1y14
Crystal structure of yeast subcomplex of Rpb4 and Rpb7
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 | 1y14 |
| 沉积日期 deposition_date | 2004-11-17 |
| 结构标题 title | Crystal structure of yeast subcomplex of Rpb4 and Rpb7 |
| 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 | 30.06 Å |
| 回转半径 Rg (电子) rg_electron | 29.28 Å |
| 零角强度 I(0) i0 | 67258600.00 |
| 分子量 molecular_weight | 65765.0 kDa |
| 排除体积 excluded_volume | 83084 ų |
| 包络体积 envelope_volume | 107690 ų |
| 水化壳体积 shell_volume | 31326 ų |
| 包络直径 envelope_diameter | 112.2 Å |
| 壳层 Rg shell_rg | 35.73 Å |
| 包络 Rg envelope_rg | 29.48 Å |
| 形状 Rg shape_rg | 29.30 Å |
| 总 Rg total_rg | 29.88 Å |
| 总原子数 total_atoms | 4622 |
| 残基数 n_residues | 583 |
| 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 | 105.7 Å |
| Rg (实空间) rg_real | 30.10 Å |
| Rg 误差 (实空间) rg_real_error | 0.90 Å |
| I(0) (实空间) i0_real | 6.7260e+07 |
| I(0) 误差 (实空间) i0_real_error | 9.6980e+05 |
| Rg (倒空间) rg_reciprocal | 30.09 Å |
| I(0) (倒空间) i0_reciprocal | 67260000.0000 |
| 解质量估计 total_estimate | 0.8708 |
| 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 | 31.9 Å |
| 偏度 Skewness skewness | 0.355 |
| 峰度 Kurtosis kurtosis | -0.391 |
| 角度范围 angular_range | — – 0.2650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 16330000.0000 |
| 实空间数据点数 n_real_points | 54 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; Smooth: 0.965 |
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) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1y14a_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.8 — HRDC-like |
| 家族 Family family | a.60.8.2 — RNA polymerase II subunit RBP4 (RpoF) |
| 结构域编号 domain_id | d1y14b1 |
| 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 | d1y14b2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.230 — Dodecin subunit-like |
| 超家族 Superfamily superfamily | d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE) |
| 家族 Family family | d.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE) |
| 结构域编号 domain_id | d1y14c_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.60 — SAM domain-like |
| 超家族 Superfamily superfamily | a.60.8 — HRDC-like |
| 家族 Family family | a.60.8.2 — RNA polymerase II subunit RBP4 (RpoF) |
| 结构域编号 domain_id | d1y14d1 |
| 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 | d1y14d2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.230 — Dodecin subunit-like |
| 超家族 Superfamily superfamily | d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE) |
| 家族 Family family | d.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE) |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1y14A01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1250 — Growth Hormone; Chain: A; |
| 同源超家族 H-superfamily homologous superfamily | 40 — RNA Polymerase II, Rpb4 subunit |
| 结构域编号 domain_id | 1y14B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 120 — RNA polymerase Rpb7-like, N-terminal domain |
| 结构域编号 domain_id | 1y14B02 |
| 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 | 1y14C01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1250 — Growth Hormone; Chain: A; |
| 同源超家族 H-superfamily homologous superfamily | 40 — RNA Polymerase II, Rpb4 subunit |
| 结构域编号 domain_id | 1y14D01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 120 — RNA polymerase Rpb7-like, N-terminal domain |
| 结构域编号 domain_id | 1y14D02 |
| 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 |