1r71
Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA
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 | 1r71 |
| 沉积日期 deposition_date | 2003-10-17 |
| 结构标题 title | Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA |
| 关键词 keywords | ;IncP, plasmid partitioning, protein-DNA complex, heilx-turn-helix motif, transcription factor, ParB homologue, TRANSCRIPTION-DNA COMPLEX ;; TRANSCRIPTION/DNA |
| 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 | 28.16 Å |
| 回转半径 Rg (电子) rg_electron | 27.57 Å |
| 零角强度 I(0) i0 | 121596000.00 |
| 分子量 molecular_weight | 73031.0 kDa |
| 排除体积 excluded_volume | 85380 ų |
| 包络体积 envelope_volume | 115730 ų |
| 水化壳体积 shell_volume | 34945 ų |
| 包络直径 envelope_diameter | 94.6 Å |
| 壳层 Rg shell_rg | 34.95 Å |
| 包络 Rg envelope_rg | 27.22 Å |
| 形状 Rg shape_rg | 27.56 Å |
| 总 Rg total_rg | 28.20 Å |
| 总原子数 total_atoms | 5040 |
| 残基数 n_residues | 519 |
| 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 | 90.0 Å |
| Rg (实空间) rg_real | 28.04 Å |
| Rg 误差 (实空间) rg_real_error | 0.57 Å |
| I(0) (实空间) i0_real | 1.2160e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.6610e+06 |
| Rg (倒空间) rg_reciprocal | 28.08 Å |
| I(0) (倒空间) i0_reciprocal | 121600000.0000 |
| 解质量估计 total_estimate | 0.8974 |
| 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 | 33.8 Å |
| 偏度 Skewness skewness | 0.230 |
| 峰度 Kurtosis kurtosis | -0.363 |
| 角度范围 angular_range | — – 0.2800 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 8379000.0000 |
| 实空间数据点数 n_real_points | 57 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.956 |
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) 12 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1r71a_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.14 — KorB DNA-binding domain-like |
| 家族 Family family | a.4.14.1 — KorB DNA-binding domain-like |
| 结构域编号 domain_id | d1r71b_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.14 — KorB DNA-binding domain-like |
| 家族 Family family | a.4.14.1 — KorB DNA-binding domain-like |
| 结构域编号 domain_id | d1r71c_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.14 — KorB DNA-binding domain-like |
| 家族 Family family | a.4.14.1 — KorB DNA-binding domain-like |
| 结构域编号 domain_id | d1r71d_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.4 — DNA/RNA-binding 3-helical bundle |
| 超家族 Superfamily superfamily | a.4.14 — KorB DNA-binding domain-like |
| 家族 Family family | a.4.14.1 — KorB DNA-binding domain-like |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1r71A01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 730 — KorB DNA-binding domain |
| 结构域编号 domain_id | 1r71A02 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 140 — |
| 结构域编号 domain_id | 1r71B01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 730 — KorB DNA-binding domain |
| 结构域编号 domain_id | 1r71B02 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 140 — |
| 结构域编号 domain_id | 1r71C01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 730 — KorB DNA-binding domain |
| 结构域编号 domain_id | 1r71C02 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 140 — |
| 结构域编号 domain_id | 1r71D01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 10 — Arc Repressor Mutant, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 730 — KorB DNA-binding domain |
| 结构域编号 domain_id | 1r71D02 |
| 类 Class class | 6 — Special |
| 架构 Architecture architecture | 10 — Helix non-globular |
| 拓扑 Topology topology | 250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces |
| 同源超家族 H-superfamily homologous superfamily | 140 — |