1u8r
Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions
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 | 1u8r |
| 沉积日期 deposition_date | 2004-08-06 |
| 结构标题 title | Crystal Structure of an IdeR-DNA Complex Reveals a Conformational Change in Activated IdeR for Base-specific Interactions |
| 关键词 keywords | ;IdeR, iron-dependent regulator, iron acquisition, siderophores, Mycobacterium tuberculosis, metal-binding protein, Transcription-DNA COMPLEX ;; metal-binding protein,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 | 45.67 Å |
| 回转半径 Rg (电子) rg_electron | 45.82 Å |
| 零角强度 I(0) i0 | 1058160000.00 |
| 分子量 molecular_weight | 237470.0 kDa |
| 排除体积 excluded_volume | 284390 ų |
| 包络体积 envelope_volume | 429810 ų |
| 水化壳体积 shell_volume | 78294 ų |
| 包络直径 envelope_diameter | 147.6 Å |
| 壳层 Rg shell_rg | 51.22 Å |
| 包络 Rg envelope_rg | 43.79 Å |
| 形状 Rg shape_rg | 45.86 Å |
| 总 Rg total_rg | 45.90 Å |
| 总原子数 total_atoms | 16430 |
| 残基数 n_residues | 1902 |
| 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 | 143.8 Å |
| Rg (实空间) rg_real | 45.46 Å |
| Rg 误差 (实空间) rg_real_error | 0.93 Å |
| I(0) (实空间) i0_real | 1.0580e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.7970e+07 |
| Rg (倒空间) rg_reciprocal | 45.67 Å |
| I(0) (倒空间) i0_reciprocal | 1058000000.0000 |
| 解质量估计 total_estimate | 0.8794 |
| 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 | 57.5 Å |
| 偏度 Skewness skewness | 0.159 |
| 峰度 Kurtosis kurtosis | -0.382 |
| 角度范围 angular_range | — – 0.1750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 42640000.0000 |
| 实空间数据点数 n_real_points | 36 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.717 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 48 domains
SCOP 2.08 (24 domains)
| 结构域编号 domain_id | d1u8ra1 |
| 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.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.24 — Iron-dependent repressor protein |
| 结构域编号 domain_id | d1u8ra2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.76 — Iron-dependent repressor protein, dimerization domain |
| 超家族 Superfamily superfamily | a.76.1 — Iron-dependent repressor protein, dimerization domain |
| 家族 Family family | a.76.1.1 — Iron-dependent repressor protein, dimerization domain |
| 结构域编号 domain_id | d1u8ra3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.1 — C-terminal domain of transcriptional repressors |
| 家族 Family family | b.34.1.2 — FeoA-like |
| 结构域编号 domain_id | d1u8rb1 |
| 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.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.24 — Iron-dependent repressor protein |
| 结构域编号 domain_id | d1u8rb2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.76 — Iron-dependent repressor protein, dimerization domain |
| 超家族 Superfamily superfamily | a.76.1 — Iron-dependent repressor protein, dimerization domain |
| 家族 Family family | a.76.1.1 — Iron-dependent repressor protein, dimerization domain |
| 结构域编号 domain_id | d1u8rb3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.1 — C-terminal domain of transcriptional repressors |
| 家族 Family family | b.34.1.2 — FeoA-like |
| 结构域编号 domain_id | d1u8rc1 |
| 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.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.24 — Iron-dependent repressor protein |
| 结构域编号 domain_id | d1u8rc2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.76 — Iron-dependent repressor protein, dimerization domain |
| 超家族 Superfamily superfamily | a.76.1 — Iron-dependent repressor protein, dimerization domain |
| 家族 Family family | a.76.1.1 — Iron-dependent repressor protein, dimerization domain |
| 结构域编号 domain_id | d1u8rc3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.1 — C-terminal domain of transcriptional repressors |
| 家族 Family family | b.34.1.2 — FeoA-like |
| 结构域编号 domain_id | d1u8rd1 |
| 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.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.24 — Iron-dependent repressor protein |
| 结构域编号 domain_id | d1u8rd2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.76 — Iron-dependent repressor protein, dimerization domain |
| 超家族 Superfamily superfamily | a.76.1 — Iron-dependent repressor protein, dimerization domain |
| 家族 Family family | a.76.1.1 — Iron-dependent repressor protein, dimerization domain |
| 结构域编号 domain_id | d1u8rd3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.1 — C-terminal domain of transcriptional repressors |
| 家族 Family family | b.34.1.2 — FeoA-like |
| 结构域编号 domain_id | d1u8rg1 |
| 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.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.24 — Iron-dependent repressor protein |
| 结构域编号 domain_id | d1u8rg2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.76 — Iron-dependent repressor protein, dimerization domain |
| 超家族 Superfamily superfamily | a.76.1 — Iron-dependent repressor protein, dimerization domain |
| 家族 Family family | a.76.1.1 — Iron-dependent repressor protein, dimerization domain |
| 结构域编号 domain_id | d1u8rg3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.1 — C-terminal domain of transcriptional repressors |
| 家族 Family family | b.34.1.2 — FeoA-like |
| 结构域编号 domain_id | d1u8rh1 |
| 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.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.24 — Iron-dependent repressor protein |
| 结构域编号 domain_id | d1u8rh2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.76 — Iron-dependent repressor protein, dimerization domain |
| 超家族 Superfamily superfamily | a.76.1 — Iron-dependent repressor protein, dimerization domain |
| 家族 Family family | a.76.1.1 — Iron-dependent repressor protein, dimerization domain |
