2kd1
;Solution NMR structure of the integrase-like domain from Bacillus cereus ordered locus BC_1272. Northeast Structural Genomics Consortium Target BcR268F ;
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 | 2kd1 |
| 沉积日期 deposition_date | 2008-12-31 |
| 结构标题 title | ;Solution NMR structure of the integrase-like domain from Bacillus cereus ordered locus BC_1272. Northeast Structural Genomics Consortium Target BcR268F ; |
| 关键词 keywords | PROTEIN STRUCTURE INITIATIVE, STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI-2, Northeast Structural Genomics Consortium, NESG; STRUCTURAL GENOMICS, UNKNOWN FUNCTION |
| 实验方法 method | SOLUTION NMR |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 16.96 Å |
| 回转半径 Rg (电子) rg_electron | 16.15 Å |
| 零角强度 I(0) i0 | 989136000.00 |
| 分子量 molecular_weight | 270980.0 kDa |
| 排除体积 excluded_volume | 342220 ų |
| 包络体积 envelope_volume | 57854 ų |
| 水化壳体积 shell_volume | 21718 ų |
| 包络直径 envelope_diameter | 81.6 Å |
| 壳层 Rg shell_rg | 29.54 Å |
| 包络 Rg envelope_rg | 24.66 Å |
| 形状 Rg shape_rg | 16.19 Å |
| 总 Rg total_rg | 16.33 Å |
| 总原子数 total_atoms | 39100 |
| 残基数 n_residues | 2360 |
| 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 | 46.2 Å |
| Rg (实空间) rg_real | 15.87 Å |
| Rg 误差 (实空间) rg_real_error | 0.07 Å |
| I(0) (实空间) i0_real | 9.4170e+08 |
| I(0) 误差 (实空间) i0_real_error | 8.4920e+06 |
| Rg (倒空间) rg_reciprocal | 17.13 Å |
| I(0) (倒空间) i0_reciprocal | 989100000.0000 |
| 解质量估计 total_estimate | 0.6682 |
| 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 | 17.6 Å |
| 偏度 Skewness skewness | 0.389 |
| 峰度 Kurtosis kurtosis | -0.169 |
| 角度范围 angular_range | — – 0.4700 Å−1 |
| 当前正则化参数 α current_alpha | 3.2980 |
| 最高正则化参数 α highest_alpha | 463500.0000 |
| 实空间数据点数 n_real_points | 77 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.005; Oscil: 0.908; Stabil: 0.989; Sysdev: 0.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (1)
6. 折叠分类 (SCOP + CATH) 1 domains
CATH v4.4 (1 domains)
| 结构域编号 domain_id | 2kd1A00 |
| 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 | 130 — Tyrosine recombinase, N-terminal domain |