1ynj
Taq RNA polymerase-Sorangicin 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 | 1ynj |
| 沉积日期 deposition_date | 2005-01-24 |
| 结构标题 title | Taq RNA polymerase-Sorangicin complex |
| 关键词 keywords | TRANSFERASE; TRANSFERASE |
| 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 | 53.49 Å |
| 回转半径 Rg (电子) rg_electron | 54.20 Å |
| 零角强度 I(0) i0 | 1686970000.00 |
| 分子量 molecular_weight | 345750.0 kDa |
| 排除体积 excluded_volume | 434650 ų |
| 包络体积 envelope_volume | 638940 ų |
| 水化壳体积 shell_volume | 102170 ų |
| 包络直径 envelope_diameter | 230.8 Å |
| 壳层 Rg shell_rg | 55.49 Å |
| 包络 Rg envelope_rg | 55.13 Å |
| 形状 Rg shape_rg | 54.23 Å |
| 总 Rg total_rg | 54.13 Å |
| 总原子数 total_atoms | 24369 |
| 残基数 n_residues | 3151 |
| 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 | 214.5 Å |
| Rg (实空间) rg_real | 54.16 Å |
| Rg 误差 (实空间) rg_real_error | 2.70 Å |
| I(0) (实空间) i0_real | 1.6870e+09 |
| I(0) 误差 (实空间) i0_real_error | 3.3100e+07 |
| Rg (倒空间) rg_reciprocal | 52.98 Å |
| I(0) (倒空间) i0_reciprocal | 1684000000.0000 |
| 解质量估计 total_estimate | 0.7452 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 59.2 Å |
| 偏度 Skewness skewness | 0.982 |
| 峰度 Kurtosis kurtosis | 1.271 |
| 角度范围 angular_range | — – 0.1450 Å−1 |
| 当前正则化参数 α current_alpha | 0.0003 |
| 最高正则化参数 α highest_alpha | 168600000.0000 |
| 实空间数据点数 n_real_points | 30 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.272; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.924 |
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) 25 domains
SCOP 2.08 (7 domains)
| 结构域编号 domain_id | d1ynja1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.74 — DCoH-like |
| 超家族 Superfamily superfamily | d.74.3 — RBP11-like subunits of RNA polymerase |
| 家族 Family family | d.74.3.1 — RNA polymerase alpha subunit dimerisation domain |
| 结构域编号 domain_id | d1ynja2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.181 — Insert subdomain of RNA polymerase alpha subunit |
| 超家族 Superfamily superfamily | d.181.1 — Insert subdomain of RNA polymerase alpha subunit |
| 家族 Family family | d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit |
| 结构域编号 domain_id | d1ynjb1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.74 — DCoH-like |
| 超家族 Superfamily superfamily | d.74.3 — RBP11-like subunits of RNA polymerase |
| 家族 Family family | d.74.3.1 — RNA polymerase alpha subunit dimerisation domain |
| 结构域编号 domain_id | d1ynjb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.181 — Insert subdomain of RNA polymerase alpha subunit |
| 超家族 Superfamily superfamily | d.181.1 — Insert subdomain of RNA polymerase alpha subunit |
| 家族 Family family | d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit |
| 结构域编号 domain_id | d1ynjc1 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase |
| 超家族 Superfamily superfamily | e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase |
| 家族 Family family | e.29.1.1 — RNA-polymerase beta |
| 结构域编号 domain_id | d1ynjd1 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase |
| 超家族 Superfamily superfamily | e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase |
| 家族 Family family | e.29.1.2 — RNA-polymerase beta-prime |
| 结构域编号 domain_id | d1ynjk1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.143 — RPB6/omega subunit-like |
| 超家族 Superfamily superfamily | a.143.1 — RPB6/omega subunit-like |
| 家族 Family family | a.143.1.1 — RNA polymerase omega subunit |
CATH v4.4 (18 domains)
| 结构域编号 domain_id | 1ynjA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1360 — Gyrase A; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — RNA polymerase, RBP11-like subunit |
| 结构域编号 domain_id | 1ynjA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 170 — Beta Complex |
| 拓扑 Topology topology | 120 — RNA Polymerase Alpha Subunit; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 12 — DNA-directed RNA polymerase, insert domain |
| 结构域编号 domain_id | 1ynjB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1360 — Gyrase A; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — RNA polymerase, RBP11-like subunit |
| 结构域编号 domain_id | 1ynjB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 170 — Beta Complex |
| 拓扑 Topology topology | 120 — RNA Polymerase Alpha Subunit; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 12 — DNA-directed RNA polymerase, insert domain |
| 结构域编号 domain_id | 1ynjC01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 270 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 |
| 同源超家族 H-superfamily homologous superfamily | 10 — DNA-directed RNA polymerase, subunit 2, domain 6 |
| 结构域编号 domain_id | 1ynjC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1100 — Rna Polymerase Beta Subunit; Chain: C,domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1ynjC03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — RNA polymerase Rpb2, domain 2 |
| 结构域编号 domain_id | 1ynjC04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 150 — Rna Polymerase Beta Subunit; Chain: C, domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — DNA-directed RNA polymerase, beta subunit, external 1 domain |
| 结构域编号 domain_id | 1ynjC05 |
| 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 | 100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain |
| 结构域编号 domain_id | 1ynjC06 |
| 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 | 150 — RNA polymerase II, Rpb2 subunit, wall domain |
| 结构域编号 domain_id | 1ynjD03 |
| 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 | 100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain |
| 结构域编号 domain_id | 1ynjD04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 40 — Barwin-like endoglucanases |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1ynjD05 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 274 — Enzyme I; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 100 — RNA polymerase Rpb1, domain 3 |
| 结构域编号 domain_id | 1ynjD06 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 132 — Topoisomerase I; Chain A, domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 30 — RNA polymerase Rpb1 funnel domain |
| 结构域编号 domain_id | 1ynjJ01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1790 — PTS-regulatory domain, PRD |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1ynjJ02 |
| 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 | 100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain |
| 结构域编号 domain_id | 1ynjJ03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 390 — |
| 结构域编号 domain_id | 1ynjK00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 940 — Eukaryotic RPB6 RNA polymerase subunit |
| 同源超家族 H-superfamily homologous superfamily | 10 — RNA polymerase subunit, RPB6/omega |