1nlt
The crystal structure of Hsp40 Ydj1
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 | 1nlt |
| 沉积日期 deposition_date | 2003-01-07 |
| 结构标题 title | The crystal structure of Hsp40 Ydj1 |
| 关键词 keywords | beta-strands, chaperone, heat shock, mitochondrion, PROTEIN TRANSPORT; PROTEIN TRANSPORT |
| 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 | 30.01 Å |
| 回转半径 Rg (电子) rg_electron | 30.50 Å |
| 零角强度 I(0) i0 | 11938500.00 |
| 分子量 molecular_weight | 26014.0 kDa |
| 排除体积 excluded_volume | 32515 ų |
| 包络体积 envelope_volume | 47927 ų |
| 水化壳体积 shell_volume | 15691 ų |
| 包络直径 envelope_diameter | 102.0 Å |
| 壳层 Rg shell_rg | 31.59 Å |
| 包络 Rg envelope_rg | 30.84 Å |
| 形状 Rg shape_rg | 30.40 Å |
| 总 Rg total_rg | 30.94 Å |
| 总原子数 total_atoms | 1815 |
| 残基数 n_residues | 235 |
| 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 | 103.1 Å |
| Rg (实空间) rg_real | 30.55 Å |
| Rg 误差 (实空间) rg_real_error | 1.17 Å |
| I(0) (实空间) i0_real | 1.1940e+07 |
| I(0) 误差 (实空间) i0_real_error | 2.3800e+05 |
| Rg (倒空间) rg_reciprocal | 30.33 Å |
| I(0) (倒空间) i0_reciprocal | 11940000.0000 |
| 解质量估计 total_estimate | 0.7203 |
| 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 | 19.5 Å |
| 偏度 Skewness skewness | 0.531 |
| 峰度 Kurtosis kurtosis | -0.636 |
| 角度范围 angular_range | — – 0.2650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 608900.0000 |
| 实空间数据点数 n_real_points | 54 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.502; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.139; Smooth: 0.712 |
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) 6 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1nlta1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.4 — HSP40/DnaJ peptide-binding domain |
| 超家族 Superfamily superfamily | b.4.1 — HSP40/DnaJ peptide-binding domain |
| 家族 Family family | b.4.1.1 — HSP40/DnaJ peptide-binding domain |
| 结构域编号 domain_id | d1nlta2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.4 — HSP40/DnaJ peptide-binding domain |
| 超家族 Superfamily superfamily | b.4.1 — HSP40/DnaJ peptide-binding domain |
| 家族 Family family | b.4.1.1 — HSP40/DnaJ peptide-binding domain |
| 结构域编号 domain_id | d1nlta3 |
| 类 Class class | g — Small proteins |
| 折叠类型 Fold fold | g.54 — DnaJ/Hsp40 cysteine-rich domain |
| 超家族 Superfamily superfamily | g.54.1 — DnaJ/Hsp40 cysteine-rich domain |
| 家族 Family family | g.54.1.1 — DnaJ/Hsp40 cysteine-rich domain |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1nltA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 260 — HSP40/DNAj peptide-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 20 — Urease metallochaperone UreE, N-terminal domain |
| 结构域编号 domain_id | 1nltA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 10 — Ribbon |
| 拓扑 Topology topology | 230 — Chaperone, DNAj Protein; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Heat shock protein DnaJ, cysteine-rich domain |
| 结构域编号 domain_id | 1nltA03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 260 — HSP40/DNAj peptide-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 20 — Urease metallochaperone UreE, N-terminal domain |