2bsd
Structure of Lactococcal Bacteriophage p2 Receptor Binding Protein
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 | 2bsd |
| 沉积日期 deposition_date | 2005-05-20 |
| 结构标题 title | Structure of Lactococcal Bacteriophage p2 Receptor Binding Protein |
| 关键词 keywords | LACTOCOCCUS LACTIS, PHAGE, LLAMA VHH, RECEPTOR BINDING PROTEIN, RECEPTOR; RECEPTOR |
| 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 | 32.29 Å |
| 回转半径 Rg (电子) rg_electron | 31.49 Å |
| 零角强度 I(0) i0 | 111395000.00 |
| 分子量 molecular_weight | 82617.0 kDa |
| 排除体积 excluded_volume | 102970 ų |
| 包络体积 envelope_volume | 127810 ų |
| 水化壳体积 shell_volume | 34217 ų |
| 包络直径 envelope_diameter | 101.4 Å |
| 壳层 Rg shell_rg | 38.17 Å |
| 包络 Rg envelope_rg | 31.10 Å |
| 形状 Rg shape_rg | 31.52 Å |
| 总 Rg total_rg | 31.96 Å |
| 总原子数 total_atoms | 5820 |
| 残基数 n_residues | 762 |
| 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 | 102.1 Å |
| Rg (实空间) rg_real | 32.22 Å |
| Rg 误差 (实空间) rg_real_error | 0.77 Å |
| I(0) (实空间) i0_real | 1.1140e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.7420e+06 |
| Rg (倒空间) rg_reciprocal | 32.26 Å |
| I(0) (倒空间) i0_reciprocal | 111400000.0000 |
| 解质量估计 total_estimate | 0.8255 |
| 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 | 33.3 Å |
| 偏度 Skewness skewness | 0.140 |
| 峰度 Kurtosis kurtosis | -0.834 |
| 角度范围 angular_range | — – 0.2450 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 13860000.0000 |
| 实空间数据点数 n_real_points | 50 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; 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) 15 domains
SCOP 2.08 (9 domains)
| 结构域编号 domain_id | d2bsda1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.21 — Virus attachment protein globular domain |
| 超家族 Superfamily superfamily | b.21.1 — Virus attachment protein globular domain |
| 家族 Family family | b.21.1.3 — Lactophage receptor-binding protein head domain |
| 结构域编号 domain_id | d2bsda2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.108 — Triple-stranded beta-helix |
| 超家族 Superfamily superfamily | b.108.1 — Phage fibre proteins |
| 家族 Family family | b.108.1.4 — Lactophage receptor-binding protein domain |
| 结构域编号 domain_id | d2bsda3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.163 — Pseudo beta-prism I |
| 超家族 Superfamily superfamily | b.163.1 — Bacteriophage trimeric proteins domain |
| 家族 Family family | b.163.1.2 — Lactophage receptor-binding protein N-terminal domain |
| 结构域编号 domain_id | d2bsdb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.21 — Virus attachment protein globular domain |
| 超家族 Superfamily superfamily | b.21.1 — Virus attachment protein globular domain |
| 家族 Family family | b.21.1.3 — Lactophage receptor-binding protein head domain |
| 结构域编号 domain_id | d2bsdb2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.108 — Triple-stranded beta-helix |
| 超家族 Superfamily superfamily | b.108.1 — Phage fibre proteins |
| 家族 Family family | b.108.1.4 — Lactophage receptor-binding protein domain |
| 结构域编号 domain_id | d2bsdb3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.163 — Pseudo beta-prism I |
| 超家族 Superfamily superfamily | b.163.1 — Bacteriophage trimeric proteins domain |
| 家族 Family family | b.163.1.2 — Lactophage receptor-binding protein N-terminal domain |
| 结构域编号 domain_id | d2bsdc1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.21 — Virus attachment protein globular domain |
| 超家族 Superfamily superfamily | b.21.1 — Virus attachment protein globular domain |
| 家族 Family family | b.21.1.3 — Lactophage receptor-binding protein head domain |
| 结构域编号 domain_id | d2bsdc2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.108 — Triple-stranded beta-helix |
| 超家族 Superfamily superfamily | b.108.1 — Phage fibre proteins |
| 家族 Family family | b.108.1.4 — Lactophage receptor-binding protein domain |
| 结构域编号 domain_id | d2bsdc3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.163 — Pseudo beta-prism I |
| 超家族 Superfamily superfamily | b.163.1 — Bacteriophage trimeric proteins domain |
| 家族 Family family | b.163.1.2 — Lactophage receptor-binding protein N-terminal domain |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2bsdA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 520 — Triple-stranded beta-helix |
| 同源超家族 H-superfamily homologous superfamily | 10 — Phage fibre proteins |
| 结构域编号 domain_id | 2bsdA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1830 — Phage tail base-plate Siphoviridae RBP, head domain |
| 结构域编号 domain_id | 2bsdB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 520 — Triple-stranded beta-helix |
| 同源超家族 H-superfamily homologous superfamily | 10 — Phage fibre proteins |
| 结构域编号 domain_id | 2bsdB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1830 — Phage tail base-plate Siphoviridae RBP, head domain |
| 结构域编号 domain_id | 2bsdC01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 520 — Triple-stranded beta-helix |
| 同源超家族 H-superfamily homologous superfamily | 10 — Phage fibre proteins |
| 结构域编号 domain_id | 2bsdC02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1830 — Phage tail base-plate Siphoviridae RBP, head domain |