1h95
;Solution structure of the single-stranded DNA-binding Cold Shock Domain (CSD) of human Y-box protein 1 (YB1) determined by NMR (10 lowest energy structures) ;
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 | 1h95 |
| 沉积日期 deposition_date | 2001-02-23 |
| 结构标题 title | ;Solution structure of the single-stranded DNA-binding Cold Shock Domain (CSD) of human Y-box protein 1 (YB1) determined by NMR (10 lowest energy structures) ; |
| 关键词 keywords | ;TRANSLATION FACTOR, TRANSCRIPTION FACTOR, OB-FOLD, 5-STRANDED ANTI-PARALLEL BETA-BARREL, SINGLE STRANDED DNA BINDING, COLD SHOCK, Y-BOX ;; TRANSLATION FACTOR |
| 实验方法 method | SOLUTION NMR |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 13.41 Å |
| 回转半径 Rg (电子) rg_electron | 13.13 Å |
| 零角强度 I(0) i0 | 112333000.00 |
| 分子量 molecular_weight | 87439.0 kDa |
| 排除体积 excluded_volume | 109430 ų |
| 包络体积 envelope_volume | 26976 ų |
| 水化壳体积 shell_volume | 14490 ų |
| 包络直径 envelope_diameter | 54.0 Å |
| 壳层 Rg shell_rg | 21.67 Å |
| 包络 Rg envelope_rg | 16.25 Å |
| 形状 Rg shape_rg | 13.05 Å |
| 总 Rg total_rg | 13.82 Å |
| 总原子数 total_atoms | 12370 |
| 残基数 n_residues | 790 |
| 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 | 55.5 Å |
| Rg (实空间) rg_real | 13.40 Å |
| Rg 误差 (实空间) rg_real_error | 0.62 Å |
| I(0) (实空间) i0_real | 1.1230e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.3170e+06 |
| Rg (倒空间) rg_reciprocal | 13.40 Å |
| I(0) (倒空间) i0_reciprocal | 112300000.0000 |
| 解质量估计 total_estimate | 0.7401 |
| 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 | 16.1 Å |
| 偏度 Skewness skewness | 0.365 |
| 峰度 Kurtosis kurtosis | 0.061 |
| 角度范围 angular_range | — – 0.5000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 277900.0000 |
| 实空间数据点数 n_real_points | 80 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.305; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.703; Smooth: 0.998 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (1)
6. 折叠分类 (SCOP + CATH) 2 domains
SCOP 2.08 (1 domains)
| 结构域编号 domain_id | d1h95a_ |
| 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 |
CATH v4.4 (1 domains)
| 结构域编号 domain_id | 1h95A00 |
| 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 |