1tjl
Crystal structure of transcription factor DksA from E. coli
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 | 1tjl |
| 沉积日期 deposition_date | 2004-06-06 |
| 结构标题 title | Crystal structure of transcription factor DksA from E. coli |
| 关键词 keywords | ;DksA, transcription factor, RNA polymerase, stringent response, ppGpp, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, 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 | 48.87 Å |
| 回转半径 Rg (电子) rg_electron | 48.97 Å |
| 零角强度 I(0) i0 | 474740000.00 |
| 分子量 molecular_weight | 168990.0 kDa |
| 排除体积 excluded_volume | 207720 ų |
| 包络体积 envelope_volume | 357630 ų |
| 水化壳体积 shell_volume | 63919 ų |
| 包络直径 envelope_diameter | 170.9 Å |
| 壳层 Rg shell_rg | 49.37 Å |
| 包络 Rg envelope_rg | 47.87 Å |
| 形状 Rg shape_rg | 48.96 Å |
| 总 Rg total_rg | 49.02 Å |
| 总原子数 total_atoms | 11800 |
| 残基数 n_residues | 1450 |
| 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 | 169.9 Å |
| Rg (实空间) rg_real | 49.04 Å |
| Rg 误差 (实空间) rg_real_error | 1.95 Å |
| I(0) (实空间) i0_real | 4.7470e+08 |
| I(0) 误差 (实空间) i0_real_error | 9.8420e+06 |
| Rg (倒空间) rg_reciprocal | 48.88 Å |
| I(0) (倒空间) i0_reciprocal | 474600000.0000 |
| 解质量估计 total_estimate | 0.8749 |
| 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 | 53.1 Å |
| 偏度 Skewness skewness | 0.383 |
| 峰度 Kurtosis kurtosis | -0.340 |
| 角度范围 angular_range | — – 0.1600 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 26730000.0000 |
| 实空间数据点数 n_real_points | 33 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.853 |
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) 30 domains
SCOP 2.08 (20 domains)
| 结构域编号 domain_id | d1tjla1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 家族 Family family | a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 结构域编号 domain_id | d1tjla2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.39 — Glucocorticoid receptor-like (DNA-binding domain) |
| 超家族 Superfamily superfamily | g.39.1 — Glucocorticoid receptor-like (DNA-binding domain) |
| 家族 Family family | g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger |
| 结构域编号 domain_id | d1tjlb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 家族 Family family | a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 结构域编号 domain_id | d1tjlb2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.39 — Glucocorticoid receptor-like (DNA-binding domain) |
| 超家族 Superfamily superfamily | g.39.1 — Glucocorticoid receptor-like (DNA-binding domain) |
| 家族 Family family | g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger |
| 结构域编号 domain_id | d1tjlc1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 家族 Family family | a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 结构域编号 domain_id | d1tjlc2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.39 — Glucocorticoid receptor-like (DNA-binding domain) |
| 超家族 Superfamily superfamily | g.39.1 — Glucocorticoid receptor-like (DNA-binding domain) |
| 家族 Family family | g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger |
| 结构域编号 domain_id | d1tjld1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 家族 Family family | a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 结构域编号 domain_id | d1tjld2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.39 — Glucocorticoid receptor-like (DNA-binding domain) |
| 超家族 Superfamily superfamily | g.39.1 — Glucocorticoid receptor-like (DNA-binding domain) |
| 家族 Family family | g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger |
| 结构域编号 domain_id | d1tjle1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 家族 Family family | a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 结构域编号 domain_id | d1tjle2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.39 — Glucocorticoid receptor-like (DNA-binding domain) |
| 超家族 Superfamily superfamily | g.39.1 — Glucocorticoid receptor-like (DNA-binding domain) |
| 家族 Family family | g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger |
| 结构域编号 domain_id | d1tjlf1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 家族 Family family | a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 结构域编号 domain_id | d1tjlf2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.39 — Glucocorticoid receptor-like (DNA-binding domain) |
| 超家族 Superfamily superfamily | g.39.1 — Glucocorticoid receptor-like (DNA-binding domain) |
| 家族 Family family | g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger |
| 结构域编号 domain_id | d1tjlg1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 家族 Family family | a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 结构域编号 domain_id | d1tjlg2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.39 — Glucocorticoid receptor-like (DNA-binding domain) |
| 超家族 Superfamily superfamily | g.39.1 — Glucocorticoid receptor-like (DNA-binding domain) |
| 家族 Family family | g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger |
| 结构域编号 domain_id | d1tjlh1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 家族 Family family | a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 结构域编号 domain_id | d1tjlh2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.39 — Glucocorticoid receptor-like (DNA-binding domain) |
| 超家族 Superfamily superfamily | g.39.1 — Glucocorticoid receptor-like (DNA-binding domain) |
| 家族 Family family | g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger |
| 结构域编号 domain_id | d1tjli1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 家族 Family family | a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 结构域编号 domain_id | d1tjli2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.39 — Glucocorticoid receptor-like (DNA-binding domain) |
| 超家族 Superfamily superfamily | g.39.1 — Glucocorticoid receptor-like (DNA-binding domain) |
| 家族 Family family | g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger |
| 结构域编号 domain_id | d1tjlj1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.2 — Long alpha-hairpin |
| 超家族 Superfamily superfamily | a.2.14 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 家族 Family family | a.2.14.1 — DnaK suppressor protein DksA, alpha-hairpin domain |
| 结构域编号 domain_id | d1tjlj2 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.39 — Glucocorticoid receptor-like (DNA-binding domain) |
| 超家族 Superfamily superfamily | g.39.1 — Glucocorticoid receptor-like (DNA-binding domain) |
| 家族 Family family | g.39.1.13 — Prokaryotic DksA/TraR C4-type zinc finger |
CATH v4.4 (10 domains)
| 结构域编号 domain_id | 1tjlA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 910 — DksA, coiled-coil domain |
| 结构域编号 domain_id | 1tjlB00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 910 — DksA, coiled-coil domain |
| 结构域编号 domain_id | 1tjlC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 910 — DksA, coiled-coil domain |
| 结构域编号 domain_id | 1tjlD00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 910 — DksA, coiled-coil domain |
| 结构域编号 domain_id | 1tjlE00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 910 — DksA, coiled-coil domain |
| 结构域编号 domain_id | 1tjlF00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 910 — DksA, coiled-coil domain |
| 结构域编号 domain_id | 1tjlG00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 910 — DksA, coiled-coil domain |
| 结构域编号 domain_id | 1tjlH00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 910 — DksA, coiled-coil domain |
| 结构域编号 domain_id | 1tjlI00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 910 — DksA, coiled-coil domain |
| 结构域编号 domain_id | 1tjlJ00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 120 — Four Helix Bundle (Hemerythrin (Met), subunit A) |
| 同源超家族 H-superfamily homologous superfamily | 910 — DksA, coiled-coil domain |