2dvq
Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide
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 | 2dvq |
| 沉积日期 deposition_date | 2006-08-01 |
| 结构标题 title | Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide |
| 关键词 keywords | ;alpha-helical domain, bromodomain, binds to acetylated histones, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSCRIPTION ;; TRANSCRIPTION |
| 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 | 23.59 Å |
| 回转半径 Rg (电子) rg_electron | 23.06 Å |
| 零角强度 I(0) i0 | 31268700.00 |
| 分子量 molecular_weight | 42470.0 kDa |
| 排除体积 excluded_volume | 52614 ų |
| 包络体积 envelope_volume | 62867 ų |
| 水化壳体积 shell_volume | 23268 ų |
| 包络直径 envelope_diameter | 82.6 Å |
| 壳层 Rg shell_rg | 29.64 Å |
| 包络 Rg envelope_rg | 23.33 Å |
| 形状 Rg shape_rg | 23.12 Å |
| 总 Rg total_rg | 23.68 Å |
| 总原子数 total_atoms | 2911 |
| 残基数 n_residues | 333 |
| 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 | 77.2 Å |
| Rg (实空间) rg_real | 24.33 Å |
| Rg 误差 (实空间) rg_real_error | 0.20 Å |
| I(0) (实空间) i0_real | 3.1040e+07 |
| I(0) 误差 (实空间) i0_real_error | 3.4820e+05 |
| Rg (倒空间) rg_reciprocal | 23.62 Å |
| I(0) (倒空间) i0_reciprocal | 31270000.0000 |
| 解质量估计 total_estimate | 0.6661 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 25.3 Å |
| 偏度 Skewness skewness | 0.440 |
| 峰度 Kurtosis kurtosis | -0.328 |
| 角度范围 angular_range | — – 0.3350 Å−1 |
| 当前正则化参数 α current_alpha | 6.2150 |
| 最高正则化参数 α highest_alpha | 13030000.0000 |
| 实空间数据点数 n_real_points | 65 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.918; Stabil: 0.906; Sysdev: 0.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.281 |
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 (3 domains)
| 结构域编号 domain_id | d2dvqa_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.29 — Bromodomain-like |
| 超家族 Superfamily superfamily | a.29.2 — Bromodomain |
| 家族 Family family | a.29.2.0 — automated matches |
| 结构域编号 domain_id | d2dvqb_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.29 — Bromodomain-like |
| 超家族 Superfamily superfamily | a.29.2 — Bromodomain |
| 家族 Family family | a.29.2.0 — automated matches |
| 结构域编号 domain_id | d2dvqc_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.29 — Bromodomain-like |
| 超家族 Superfamily superfamily | a.29.2 — Bromodomain |
| 家族 Family family | a.29.2.0 — automated matches |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 2dvqA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 920 — Histone Acetyltransferase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bromodomain-like |
| 结构域编号 domain_id | 2dvqB00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 920 — Histone Acetyltransferase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bromodomain-like |
| 结构域编号 domain_id | 2dvqC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 920 — Histone Acetyltransferase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Bromodomain-like |