1nxz
X-Ray Crystal Structure of Protein yggj_haein of Haemophilus influenzae. Northeast Structural Genomics Consortium Target IR73.
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 | 1nxz |
| 沉积日期 deposition_date | 2003-02-11 |
| 结构标题 title | X-Ray Crystal Structure of Protein yggj_haein of Haemophilus influenzae. Northeast Structural Genomics Consortium Target IR73. |
| 关键词 keywords | STRUCTURAL GENOMICS, dimer, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, Unknown function; STRUCTURAL GENOMICS, Unknown function |
| 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 | 25.59 Å |
| 回转半径 Rg (电子) rg_electron | 24.61 Å |
| 零角强度 I(0) i0 | 51710500.00 |
| 分子量 molecular_weight | 55044.0 kDa |
| 排除体积 excluded_volume | 68609 ų |
| 包络体积 envelope_volume | 84106 ų |
| 水化壳体积 shell_volume | 28735 ų |
| 包络直径 envelope_diameter | 87.6 Å |
| 壳层 Rg shell_rg | 31.74 Å |
| 包络 Rg envelope_rg | 24.73 Å |
| 形状 Rg shape_rg | 24.62 Å |
| 总 Rg total_rg | 25.33 Å |
| 总原子数 total_atoms | 3835 |
| 残基数 n_residues | 483 |
| 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 | 85.0 Å |
| Rg (实空间) rg_real | 25.52 Å |
| Rg 误差 (实空间) rg_real_error | 0.56 Å |
| I(0) (实空间) i0_real | 5.1710e+07 |
| I(0) 误差 (实空间) i0_real_error | 7.1870e+05 |
| Rg (倒空间) rg_reciprocal | 25.54 Å |
| I(0) (倒空间) i0_reciprocal | 51710000.0000 |
| 解质量估计 total_estimate | 0.8877 |
| 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 | 31.5 Å |
| 偏度 Skewness skewness | 0.278 |
| 峰度 Kurtosis kurtosis | -0.231 |
| 角度范围 angular_range | — – 0.3100 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 5921000.0000 |
| 实空间数据点数 n_real_points | 63 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.984 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 10 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1nxza1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.122 — PUA domain-like |
| 超家族 Superfamily superfamily | b.122.1 — PUA domain-like |
| 家族 Family family | b.122.1.2 — YggJ N-terminal domain-like |
| 结构域编号 domain_id | d1nxza2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.116 — alpha/beta knot |
| 超家族 Superfamily superfamily | c.116.1 — alpha/beta knot |
| 家族 Family family | c.116.1.5 — YggJ C-terminal domain-like |
| 结构域编号 domain_id | d1nxza3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1nxzb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.122 — PUA domain-like |
| 超家族 Superfamily superfamily | b.122.1 — PUA domain-like |
| 家族 Family family | b.122.1.2 — YggJ N-terminal domain-like |
| 结构域编号 domain_id | d1nxzb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.116 — alpha/beta knot |
| 超家族 Superfamily superfamily | c.116.1 — alpha/beta knot |
| 家族 Family family | c.116.1.5 — YggJ C-terminal domain-like |
| 结构域编号 domain_id | d1nxzb3 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1nxzA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 240 — Ribosomal Protein L25; Chain P |
| 同源超家族 H-superfamily homologous superfamily | 20 — Hypothetical PUA domain-like; domain 1 |
| 结构域编号 domain_id | 1nxzA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1280 — Alpha/beta knot |
| 同源超家族 H-superfamily homologous superfamily | 10 — SPOUT methyltransferase, trefoil knot domain |
| 结构域编号 domain_id | 1nxzB01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 240 — Ribosomal Protein L25; Chain P |
| 同源超家族 H-superfamily homologous superfamily | 20 — Hypothetical PUA domain-like; domain 1 |
| 结构域编号 domain_id | 1nxzB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1280 — Alpha/beta knot |
| 同源超家族 H-superfamily homologous superfamily | 10 — SPOUT methyltransferase, trefoil knot domain |