1dky
THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE PEPTIDE, DETERMINED FROM TYPE 2 NATIVE CRYSTALS
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 | 1dky |
| 沉积日期 deposition_date | 1996-06-03 |
| 结构标题 title | THE SUBSTRATE BINDING DOMAIN OF DNAK IN COMPLEX WITH A SUBSTRATE PEPTIDE, DETERMINED FROM TYPE 2 NATIVE CRYSTALS |
| 关键词 keywords | DNAK, HEAT SHOCK PROTEIN 70 KDA (HSP70), COMPLEX (MOLECULAR CHAPERONE-PEPTIDE), COMPLEX (MOLECULAR CHAPERONE-PEPTIDE) complex; COMPLEX (MOLECULAR CHAPERONE/PEPTIDE) |
| 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 | 23.32 Å |
| 回转半径 Rg (电子) rg_electron | 22.40 Å |
| 零角强度 I(0) i0 | 33145200.00 |
| 分子量 molecular_weight | 42298.0 kDa |
| 排除体积 excluded_volume | 52252 ų |
| 包络体积 envelope_volume | 67397 ų |
| 水化壳体积 shell_volume | 25249 ų |
| 包络直径 envelope_diameter | 80.7 Å |
| 壳层 Rg shell_rg | 29.41 Å |
| 包络 Rg envelope_rg | 22.43 Å |
| 形状 Rg shape_rg | 22.41 Å |
| 总 Rg total_rg | 23.26 Å |
| 总原子数 total_atoms | 2971 |
| 残基数 n_residues | 422 |
| 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 | 78.6 Å |
| Rg (实空间) rg_real | 23.19 Å |
| Rg 误差 (实空间) rg_real_error | 0.48 Å |
| I(0) (实空间) i0_real | 3.3150e+07 |
| I(0) 误差 (实空间) i0_real_error | 4.7260e+05 |
| Rg (倒空间) rg_reciprocal | 23.22 Å |
| I(0) (倒空间) i0_reciprocal | 33150000.0000 |
| 解质量估计 total_estimate | 0.8754 |
| 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 | 30.2 Å |
| 偏度 Skewness skewness | 0.179 |
| 峰度 Kurtosis kurtosis | -0.357 |
| 角度范围 angular_range | — – 0.3400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 4829000.0000 |
| 实空间数据点数 n_real_points | 66 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.987 |
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) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1dkya1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.8 — immunoglobulin/albumin-binding domain-like |
| 超家族 Superfamily superfamily | a.8.4 — Heat shock protein 70kD (HSP70), C-terminal subdomain |
| 家族 Family family | a.8.4.1 — Heat shock protein 70kD (HSP70), C-terminal subdomain |
| 结构域编号 domain_id | d1dkya2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.130 — Heat shock protein 70kD (HSP70), peptide-binding domain |
| 超家族 Superfamily superfamily | b.130.1 — Heat shock protein 70kD (HSP70), peptide-binding domain |
| 家族 Family family | b.130.1.1 — Heat shock protein 70kD (HSP70), peptide-binding domain |
| 结构域编号 domain_id | d1dkyb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.8 — immunoglobulin/albumin-binding domain-like |
| 超家族 Superfamily superfamily | a.8.4 — Heat shock protein 70kD (HSP70), C-terminal subdomain |
| 家族 Family family | a.8.4.1 — Heat shock protein 70kD (HSP70), C-terminal subdomain |
| 结构域编号 domain_id | d1dkyb2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.130 — Heat shock protein 70kD (HSP70), peptide-binding domain |
| 超家族 Superfamily superfamily | b.130.1 — Heat shock protein 70kD (HSP70), peptide-binding domain |
| 家族 Family family | b.130.1.1 — Heat shock protein 70kD (HSP70), peptide-binding domain |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1dkyA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 34 — Substrate Binding Domain Of DNAk; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Substrate Binding Domain Of DNAk; Chain A, domain 1 |
| 结构域编号 domain_id | 1dkyA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |
| 结构域编号 domain_id | 1dkyB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 34 — Substrate Binding Domain Of DNAk; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Substrate Binding Domain Of DNAk; Chain A, domain 1 |
| 结构域编号 domain_id | 1dkyB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — |