2gum
Crystal structure of the extracellular domain of glycoprotein B from Herpes Simplex Virus type I
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 | 2gum |
| 沉积日期 deposition_date | 2006-05-01 |
| 结构标题 title | Crystal structure of the extracellular domain of glycoprotein B from Herpes Simplex Virus type I |
| 关键词 keywords | ENVELOPE GLYCOPROTEIN, MEMBRANE FUSION, VIRAL PROTEIN; VIRAL 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 | 50.56 Å |
| 回转半径 Rg (电子) rg_electron | 50.93 Å |
| 零角强度 I(0) i0 | 599537000.00 |
| 分子量 molecular_weight | 198520.0 kDa |
| 排除体积 excluded_volume | 246500 ų |
| 包络体积 envelope_volume | 352540 ų |
| 水化壳体积 shell_volume | 62296 ų |
| 包络直径 envelope_diameter | 172.0 Å |
| 壳层 Rg shell_rg | 48.23 Å |
| 包络 Rg envelope_rg | 50.33 Å |
| 形状 Rg shape_rg | 50.91 Å |
| 总 Rg total_rg | 50.86 Å |
| 总原子数 total_atoms | 14000 |
| 残基数 n_residues | 1732 |
| 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 | 160.7 Å |
| Rg (实空间) rg_real | 50.98 Å |
| Rg 误差 (实空间) rg_real_error | 1.49 Å |
| I(0) (实空间) i0_real | 5.9950e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.1290e+07 |
| Rg (倒空间) rg_reciprocal | 50.20 Å |
| I(0) (倒空间) i0_reciprocal | 598900000.0000 |
| 解质量估计 total_estimate | 0.7752 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 41.5 Å |
| 偏度 Skewness skewness | 0.552 |
| 峰度 Kurtosis kurtosis | -0.530 |
| 角度范围 angular_range | — – 0.1550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 56570000.0000 |
| 实空间数据点数 n_real_points | 32 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.752; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.812; Smooth: 0.007 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 15 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d2guma1 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.76 — Viral glycoprotein ectodomain-like |
| 超家族 Superfamily superfamily | e.76.1 — Viral glycoprotein ectodomain-like |
| 家族 Family family | e.76.1.1 — Glycoprotein B-like |
| 结构域编号 domain_id | d2gumb_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.76 — Viral glycoprotein ectodomain-like |
| 超家族 Superfamily superfamily | e.76.1 — Viral glycoprotein ectodomain-like |
| 家族 Family family | e.76.1.1 — Glycoprotein B-like |
| 结构域编号 domain_id | d2gumc_ |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.76 — Viral glycoprotein ectodomain-like |
| 超家族 Superfamily superfamily | e.76.1 — Viral glycoprotein ectodomain-like |
| 家族 Family family | e.76.1.1 — Glycoprotein B-like |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 2gumA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 1230 — |
| 结构域编号 domain_id | 2gumA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 1890 — |
| 结构域编号 domain_id | 2gumA03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 29 — PH-domain like |
| 同源超家族 H-superfamily homologous superfamily | 100 — |
| 结构域编号 domain_id | 2gumA05 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 3280 — |
| 结构域编号 domain_id | 2gumB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 1230 — |
| 结构域编号 domain_id | 2gumB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 1890 — |
| 结构域编号 domain_id | 2gumB03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 29 — PH-domain like |
| 同源超家族 H-superfamily homologous superfamily | 100 — |
| 结构域编号 domain_id | 2gumB05 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 3280 — |
| 结构域编号 domain_id | 2gumC01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 1230 — |
| 结构域编号 domain_id | 2gumC02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 1890 — |
| 结构域编号 domain_id | 2gumC03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 29 — PH-domain like |
| 同源超家族 H-superfamily homologous superfamily | 100 — |
| 结构域编号 domain_id | 2gumC05 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 3280 — |