1upg
Crystal structure of the quorum-sensing protein TraM from Agrobacterium tumefaciens
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 | 1upg |
| 沉积日期 deposition_date | 2003-09-30 |
| 结构标题 title | Crystal structure of the quorum-sensing protein TraM from Agrobacterium tumefaciens |
| 关键词 keywords | TRANSCRIPTION REPRESSOR, NEGATIVE REGULATOR, QUORUM-SENSING, CONJUGATION, TRANSCRIPTION REGULATION, REPRESSOR; TRANSCRIPTION REPRESSOR |
| 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 | 18.88 Å |
| 回转半径 Rg (电子) rg_electron | 18.06 Å |
| 零角强度 I(0) i0 | 8279080.00 |
| 分子量 molecular_weight | 21348.0 kDa |
| 排除体积 excluded_volume | 26775 ų |
| 包络体积 envelope_volume | 31610 ų |
| 水化壳体积 shell_volume | 15255 ų |
| 包络直径 envelope_diameter | 66.5 Å |
| 壳层 Rg shell_rg | 23.36 Å |
| 包络 Rg envelope_rg | 18.23 Å |
| 形状 Rg shape_rg | 18.10 Å |
| 总 Rg total_rg | 18.81 Å |
| 总原子数 total_atoms | 1483 |
| 残基数 n_residues | 186 |
| 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 | 64.2 Å |
| Rg (实空间) rg_real | 18.85 Å |
| Rg 误差 (实空间) rg_real_error | 0.56 Å |
| I(0) (实空间) i0_real | 8.2790e+06 |
| I(0) 误差 (实空间) i0_real_error | 1.1780e+05 |
| Rg (倒空间) rg_reciprocal | 18.86 Å |
| I(0) (倒空间) i0_reciprocal | 8279000.0000 |
| 解质量估计 total_estimate | 0.8002 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 23.2 Å |
| 偏度 Skewness skewness | 0.299 |
| 峰度 Kurtosis kurtosis | -0.313 |
| 角度范围 angular_range | — – 0.4200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 1391000.0000 |
| 实空间数据点数 n_real_points | 73 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.810; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; 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) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1upga_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.13 — Transcriptional repressor TraM |
| 家族 Family family | a.2.13.1 — Transcriptional repressor TraM |
| 结构域编号 domain_id | d1upgb_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.13 — Transcriptional repressor TraM |
| 家族 Family family | a.2.13.1 — Transcriptional repressor TraM |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1upgA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 160 — HR1 repeat |
| 结构域编号 domain_id | 1upgB00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 160 — HR1 repeat |