1pv4
X-ray crystal structure of the Rho transcription termination factor in complex with single stranded DNA
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 | 1pv4 |
| 沉积日期 deposition_date | 2003-06-26 |
| 结构标题 title | X-ray crystal structure of the Rho transcription termination factor in complex with single stranded DNA |
| 关键词 keywords | PROTEIN-ssDNA 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 | 46.94 Å |
| 回转半径 Rg (电子) rg_electron | 46.20 Å |
| 零角强度 I(0) i0 | 1151420000.00 |
| 分子量 molecular_weight | 275900.0 kDa |
| 排除体积 excluded_volume | 341910 ų |
| 包络体积 envelope_volume | 487760 ų |
| 水化壳体积 shell_volume | 84092 ų |
| 包络直径 envelope_diameter | 152.8 Å |
| 壳层 Rg shell_rg | 54.93 Å |
| 包络 Rg envelope_rg | 45.04 Å |
| 形状 Rg shape_rg | 46.16 Å |
| 总 Rg total_rg | 46.64 Å |
| 总原子数 total_atoms | 19036 |
| 残基数 n_residues | 2314 |
| 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 | 149.2 Å |
| Rg (实空间) rg_real | 46.65 Å |
| Rg 误差 (实空间) rg_real_error | 1.04 Å |
| I(0) (实空间) i0_real | 1.1510e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.1000e+07 |
| Rg (倒空间) rg_reciprocal | 46.94 Å |
| I(0) (倒空间) i0_reciprocal | 1152000000.0000 |
| 解质量估计 total_estimate | 0.8948 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 65.8 Å |
| 偏度 Skewness skewness | 0.052 |
| 峰度 Kurtosis kurtosis | -0.609 |
| 角度范围 angular_range | — – 0.1700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 128400000.0000 |
| 实空间数据点数 n_real_points | 35 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.929 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 29 domains
SCOP 2.08 (17 domains)
| 结构域编号 domain_id | d1pv4a1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.140 — LEM/SAP HeH motif |
| 超家族 Superfamily superfamily | a.140.3 — Rho N-terminal domain-like |
| 家族 Family family | a.140.3.1 — Rho termination factor, N-terminal domain |
| 结构域编号 domain_id | d1pv4a2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.40 — OB-fold |
| 超家族 Superfamily superfamily | b.40.4 — Nucleic acid-binding proteins |
| 家族 Family family | b.40.4.5 — Cold shock DNA-binding domain-like |
| 结构域编号 domain_id | d1pv4a3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.11 — RecA protein-like (ATPase-domain) |
| 结构域编号 domain_id | d1pv4b1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.40 — OB-fold |
| 超家族 Superfamily superfamily | b.40.4 — Nucleic acid-binding proteins |
| 家族 Family family | b.40.4.5 — Cold shock DNA-binding domain-like |
| 结构域编号 domain_id | d1pv4b2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.11 — RecA protein-like (ATPase-domain) |
| 结构域编号 domain_id | d1pv4c1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.140 — LEM/SAP HeH motif |
| 超家族 Superfamily superfamily | a.140.3 — Rho N-terminal domain-like |
| 家族 Family family | a.140.3.1 — Rho termination factor, N-terminal domain |
| 结构域编号 domain_id | d1pv4c2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.40 — OB-fold |
| 超家族 Superfamily superfamily | b.40.4 — Nucleic acid-binding proteins |
| 家族 Family family | b.40.4.5 — Cold shock DNA-binding domain-like |
| 结构域编号 domain_id | d1pv4c3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.11 — RecA protein-like (ATPase-domain) |
| 结构域编号 domain_id | d1pv4d1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.140 — LEM/SAP HeH motif |
| 超家族 Superfamily superfamily | a.140.3 — Rho N-terminal domain-like |
| 家族 Family family | a.140.3.1 — Rho termination factor, N-terminal domain |
| 结构域编号 domain_id | d1pv4d2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.40 — OB-fold |
| 超家族 Superfamily superfamily | b.40.4 — Nucleic acid-binding proteins |
| 家族 Family family | b.40.4.5 — Cold shock DNA-binding domain-like |
| 结构域编号 domain_id | d1pv4d3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.11 — RecA protein-like (ATPase-domain) |
| 结构域编号 domain_id | d1pv4e1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.140 — LEM/SAP HeH motif |
| 超家族 Superfamily superfamily | a.140.3 — Rho N-terminal domain-like |
| 家族 Family family | a.140.3.1 — Rho termination factor, N-terminal domain |
| 结构域编号 domain_id | d1pv4e2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.40 — OB-fold |
| 超家族 Superfamily superfamily | b.40.4 — Nucleic acid-binding proteins |
| 家族 Family family | b.40.4.5 — Cold shock DNA-binding domain-like |
| 结构域编号 domain_id | d1pv4e3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.11 — RecA protein-like (ATPase-domain) |
| 结构域编号 domain_id | d1pv4f1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.140 — LEM/SAP HeH motif |
| 超家族 Superfamily superfamily | a.140.3 — Rho N-terminal domain-like |
| 家族 Family family | a.140.3.1 — Rho termination factor, N-terminal domain |
| 结构域编号 domain_id | d1pv4f2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.40 — OB-fold |
| 超家族 Superfamily superfamily | b.40.4 — Nucleic acid-binding proteins |
| 家族 Family family | b.40.4.5 — Cold shock DNA-binding domain-like |
| 结构域编号 domain_id | d1pv4f3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.11 — RecA protein-like (ATPase-domain) |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 1pv4A01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 140 — Nucleic acid-binding proteins |
| 结构域编号 domain_id | 1pv4A02 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1pv4B01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 140 — Nucleic acid-binding proteins |
| 结构域编号 domain_id | 1pv4B02 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1pv4C01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 140 — Nucleic acid-binding proteins |
| 结构域编号 domain_id | 1pv4C02 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1pv4D01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 140 — Nucleic acid-binding proteins |
| 结构域编号 domain_id | 1pv4D02 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1pv4E01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 140 — Nucleic acid-binding proteins |
| 结构域编号 domain_id | 1pv4E02 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1pv4F01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P) |
| 同源超家族 H-superfamily homologous superfamily | 140 — Nucleic acid-binding proteins |
| 结构域编号 domain_id | 1pv4F02 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |