2kho
NMR-RDC / XRAY structure of E. coli HSP70 (DNAK) chaperone (1-605) complexed with ADP and substrate
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 | 2kho |
| 沉积日期 deposition_date | 2009-04-10 |
| 结构标题 title | NMR-RDC / XRAY structure of E. coli HSP70 (DNAK) chaperone (1-605) complexed with ADP and substrate |
| 关键词 keywords | ;MOLECULAR CHAPERONE, HSP70, PEPTIDE BINDING, PROTEIN FOLDING, ATP-binding, Cell inner membrane, Cell membrane, Chaperone, DNA replication, Membrane, Nucleotide-binding, Phosphoprotein, Stress response, TRANSCRIPTION ;; CHAPERONE |
| 实验方法 method | SOLUTION NMR |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 37.11 Å |
| 回转半径 Rg (电子) rg_electron | 37.63 Å |
| 零角强度 I(0) i0 | 64753500.00 |
| 分子量 molecular_weight | 64024.0 kDa |
| 排除体积 excluded_volume | 80246 ų |
| 包络体积 envelope_volume | 114370 ų |
| 水化壳体积 shell_volume | 28883 ų |
| 包络直径 envelope_diameter | 144.9 Å |
| 壳层 Rg shell_rg | 37.47 Å |
| 包络 Rg envelope_rg | 38.14 Å |
| 形状 Rg shape_rg | 37.61 Å |
| 总 Rg total_rg | 37.69 Å |
| 总原子数 total_atoms | 5078 |
| 残基数 n_residues | 600 |
| 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 | 136.8 Å |
| Rg (实空间) rg_real | 37.90 Å |
| Rg 误差 (实空间) rg_real_error | 1.82 Å |
| I(0) (实空间) i0_real | 6.4750e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.2970e+06 |
| Rg (倒空间) rg_reciprocal | 37.41 Å |
| I(0) (倒空间) i0_reciprocal | 64720000.0000 |
| 解质量估计 total_estimate | 0.7023 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 31.8 Å |
| 偏度 Skewness skewness | 0.695 |
| 峰度 Kurtosis kurtosis | -0.195 |
| 角度范围 angular_range | — – 0.2150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 6196000.0000 |
| 实空间数据点数 n_real_points | 44 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.389; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.187; Smooth: 0.773 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (1)
6. 折叠分类 (SCOP + CATH) 6 domains
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2khoA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 40 — ATPase, nucleotide binding domain |
| 结构域编号 domain_id | 2khoA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 30 — Defensin A-like |
| 同源超家族 H-superfamily homologous superfamily | 30 — |
| 结构域编号 domain_id | 2khoA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 40 — ATPase, nucleotide binding domain |
| 结构域编号 domain_id | 2khoA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 640 — Actin; Chain A, domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — ATPase, substrate binding domain, subdomain 4 |
| 结构域编号 domain_id | 2khoA05 |
| 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 | 2khoA06 |
| 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 — |