1kk5
Crystal Structure of Vat(D) (Form II)
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 | 1kk5 |
| 沉积日期 deposition_date | 2001-12-06 |
| 结构标题 title | Crystal Structure of Vat(D) (Form II) |
| 关键词 keywords | Antibiotic resistance, acyltransferase, TRANSFERASE; TRANSFERASE |
| 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 | 59.82 Å |
| 回转半径 Rg (电子) rg_electron | 60.14 Å |
| 零角强度 I(0) i0 | 250704000.00 |
| 分子量 molecular_weight | 137660.0 kDa |
| 排除体积 excluded_volume | 173850 ų |
| 包络体积 envelope_volume | 286280 ų |
| 水化壳体积 shell_volume | 39478 ų |
| 包络直径 envelope_diameter | 183.2 Å |
| 壳层 Rg shell_rg | 67.26 Å |
| 包络 Rg envelope_rg | 55.52 Å |
| 形状 Rg shape_rg | 60.15 Å |
| 总 Rg total_rg | 60.26 Å |
| 总原子数 total_atoms | 9700 |
| 残基数 n_residues | 1236 |
| 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 | 176.3 Å |
| Rg (实空间) rg_real | 60.36 Å |
| Rg 误差 (实空间) rg_real_error | 1.79 Å |
| I(0) (实空间) i0_real | 2.5070e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.6270e+06 |
| Rg (倒空间) rg_reciprocal | 59.25 Å |
| I(0) (倒空间) i0_reciprocal | 250200000.0000 |
| 解质量估计 total_estimate | 0.5772 |
| 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 | 33.9 Å |
| 偏度 Skewness skewness | 0.149 |
| 峰度 Kurtosis kurtosis | -1.317 |
| 角度范围 angular_range | — – 0.1300 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 9820000.0000 |
| 实空间数据点数 n_real_points | 27 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.058; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.326; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1kk5a_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.81 — Single-stranded left-handed beta-helix |
| 超家族 Superfamily superfamily | b.81.1 — Trimeric LpxA-like enzymes |
| 家族 Family family | b.81.1.3 — Galactoside acetyltransferase-like |
| 结构域编号 domain_id | d1kk5b_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.81 — Single-stranded left-handed beta-helix |
| 超家族 Superfamily superfamily | b.81.1 — Trimeric LpxA-like enzymes |
| 家族 Family family | b.81.1.3 — Galactoside acetyltransferase-like |
| 结构域编号 domain_id | d1kk5c_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.81 — Single-stranded left-handed beta-helix |
| 超家族 Superfamily superfamily | b.81.1 — Trimeric LpxA-like enzymes |
| 家族 Family family | b.81.1.3 — Galactoside acetyltransferase-like |
| 结构域编号 domain_id | d1kk5d_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.81 — Single-stranded left-handed beta-helix |
| 超家族 Superfamily superfamily | b.81.1 — Trimeric LpxA-like enzymes |
| 家族 Family family | b.81.1.3 — Galactoside acetyltransferase-like |
| 结构域编号 domain_id | d1kk5e_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.81 — Single-stranded left-handed beta-helix |
| 超家族 Superfamily superfamily | b.81.1 — Trimeric LpxA-like enzymes |
| 家族 Family family | b.81.1.3 — Galactoside acetyltransferase-like |
| 结构域编号 domain_id | d1kk5f_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.81 — Single-stranded left-handed beta-helix |
| 超家族 Superfamily superfamily | b.81.1 — Trimeric LpxA-like enzymes |
| 家族 Family family | b.81.1.3 — Galactoside acetyltransferase-like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1kk5A00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 160 — 3 Solenoid |
| 拓扑 Topology topology | 10 — UDP N-Acetylglucosamine Acyltransferase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hexapeptide repeat proteins |
| 结构域编号 domain_id | 1kk5B00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 160 — 3 Solenoid |
| 拓扑 Topology topology | 10 — UDP N-Acetylglucosamine Acyltransferase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hexapeptide repeat proteins |
| 结构域编号 domain_id | 1kk5C00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 160 — 3 Solenoid |
| 拓扑 Topology topology | 10 — UDP N-Acetylglucosamine Acyltransferase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hexapeptide repeat proteins |
| 结构域编号 domain_id | 1kk5D00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 160 — 3 Solenoid |
| 拓扑 Topology topology | 10 — UDP N-Acetylglucosamine Acyltransferase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hexapeptide repeat proteins |
| 结构域编号 domain_id | 1kk5E00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 160 — 3 Solenoid |
| 拓扑 Topology topology | 10 — UDP N-Acetylglucosamine Acyltransferase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hexapeptide repeat proteins |
| 结构域编号 domain_id | 1kk5F00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 160 — 3 Solenoid |
| 拓扑 Topology topology | 10 — UDP N-Acetylglucosamine Acyltransferase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hexapeptide repeat proteins |