| 结构域编号 domain_id | d1u8rh3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.1 — C-terminal domain of transcriptional repressors |
| 家族 Family family | b.34.1.2 — FeoA-like |
| 结构域编号 domain_id | d1u8ri1 |
| 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.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.24 — Iron-dependent repressor protein |
| 结构域编号 domain_id | d1u8ri2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.76 — Iron-dependent repressor protein, dimerization domain |
| 超家族 Superfamily superfamily | a.76.1 — Iron-dependent repressor protein, dimerization domain |
| 家族 Family family | a.76.1.1 — Iron-dependent repressor protein, dimerization domain |
| 结构域编号 domain_id | d1u8ri3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.1 — C-terminal domain of transcriptional repressors |
| 家族 Family family | b.34.1.2 — FeoA-like |
| 结构域编号 domain_id | d1u8rj1 |
| 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.4.5 — 'Winged helix' DNA-binding domain |
| 家族 Family family | a.4.5.24 — Iron-dependent repressor protein |
| 结构域编号 domain_id | d1u8rj2 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.76 — Iron-dependent repressor protein, dimerization domain |
| 超家族 Superfamily superfamily | a.76.1 — Iron-dependent repressor protein, dimerization domain |
| 家族 Family family | a.76.1.1 — Iron-dependent repressor protein, dimerization domain |
| 结构域编号 domain_id | d1u8rj3 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.34 — SH3-like barrel |
| 超家族 Superfamily superfamily | b.34.1 — C-terminal domain of transcriptional repressors |
| 家族 Family family | b.34.1.2 — FeoA-like |
CATH v4.4 (24 domains)
| 结构域编号 domain_id | 1u8rA01 |
| 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 | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1u8rA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 60 — Diphtheria Toxin Repressor; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Iron dependent repressor, metal binding and dimerisation domain |
| 结构域编号 domain_id | 1u8rA03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 90 — Ferrous iron transport protein A (FeoA) |
| 结构域编号 domain_id | 1u8rB01 |
| 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 | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1u8rB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 60 — Diphtheria Toxin Repressor; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Iron dependent repressor, metal binding and dimerisation domain |
| 结构域编号 domain_id | 1u8rB03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 90 — Ferrous iron transport protein A (FeoA) |
| 结构域编号 domain_id | 1u8rC01 |
| 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 | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1u8rC02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 60 — Diphtheria Toxin Repressor; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Iron dependent repressor, metal binding and dimerisation domain |
| 结构域编号 domain_id | 1u8rC03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 90 — Ferrous iron transport protein A (FeoA) |
| 结构域编号 domain_id | 1u8rD01 |
| 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 | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1u8rD02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 60 — Diphtheria Toxin Repressor; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Iron dependent repressor, metal binding and dimerisation domain |
| 结构域编号 domain_id | 1u8rD03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 90 — Ferrous iron transport protein A (FeoA) |
| 结构域编号 domain_id | 1u8rG01 |
| 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 | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1u8rG02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 60 — Diphtheria Toxin Repressor; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Iron dependent repressor, metal binding and dimerisation domain |
| 结构域编号 domain_id | 1u8rG03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 90 — Ferrous iron transport protein A (FeoA) |
| 结构域编号 domain_id | 1u8rH01 |
| 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 | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1u8rH02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 60 — Diphtheria Toxin Repressor; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Iron dependent repressor, metal binding and dimerisation domain |
| 结构域编号 domain_id | 1u8rH03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 90 — Ferrous iron transport protein A (FeoA) |
| 结构域编号 domain_id | 1u8rI01 |
| 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 | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1u8rI02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 60 — Diphtheria Toxin Repressor; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Iron dependent repressor, metal binding and dimerisation domain |
| 结构域编号 domain_id | 1u8rI03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 90 — Ferrous iron transport protein A (FeoA) |
| 结构域编号 domain_id | 1u8rJ01 |
| 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 | 10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain |
| 结构域编号 domain_id | 1u8rJ02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 60 — Diphtheria Toxin Repressor; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Iron dependent repressor, metal binding and dimerisation domain |
| 结构域编号 domain_id | 1u8rJ03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 30 — Roll |
| 拓扑 Topology topology | 30 — SH3 type barrels. |
| 同源超家族 H-superfamily homologous superfamily | 90 — Ferrous iron transport protein A (FeoA) |