1k28
The Structure of the Bacteriophage T4 Cell-Puncturing Device
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 | 1k28 |
| 沉积日期 deposition_date | 2001-09-26 |
| 结构标题 title | The Structure of the Bacteriophage T4 Cell-Puncturing Device |
| 关键词 keywords | Triple-stranded beta-helix, OB fold, pseudohexamer, T4 tail lysozyme, HUB, gp27-gp5*-gp5C, HYDROLASE-STRUCTURAL PROTEIN COMPLEX; HYDROLASE/STRUCTURAL 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 | 48.90 Å |
| 回转半径 Rg (电子) rg_electron | 50.45 Å |
| 零角强度 I(0) i0 | 170704000.00 |
| 分子量 molecular_weight | 103520.0 kDa |
| 排除体积 excluded_volume | 127910 ų |
| 包络体积 envelope_volume | 215890 ų |
| 水化壳体积 shell_volume | 39492 ų |
| 包络直径 envelope_diameter | 197.6 Å |
| 壳层 Rg shell_rg | 45.21 Å |
| 包络 Rg envelope_rg | 54.33 Å |
| 形状 Rg shape_rg | 50.44 Å |
| 总 Rg total_rg | 50.24 Å |
| 总原子数 total_atoms | 7225 |
| 残基数 n_residues | 906 |
| 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 | 190.0 Å |
| Rg (实空间) rg_real | 50.37 Å |
| Rg 误差 (实空间) rg_real_error | 3.50 Å |
| I(0) (实空间) i0_real | 1.7070e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.8040e+06 |
| Rg (倒空间) rg_reciprocal | 48.91 Å |
| I(0) (倒空间) i0_reciprocal | 170400000.0000 |
| 解质量估计 total_estimate | 0.6562 |
| 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 | 29.7 Å |
| 偏度 Skewness skewness | 0.745 |
| 峰度 Kurtosis kurtosis | 0.055 |
| 角度范围 angular_range | — – 0.1600 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 10640000.0000 |
| 实空间数据点数 n_real_points | 33 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.252; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.108; Smooth: 0.666 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 13 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1k28a1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.40 — OB-fold |
| 超家族 Superfamily superfamily | b.40.8 — gp5 N-terminal domain-like |
| 家族 Family family | b.40.8.1 — gp4 N-terminal domain-like |
| 结构域编号 domain_id | d1k28a2 |
| 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.108.1.2 — Tail-associated lysozyme gp5, C-terminal domain |
| 结构域编号 domain_id | d1k28a3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.2 — Lysozyme-like |
| 超家族 Superfamily superfamily | d.2.1 — Lysozyme-like |
| 家族 Family family | d.2.1.3 — Phage lysozyme |
| 结构域编号 domain_id | d1k28a4 |
| 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 |
| 结构域编号 domain_id | d1k28d1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.106 — Phage tail proteins |
| 超家族 Superfamily superfamily | b.106.1 — Phage tail proteins |
| 家族 Family family | b.106.1.1 — Baseplate protein-like |
| 结构域编号 domain_id | d1k28d2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.106 — Phage tail proteins |
| 超家族 Superfamily superfamily | b.106.1 — Phage tail proteins |
| 家族 Family family | b.106.1.1 — Baseplate protein-like |
CATH v4.4 (7 domains)
| 结构域编号 domain_id | 1k28A01 |
| 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 | 260 — Nucleic acid-binding protein domain |
| 结构域编号 domain_id | 1k28A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 450 — Nuclear Transport Factor 2; Chain: A, |
| 同源超家族 H-superfamily homologous superfamily | 190 — |
| 结构域编号 domain_id | 1k28A03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 530 — Lysozyme |
| 同源超家族 H-superfamily homologous superfamily | 40 — |
| 结构域编号 domain_id | 1k28D01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 10 — Thrombin, subunit H |
| 同源超家族 H-superfamily homologous superfamily | 10 — Trypsin-like serine proteases |
| 结构域编号 domain_id | 1k28D02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 55 — 3-Layer(bab) Sandwich |
| 拓扑 Topology topology | 50 — Phage tail protein beta-alpha-beta fold |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1k28D03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 30 — Elongation Factor Tu (Ef-tu); domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 150 — Bacteriophage T4, Gp27, baseplate hub, domain 3 |
| 结构域编号 domain_id | 1k28D04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1920 — Phage tail proteins - 2 layer sandwich fold |
| 同源超家族 H-superfamily homologous superfamily | 40 — |