1f5y
NMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND LIGAND-BINDING MODULES OF THE HUMAN LDL RECEPTOR
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 | 1f5y |
| 沉积日期 deposition_date | 2000-06-18 |
| 结构标题 title | NMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND LIGAND-BINDING MODULES OF THE HUMAN LDL RECEPTOR |
| 关键词 keywords | Beta hairpin, 3-10 helix, calcium binding, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN |
| 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 | 30.86 Å |
| 回转半径 Rg (电子) rg_electron | 30.31 Å |
| 零角强度 I(0) i0 | 732574000.00 |
| 分子量 molecular_weight | 186120.0 kDa |
| 排除体积 excluded_volume | 217110 ų |
| 包络体积 envelope_volume | 201620 ų |
| 水化壳体积 shell_volume | 49733 ų |
| 包络直径 envelope_diameter | 108.7 Å |
| 壳层 Rg shell_rg | 40.58 Å |
| 包络 Rg envelope_rg | 33.37 Å |
| 形状 Rg shape_rg | 30.29 Å |
| 总 Rg total_rg | 30.85 Å |
| 总原子数 total_atoms | 23660 |
| 残基数 n_residues | 1700 |
| 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 | 102.5 Å |
| Rg (实空间) rg_real | 30.90 Å |
| Rg 误差 (实空间) rg_real_error | 0.76 Å |
| I(0) (实空间) i0_real | 7.3260e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.1450e+07 |
| Rg (倒空间) rg_reciprocal | 30.89 Å |
| I(0) (倒空间) i0_reciprocal | 732600000.0000 |
| 解质量估计 total_estimate | 0.8869 |
| 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 | 34.2 Å |
| 偏度 Skewness skewness | 0.377 |
| 峰度 Kurtosis kurtosis | -0.278 |
| 角度范围 angular_range | — – 0.2550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 11870000.0000 |
| 实空间数据点数 n_real_points | 52 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.903 |
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) 5 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1f5ya1 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.12 — LDL receptor-like module |
| 超家族 Superfamily superfamily | g.12.1 — LDL receptor-like module |
| 家族 Family family | g.12.1.1 — LDL receptor-like module |
| 结构域编号 domain_id | d1f5ya2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.12 — LDL receptor-like module |
| 超家族 Superfamily superfamily | g.12.1 — LDL receptor-like module |
| 家族 Family family | g.12.1.1 — LDL receptor-like module |
| 结构域编号 domain_id | d1f5ya3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1f5yA01 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 400 — Low-density Lipoprotein Receptor |
| 同源超家族 H-superfamily homologous superfamily | 10 — Low-density Lipoprotein Receptor |
| 结构域编号 domain_id | 1f5yA02 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 400 — Low-density Lipoprotein Receptor |
| 同源超家族 H-superfamily homologous superfamily | 10 — Low-density Lipoprotein Receptor |