2k2q
complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain
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 | 2k2q |
| 沉积日期 deposition_date | 2008-04-10 |
| 结构标题 title | complex structure of the external thioesterase of the Surfactin-synthetase with a carrier domain |
| 关键词 keywords | ;thioesterase, a/b-hydrolase, NRPS, non-ribosomal peptide synthetase, type II thioesterase, Antibiotic biosynthesis, Ligase, Multifunctional enzyme, Phosphopantetheine, Sporulation, Stress response, Ligase-Hydrolase COMPLEX ;; Ligase/Hydrolase |
| 实验方法 method | SOLUTION NMR |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 20.93 Å |
| 回转半径 Rg (电子) rg_electron | 20.71 Å |
| 零角强度 I(0) i0 | 5589650000.00 |
| 分子量 molecular_weight | 657110.0 kDa |
| 排除体积 excluded_volume | 829240 ų |
| 包络体积 envelope_volume | 84711 ų |
| 水化壳体积 shell_volume | 30130 ų |
| 包络直径 envelope_diameter | 73.7 Å |
| 壳层 Rg shell_rg | 30.79 Å |
| 包络 Rg envelope_rg | 22.81 Å |
| 形状 Rg shape_rg | 20.70 Å |
| 总 Rg total_rg | 20.86 Å |
| 总原子数 total_atoms | 92270 |
| 残基数 n_residues | 5832 |
| 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 | 65.2 Å |
| Rg (实空间) rg_real | 20.78 Å |
| Rg 误差 (实空间) rg_real_error | 0.34 Å |
| I(0) (实空间) i0_real | 5.5900e+09 |
| I(0) 误差 (实空间) i0_real_error | 7.1570e+07 |
| Rg (倒空间) rg_reciprocal | 20.81 Å |
| I(0) (倒空间) i0_reciprocal | 5590000000.0000 |
| 解质量估计 total_estimate | 0.9004 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 64.3 Å |
| 偏度 Skewness skewness | 0.101 |
| 峰度 Kurtosis kurtosis | -0.510 |
| 角度范围 angular_range | — – 0.3800 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 3780000.0000 |
| 实空间数据点数 n_real_points | 70 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.996 |
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) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d2k2qa1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.28 — Acyl carrier protein-like |
| 超家族 Superfamily superfamily | a.28.1 — ACP-like |
| 家族 Family family | a.28.1.2 — Peptidyl carrier domain |
| 结构域编号 domain_id | d2k2qa2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 2k2qA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — ACP-like |
| 结构域编号 domain_id | 2k2qB00 |
| 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 | 1820 — Alpha/Beta hydrolase fold, catalytic domain |