1udx
Crystal structure of the conserved protein TT1381 from Thermus thermophilus HB8
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 | 1udx |
| 沉积日期 deposition_date | 2003-05-07 |
| 结构标题 title | Crystal structure of the conserved protein TT1381 from Thermus thermophilus HB8 |
| 关键词 keywords | GTP-binding protein, Obg, TGS domain, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, PROTEIN BINDING; PROTEIN BINDING |
| 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 | 32.18 Å |
| 回转半径 Rg (电子) rg_electron | 32.63 Å |
| 零角强度 I(0) i0 | 32144400.00 |
| 分子量 molecular_weight | 44216.0 kDa |
| 排除体积 excluded_volume | 55447 ų |
| 包络体积 envelope_volume | 74662 ų |
| 水化壳体积 shell_volume | 22024 ų |
| 包络直径 envelope_diameter | 119.5 Å |
| 壳层 Rg shell_rg | 34.48 Å |
| 包络 Rg envelope_rg | 32.79 Å |
| 形状 Rg shape_rg | 32.64 Å |
| 总 Rg total_rg | 32.76 Å |
| 总原子数 total_atoms | 3115 |
| 残基数 n_residues | 412 |
| 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 | 111.9 Å |
| Rg (实空间) rg_real | 32.72 Å |
| Rg 误差 (实空间) rg_real_error | 1.42 Å |
| I(0) (实空间) i0_real | 3.2140e+07 |
| I(0) 误差 (实空间) i0_real_error | 5.7970e+05 |
| Rg (倒空间) rg_reciprocal | 32.50 Å |
| I(0) (倒空间) i0_reciprocal | 32140000.0000 |
| 解质量估计 total_estimate | 0.7647 |
| 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 | 25.1 Å |
| 偏度 Skewness skewness | 0.516 |
| 峰度 Kurtosis kurtosis | -0.614 |
| 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 | 3002000.0000 |
| 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: 0.565; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.340; Smooth: 0.903 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 6 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1udxa1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.117 — Obg-fold |
| 超家族 Superfamily superfamily | b.117.1 — Obg GTP-binding protein N-terminal domain |
| 家族 Family family | b.117.1.1 — Obg GTP-binding protein N-terminal domain |
| 结构域编号 domain_id | d1udxa2 |
| 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.37.1.8 — G proteins |
| 结构域编号 domain_id | d1udxa3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.242 — Obg GTP-binding protein C-terminal domain |
| 超家族 Superfamily superfamily | d.242.1 — Obg GTP-binding protein C-terminal domain |
| 家族 Family family | d.242.1.1 — Obg GTP-binding protein C-terminal domain |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1udxA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 70 — Distorted Sandwich |
| 拓扑 Topology topology | 210 — Spo0b-associated Gtp-binding Protein; Chain: A, |
| 同源超家族 H-superfamily homologous superfamily | 12 — GTP1/OBG domain |
| 结构域编号 domain_id | 1udxA02 |
| 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 | 1udxA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 300 — GMP Synthetase; Chain A, domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 350 — GTP-binding protein OBG, C-terminal domain |