurtosis kurtosis | -0.554 |
| 角度范围 angular_range | — – 0.3000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 23950000.0000 |
| 实空间数据点数 n_real_points | 61 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.992 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 5 domains
SCOP 2.08 (1 domains)
| 结构域编号 domain_id | d1ghd.1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.153 — Ntn hydrolase-like |
| 超家族 Superfamily superfamily | d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases) |
| 家族 Family family | d.153.1.2 — Penicillin acylase, catalytic domain |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1ghdA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 439 — Penicillin Amidohydrolase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Penicillin Amidohydrolase, domain 1 |
| 结构域编号 domain_id | 1ghdB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 60 — 4-Layer Sandwich |
| 拓扑 Topology topology | 20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain |
| 结构域编号 domain_id | 1ghdB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1400 — Penicillin amidase (Acylase) alpha subunit, N-terminal domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aminohydrolase, alpha-helical knob region |
| 结构域编号 domain_id | 1ghdB03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 120 — Penicillin G acylase, beta-roll domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region |