1ytf
YEAST TFIIA/TBP/DNA COMPLEX
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 | 1ytf |
| 沉积日期 deposition_date | 1996-04-05 |
| 结构标题 title | YEAST TFIIA/TBP/DNA COMPLEX |
| 关键词 keywords | TRANSCRIPTION REGULATION, DNA, COMPLEX, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA |
| 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 | 27.87 Å |
| 回转半径 Rg (电子) rg_electron | 28.18 Å |
| 零角强度 I(0) i0 | 52284300.00 |
| 分子量 molecular_weight | 51812.0 kDa |
| 排除体积 excluded_volume | 62876 ų |
| 包络体积 envelope_volume | 80277 ų |
| 水化壳体积 shell_volume | 25829 ų |
| 包络直径 envelope_diameter | 102.4 Å |
| 壳层 Rg shell_rg | 32.54 Å |
| 包络 Rg envelope_rg | 28.14 Å |
| 形状 Rg shape_rg | 28.22 Å |
| 总 Rg total_rg | 28.50 Å |
| 总原子数 total_atoms | 3605 |
| 残基数 n_residues | 404 |
| 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 | 99.5 Å |
| Rg (实空间) rg_real | 28.15 Å |
| Rg 误差 (实空间) rg_real_error | 0.98 Å |
| I(0) (实空间) i0_real | 5.2280e+07 |
| I(0) 误差 (实空间) i0_real_error | 8.6530e+05 |
| Rg (倒空间) rg_reciprocal | 28.06 Å |
| I(0) (倒空间) i0_reciprocal | 52280000.0000 |
| 解质量估计 total_estimate | 0.8248 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 27.9 Å |
| 偏度 Skewness skewness | 0.586 |
| 峰度 Kurtosis kurtosis | 0.003 |
| 角度范围 angular_range | — – 0.2850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 13340000.0000 |
| 实空间数据点数 n_real_points | 58 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.720; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.762; Smooth: 0.796 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1ytfa1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.129 — TBP-like |
| 超家族 Superfamily superfamily | d.129.1 — TATA-box binding protein-like |
| 家族 Family family | d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain |
| 结构域编号 domain_id | d1ytfa2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.129 — TBP-like |
| 超家族 Superfamily superfamily | d.129.1 — TATA-box binding protein-like |
| 家族 Family family | d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain |
| 结构域编号 domain_id | d1ytfb_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.32 — Transcription factor IIA (TFIIA), alpha-helical domain |
| 超家族 Superfamily superfamily | a.32.1 — Transcription factor IIA (TFIIA), alpha-helical domain |
| 家族 Family family | a.32.1.1 — Transcription factor IIA (TFIIA), alpha-helical domain |
| 结构域编号 domain_id | d1ytfc_ |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.56 — Transcription factor IIA (TFIIA), beta-barrel domain |
| 超家族 Superfamily superfamily | b.56.1 — Transcription factor IIA (TFIIA), beta-barrel domain |
| 家族 Family family | b.56.1.1 — Transcription factor IIA (TFIIA), beta-barrel domain |
| 结构域编号 domain_id | d1ytfd1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.32 — Transcription factor IIA (TFIIA), alpha-helical domain |
| 超家族 Superfamily superfamily | a.32.1 — Transcription factor IIA (TFIIA), alpha-helical domain |
| 家族 Family family | a.32.1.1 — Transcription factor IIA (TFIIA), alpha-helical domain |
| 结构域编号 domain_id | d1ytfd2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.56 — Transcription factor IIA (TFIIA), beta-barrel domain |
| 超家族 Superfamily superfamily | b.56.1 — Transcription factor IIA (TFIIA), beta-barrel domain |
| 家族 Family family | b.56.1.1 — Transcription factor IIA (TFIIA), beta-barrel domain |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1ytfA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 310 — TATA-Binding Protein |
| 同源超家族 H-superfamily homologous superfamily | 10 — TATA-Binding Protein |
| 结构域编号 domain_id | 1ytfA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 310 — TATA-Binding Protein |
| 同源超家族 H-superfamily homologous superfamily | 10 — TATA-Binding Protein |
| 结构域编号 domain_id | 1ytfB00 |
| 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 | 100 — |
| 结构域编号 domain_id | 1ytfC00 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 18 — TATA box binding Protein, subunit D; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Transcription factor IIA (TFIIA), beta-barrel domain |
| 结构域编号 domain_id | 1ytfD01 |
| 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 | 190 — Transcription factor IIA gamma subunit, alpha-helical domain |
| 结构域编号 domain_id | 1ytfD02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 18 — TATA box binding Protein, subunit D; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Transcription factor IIA (TFIIA), beta-barrel domain |