1w26
Trigger Factor in Complex with the Ribosome forms a Molecular Cradle for Nascent Proteins
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 | 1w26 |
| 沉积日期 deposition_date | 2004-06-28 |
| 结构标题 title | Trigger Factor in Complex with the Ribosome forms a Molecular Cradle for Nascent Proteins |
| 关键词 keywords | CHAPERONE, PROTEIN FOLDING, RIBOSOME ASSOCIATED PROTEIN, NASCENT CHAIN, CELL DIVISION, ISOMERASE; CHAPERONE |
| 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 | 45.26 Å |
| 回转半径 Rg (电子) rg_electron | 45.67 Å |
| 零角强度 I(0) i0 | 152709000.00 |
| 分子量 molecular_weight | 97391.0 kDa |
| 排除体积 excluded_volume | 120740 ų |
| 包络体积 envelope_volume | 206400 ų |
| 水化壳体积 shell_volume | 41268 ų |
| 包络直径 envelope_diameter | 158.8 Å |
| 壳层 Rg shell_rg | 44.21 Å |
| 包络 Rg envelope_rg | 45.29 Å |
| 形状 Rg shape_rg | 45.68 Å |
| 总 Rg total_rg | 45.54 Å |
| 总原子数 total_atoms | 6772 |
| 残基数 n_residues | 842 |
| 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 | 163.0 Å |
| Rg (实空间) rg_real | 45.42 Å |
| Rg 误差 (实空间) rg_real_error | 1.80 Å |
| I(0) (实空间) i0_real | 1.5270e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.2570e+06 |
| Rg (倒空间) rg_reciprocal | 45.26 Å |
| I(0) (倒空间) i0_reciprocal | 152700000.0000 |
| 解质量估计 total_estimate | 0.7930 |
| 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 | 51.2 Å |
| 偏度 Skewness skewness | 0.370 |
| 峰度 Kurtosis kurtosis | -0.236 |
| 角度范围 angular_range | — – 0.1750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 7875000.0000 |
| 实空间数据点数 n_real_points | 36 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.925; 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) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1w26a1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.223 — Triger factor/SurA peptide-binding domain-like |
| 超家族 Superfamily superfamily | a.223.1 — Triger factor/SurA peptide-binding domain-like |
| 家族 Family family | a.223.1.1 — TF C-terminus |
| 结构域编号 domain_id | d1w26a2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.241 — Ribosome binding domain-like |
| 超家族 Superfamily superfamily | d.241.2 — Trigger factor ribosome-binding domain |
| 家族 Family family | d.241.2.1 — Trigger factor ribosome-binding domain |
| 结构域编号 domain_id | d1w26a3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.26 — FKBP-like |
| 超家族 Superfamily superfamily | d.26.1 — FKBP-like |
| 家族 Family family | d.26.1.1 — FKBP immunophilin/proline isomerase |
| 结构域编号 domain_id | d1w26b1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.223 — Triger factor/SurA peptide-binding domain-like |
| 超家族 Superfamily superfamily | a.223.1 — Triger factor/SurA peptide-binding domain-like |
| 家族 Family family | a.223.1.1 — TF C-terminus |
| 结构域编号 domain_id | d1w26b2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.241 — Ribosome binding domain-like |
| 超家族 Superfamily superfamily | d.241.2 — Trigger factor ribosome-binding domain |
| 家族 Family family | d.241.2.1 — Trigger factor ribosome-binding domain |
| 结构域编号 domain_id | d1w26b3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.26 — FKBP-like |
| 超家族 Superfamily superfamily | d.26.1 — FKBP-like |
| 家族 Family family | d.26.1.1 — FKBP immunophilin/proline isomerase |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1w26A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 1050 — Trigger factor ribosome-binding domain |
| 结构域编号 domain_id | 1w26A02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3120 — Trigger factor, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Trigger factor, C-terminal domain |
| 结构域编号 domain_id | 1w26A03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 50 — Chitinase A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 40 — |
| 结构域编号 domain_id | 1w26B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 1050 — Trigger factor ribosome-binding domain |
| 结构域编号 domain_id | 1w26B02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3120 — Trigger factor, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Trigger factor, C-terminal domain |
| 结构域编号 domain_id | 1w26B03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 50 — Chitinase A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 40 — |