1yra
PAB0955 crystal structure : a GTPase in GDP bound form from Pyrococcus abyssi
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 | 1yra |
| 沉积日期 deposition_date | 2005-02-03 |
| 结构标题 title | PAB0955 crystal structure : a GTPase in GDP bound form from Pyrococcus abyssi |
| 关键词 keywords | GTP binding protein, GTPase, P-loop, Rossmann Fold, GDP, HYDROLASE; HYDROLASE |
| 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 | 24.69 Å |
| 回转半径 Rg (电子) rg_electron | 23.25 Å |
| 零角强度 I(0) i0 | 60763100.00 |
| 分子量 molecular_weight | 61105.0 kDa |
| 排除体积 excluded_volume | 76463 ų |
| 包络体积 envelope_volume | 89027 ų |
| 水化壳体积 shell_volume | 30908 ų |
| 包络直径 envelope_diameter | 85.3 Å |
| 壳层 Rg shell_rg | 31.27 Å |
| 包络 Rg envelope_rg | 23.54 Å |
| 形状 Rg shape_rg | 23.27 Å |
| 总 Rg total_rg | 24.05 Å |
| 总原子数 total_atoms | 4288 |
| 残基数 n_residues | 521 |
| 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 | 85.1 Å |
| Rg (实空间) rg_real | 24.57 Å |
| Rg 误差 (实空间) rg_real_error | 0.51 Å |
| I(0) (实空间) i0_real | 6.0760e+07 |
| I(0) 误差 (实空间) i0_real_error | 8.8290e+05 |
| Rg (倒空间) rg_reciprocal | 24.60 Å |
| I(0) (倒空间) i0_reciprocal | 60760000.0000 |
| 解质量估计 total_estimate | 0.8566 |
| 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 | 31.1 Å |
| 偏度 Skewness skewness | 0.280 |
| 峰度 Kurtosis kurtosis | -0.139 |
| 角度范围 angular_range | — – 0.3200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 14960000.0000 |
| 实空间数据点数 n_real_points | 64 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.993 |
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) 6 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1yraa2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.10 — Nitrogenase iron protein-like |
| 结构域编号 domain_id | d1yraa3 |
| 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 | d1yrab2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.10 — Nitrogenase iron protein-like |
| 结构域编号 domain_id | d1yrab3 |
| 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 |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1yraA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 1yraB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 300 — P-loop containing nucleotide triphosphate hydrolases |