1pp8
crystal structure of the T. vaginalis IBP39 Initiator binding domain (IBD) bound to the alpha-SCS Inr element
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 | 1pp8 |
| 沉积日期 deposition_date | 2003-06-16 |
| 结构标题 title | crystal structure of the T. vaginalis IBP39 Initiator binding domain (IBD) bound to the alpha-SCS Inr element |
| 关键词 keywords | IBP39, Initiator binding protein, Inr, core promoter, transcription, T. vaginalis, 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 | 51.43 Å |
| 回转半径 Rg (电子) rg_electron | 53.26 Å |
| 零角强度 I(0) i0 | 223471000.00 |
| 分子量 molecular_weight | 104870.0 kDa |
| 排除体积 excluded_volume | 123630 ų |
| 包络体积 envelope_volume | 204600 ų |
| 水化壳体积 shell_volume | 36953 ų |
| 包络直径 envelope_diameter | 178.5 Å |
| 壳层 Rg shell_rg | 46.40 Å |
| 包络 Rg envelope_rg | 51.80 Å |
| 形状 Rg shape_rg | 53.30 Å |
| 总 Rg total_rg | 52.91 Å |
| 总原子数 total_atoms | 7268 |
| 残基数 n_residues | 751 |
| 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 | 170.3 Å |
| Rg (实空间) rg_real | 52.05 Å |
| Rg 误差 (实空间) rg_real_error | 2.28 Å |
| I(0) (实空间) i0_real | 2.2350e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.5450e+06 |
| Rg (倒空间) rg_reciprocal | 50.89 Å |
| I(0) (倒空间) i0_reciprocal | 223100000.0000 |
| 解质量估计 total_estimate | 0.7019 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 4 |
| 主峰位置 r_peak_primary | 33.0 Å |
| 偏度 Skewness skewness | 0.514 |
| 峰度 Kurtosis kurtosis | -0.652 |
| 角度范围 angular_range | — – 0.1550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 5143000.0000 |
| 实空间数据点数 n_real_points | 32 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.589; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.329; Smooth: 0.029 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1pp8f_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain |
| 结构域编号 domain_id | d1pp8m_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain |
| 结构域编号 domain_id | d1pp8o_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain |
| 结构域编号 domain_id | d1pp8p_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain |
| 结构域编号 domain_id | d1pp8u_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain |
| 结构域编号 domain_id | d1pp8v_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.44 — 39 kda initiator binding protein, IBP39, N-terminal domain |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1pp8F00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1pp8M00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1pp8O00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1pp8P00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1pp8U00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1pp8V00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |