2dwq
Thermus thermophilus YchF GTP-binding protein
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 | 2dwq |
| 沉积日期 deposition_date | 2006-08-16 |
| 结构标题 title | Thermus thermophilus YchF GTP-binding protein |
| 关键词 keywords | ;GTP-binding, signal transduction, TGS domain, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, 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 | 33.24 Å |
| 回转半径 Rg (电子) rg_electron | 32.75 Å |
| 零角强度 I(0) i0 | 90255200.00 |
| 分子量 molecular_weight | 76117.0 kDa |
| 排除体积 excluded_volume | 95807 ų |
| 包络体积 envelope_volume | 133100 ų |
| 水化壳体积 shell_volume | 35057 ų |
| 包络直径 envelope_diameter | 111.9 Å |
| 壳层 Rg shell_rg | 38.42 Å |
| 包络 Rg envelope_rg | 32.31 Å |
| 形状 Rg shape_rg | 32.71 Å |
| 总 Rg total_rg | 33.37 Å |
| 总原子数 total_atoms | 5379 |
| 残基数 n_residues | 691 |
| 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 | 107.1 Å |
| Rg (实空间) rg_real | 33.36 Å |
| Rg 误差 (实空间) rg_real_error | 0.72 Å |
| I(0) (实空间) i0_real | 9.0260e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.3340e+06 |
| Rg (倒空间) rg_reciprocal | 33.32 Å |
| I(0) (倒空间) i0_reciprocal | 90250000.0000 |
| 解质量估计 total_estimate | 0.8883 |
| 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 | 37.9 Å |
| 偏度 Skewness skewness | 0.357 |
| 峰度 Kurtosis kurtosis | -0.571 |
| 角度范围 angular_range | — – 0.2400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 12660000.0000 |
| 实空间数据点数 n_real_points | 49 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.912 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 10 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2dwqa1 |
| 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.37.1.0 — automated matches |
| 结构域编号 domain_id | d2dwqa2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.10 — TGS-like |
| 家族 Family family | d.15.10.0 — automated matches |
| 结构域编号 domain_id | d2dwqb1 |
| 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.37.1.0 — automated matches |
| 结构域编号 domain_id | d2dwqb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.15 — beta-Grasp (ubiquitin-like) |
| 超家族 Superfamily superfamily | d.15.10 — TGS-like |
| 家族 Family family | d.15.10.0 — automated matches |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2dwqA01 |
| 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 | 2dwqA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 30 — Beta-grasp domain |
| 结构域编号 domain_id | 2dwqA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 300 — Obg-related GTPase Ych/YyaF, coiled-coil domain |
| 结构域编号 domain_id | 2dwqB01 |
| 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 | 2dwqB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 20 — Ubiquitin-like (UB roll) |
| 同源超家族 H-superfamily homologous superfamily | 30 — Beta-grasp domain |
| 结构域编号 domain_id | 2dwqB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 300 — Obg-related GTPase Ych/YyaF, coiled-coil domain |