1vki
;Crystal structure of a putative oligo-nucleotide binding protein (atu3699, agr_l_2275) from agrobacterium tumefaciens str. c58 at 1.60 A resolution ;
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 | 1vki |
| 沉积日期 deposition_date | 2004-05-24 |
| 结构标题 title | ;Crystal structure of a putative oligo-nucleotide binding protein (atu3699, agr_l_2275) from agrobacterium tumefaciens str. c58 at 1.60 A resolution ; |
| 关键词 keywords | Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, translation; TRANSLATION |
| 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 | 21.59 Å |
| 回转半径 Rg (电子) rg_electron | 20.79 Å |
| 零角强度 I(0) i0 | 22672600.00 |
| 分子量 molecular_weight | 36666.0 kDa |
| 排除体积 excluded_volume | 46094 ų |
| 包络体积 envelope_volume | 53894 ų |
| 水化壳体积 shell_volume | 21905 ų |
| 包络直径 envelope_diameter | 69.7 Å |
| 壳层 Rg shell_rg | 26.95 Å |
| 包络 Rg envelope_rg | 20.64 Å |
| 形状 Rg shape_rg | 20.80 Å |
| 总 Rg total_rg | 21.57 Å |
| 总原子数 total_atoms | 2584 |
| 残基数 n_residues | 331 |
| 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 | 68.6 Å |
| Rg (实空间) rg_real | 21.53 Å |
| Rg 误差 (实空间) rg_real_error | 0.38 Å |
| I(0) (实空间) i0_real | 2.2670e+07 |
| I(0) 误差 (实空间) i0_real_error | 2.8680e+05 |
| Rg (倒空间) rg_reciprocal | 21.54 Å |
| I(0) (倒空间) i0_reciprocal | 22670000.0000 |
| 解质量估计 total_estimate | 0.8999 |
| 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 | 25.2 Å |
| 偏度 Skewness skewness | 0.272 |
| 峰度 Kurtosis kurtosis | -0.440 |
| 角度范围 angular_range | — – 0.3700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 5903000.0000 |
| 实空间数据点数 n_real_points | 69 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.996 |
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) 4 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1vkia_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.116 — YbaK/ProRS associated domain |
| 超家族 Superfamily superfamily | d.116.1 — YbaK/ProRS associated domain |
| 家族 Family family | d.116.1.1 — YbaK/ProRS associated domain |
| 结构域编号 domain_id | d1vkib_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.116 — YbaK/ProRS associated domain |
| 超家族 Superfamily superfamily | d.116.1 — YbaK/ProRS associated domain |
| 家族 Family family | d.116.1.1 — YbaK/ProRS associated domain |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1vkiA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 960 — YbaK protein |
| 同源超家族 H-superfamily homologous superfamily | 10 — YbaK/aminoacyl-tRNA synthetase-associated domain |
| 结构域编号 domain_id | 1vkiB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 960 — YbaK protein |
| 同源超家族 H-superfamily homologous superfamily | 10 — YbaK/aminoacyl-tRNA synthetase-associated domain |