2ddb
Crystal structure of pseudecin from Pseudechis porphyriacus
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 | 2ddb |
| 沉积日期 deposition_date | 2006-01-25 |
| 结构标题 title | Crystal structure of pseudecin from Pseudechis porphyriacus |
| 关键词 keywords | CRISP, snake venom, CNG channel, TOXIN; TOXIN |
| 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 | 41.51 Å |
| 回转半径 Rg (电子) rg_electron | 42.54 Å |
| 零角强度 I(0) i0 | 147302000.00 |
| 分子量 molecular_weight | 95068.0 kDa |
| 排除体积 excluded_volume | 117690 ų |
| 包络体积 envelope_volume | 155340 ų |
| 水化壳体积 shell_volume | 36110 ų |
| 包络直径 envelope_diameter | 174.3 Å |
| 壳层 Rg shell_rg | 38.78 Å |
| 包络 Rg envelope_rg | 43.32 Å |
| 形状 Rg shape_rg | 42.48 Å |
| 总 Rg total_rg | 42.55 Å |
| 总原子数 total_atoms | 6635 |
| 残基数 n_residues | 832 |
| 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 | 164.6 Å |
| Rg (实空间) rg_real | 42.35 Å |
| Rg 误差 (实空间) rg_real_error | 2.88 Å |
| I(0) (实空间) i0_real | 1.4730e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.2580e+06 |
| Rg (倒空间) rg_reciprocal | 41.52 Å |
| I(0) (倒空间) i0_reciprocal | 147200000.0000 |
| 解质量估计 total_estimate | 0.6826 |
| 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 | 30.3 Å |
| 偏度 Skewness skewness | 0.777 |
| 峰度 Kurtosis kurtosis | 0.076 |
| 角度范围 angular_range | — – 0.1900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 9645000.0000 |
| 实空间数据点数 n_real_points | 39 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.260; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.174; Smooth: 0.915 |
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) 16 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d2ddba1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.111 — PR-1-like |
| 超家族 Superfamily superfamily | d.111.1 — PR-1-like |
| 家族 Family family | d.111.1.0 — automated matches |
| 结构域编号 domain_id | d2ddba2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.19 — Crisp domain-like |
| 超家族 Superfamily superfamily | g.19.1 — Crisp domain-like |
| 家族 Family family | g.19.1.0 — automated matches |
| 结构域编号 domain_id | d2ddbb1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.111 — PR-1-like |
| 超家族 Superfamily superfamily | d.111.1 — PR-1-like |
| 家族 Family family | d.111.1.0 — automated matches |
| 结构域编号 domain_id | d2ddbb2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.19 — Crisp domain-like |
| 超家族 Superfamily superfamily | g.19.1 — Crisp domain-like |
| 家族 Family family | g.19.1.0 — automated matches |
| 结构域编号 domain_id | d2ddbc1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.111 — PR-1-like |
| 超家族 Superfamily superfamily | d.111.1 — PR-1-like |
| 家族 Family family | d.111.1.0 — automated matches |
| 结构域编号 domain_id | d2ddbc2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.19 — Crisp domain-like |
| 超家族 Superfamily superfamily | g.19.1 — Crisp domain-like |
| 家族 Family family | g.19.1.0 — automated matches |
| 结构域编号 domain_id | d2ddbd1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.111 — PR-1-like |
| 超家族 Superfamily superfamily | d.111.1 — PR-1-like |
| 家族 Family family | d.111.1.0 — automated matches |
| 结构域编号 domain_id | d2ddbd2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.19 — Crisp domain-like |
| 超家族 Superfamily superfamily | g.19.1 — Crisp domain-like |
| 家族 Family family | g.19.1.0 — automated matches |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 2ddbA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 33 — Pathogenesis-related Protein p14a |
| 同源超家族 H-superfamily homologous superfamily | 10 — CAP |
| 结构域编号 domain_id | 2ddbA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 740 — Crisp domain |
| 结构域编号 domain_id | 2ddbB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 33 — Pathogenesis-related Protein p14a |
| 同源超家族 H-superfamily homologous superfamily | 10 — CAP |
| 结构域编号 domain_id | 2ddbB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 740 — Crisp domain |
| 结构域编号 domain_id | 2ddbC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 33 — Pathogenesis-related Protein p14a |
| 同源超家族 H-superfamily homologous superfamily | 10 — CAP |
| 结构域编号 domain_id | 2ddbC02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 740 — Crisp domain |
| 结构域编号 domain_id | 2ddbD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 33 — Pathogenesis-related Protein p14a |
| 同源超家族 H-superfamily homologous superfamily | 10 — CAP |
| 结构域编号 domain_id | 2ddbD02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 740 — Crisp domain |