2d5w
The crystal structure of oligopeptide binding protein from Thermus thermophilus HB8 complexed with pentapeptide
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 | 2d5w |
| 沉积日期 deposition_date | 2005-11-07 |
| 结构标题 title | The crystal structure of oligopeptide binding protein from Thermus thermophilus HB8 complexed with pentapeptide |
| 关键词 keywords | PROTEIN-PEPTIDE COMPLEX, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN |
| 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 | 36.08 Å |
| 回转半径 Rg (电子) rg_electron | 35.40 Å |
| 零角强度 I(0) i0 | 277145000.00 |
| 分子量 molecular_weight | 137980.0 kDa |
| 排除体积 excluded_volume | 173760 ų |
| 包络体积 envelope_volume | 207090 ų |
| 水化壳体积 shell_volume | 47883 ų |
| 包络直径 envelope_diameter | 121.2 Å |
| 壳层 Rg shell_rg | 42.62 Å |
| 包络 Rg envelope_rg | 35.12 Å |
| 形状 Rg shape_rg | 35.38 Å |
| 总 Rg total_rg | 35.93 Å |
| 总原子数 total_atoms | 9772 |
| 残基数 n_residues | 1214 |
| 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 | 117.3 Å |
| Rg (实空间) rg_real | 36.12 Å |
| Rg 误差 (实空间) rg_real_error | 1.16 Å |
| I(0) (实空间) i0_real | 2.7710e+08 |
| I(0) 误差 (实空间) i0_real_error | 5.1700e+06 |
| Rg (倒空间) rg_reciprocal | 36.10 Å |
| I(0) (倒空间) i0_reciprocal | 277100000.0000 |
| 解质量估计 total_estimate | 0.8854 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 37.3 Å |
| 偏度 Skewness skewness | 0.336 |
| 峰度 Kurtosis kurtosis | -0.524 |
| 角度范围 angular_range | — – 0.2200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 67970000.0000 |
| 实空间数据点数 n_real_points | 45 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.839 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 6 domains
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2d5wA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 190 — D-Maltodextrin-Binding Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Periplasmic binding protein-like II |
| 结构域编号 domain_id | 2d5wA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 76 — Dipeptide-binding Protein; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dipeptide-binding Protein; Domain 1 |
| 结构域编号 domain_id | 2d5wA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 105 — Dipeptide-binding Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dipeptide-binding Protein; Domain 3 |
| 结构域编号 domain_id | 2d5wB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 190 — D-Maltodextrin-Binding Protein; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Periplasmic binding protein-like II |
| 结构域编号 domain_id | 2d5wB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 76 — Dipeptide-binding Protein; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dipeptide-binding Protein; Domain 1 |
| 结构域编号 domain_id | 2d5wB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 105 — Dipeptide-binding Protein; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dipeptide-binding Protein; Domain 3 |