2jaz
CRYSTAL STRUCTURE OF THE MUTANT N560D OF THE NUCLEASE DOMAIN OF COLE7 IN COMPLEX WITH IM7
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 | 2jaz |
| 沉积日期 deposition_date | 2006-12-01 |
| 结构标题 title | CRYSTAL STRUCTURE OF THE MUTANT N560D OF THE NUCLEASE DOMAIN OF COLE7 IN COMPLEX WITH IM7 |
| 关键词 keywords | ;HYDROLASE/INHIBITOR, HYDROLASE-INHIBITOR COMPLEX, ZINC, TOXIN, PLASMID, NUCLEASE, HYDROLASE, ANTIBIOTIC, H-N-H MOTIF, BACTERIOCIN, ENDONUCLEASE, METAL-BINDING, ANTIMICROBIAL, DNA HYDROLYSIS, BACTERIOCIN IMMUNITY, HIS METAL FINGER MOTIF ;; HYDROLASE/INHIBITOR |
| 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 | 24.69 Å |
| 回转半径 Rg (电子) rg_electron | 23.74 Å |
| 零角强度 I(0) i0 | 40056000.00 |
| 分子量 molecular_weight | 47295.0 kDa |
| 排除体积 excluded_volume | 58624 ų |
| 包络体积 envelope_volume | 71248 ų |
| 水化壳体积 shell_volume | 25618 ų |
| 包络直径 envelope_diameter | 88.1 Å |
| 壳层 Rg shell_rg | 30.52 Å |
| 包络 Rg envelope_rg | 23.87 Å |
| 形状 Rg shape_rg | 23.70 Å |
| 总 Rg total_rg | 24.67 Å |
| 总原子数 total_atoms | 3329 |
| 残基数 n_residues | 411 |
| 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 | 86.1 Å |
| Rg (实空间) rg_real | 24.74 Å |
| Rg 误差 (实空间) rg_real_error | 0.69 Å |
| I(0) (实空间) i0_real | 4.0060e+07 |
| I(0) 误差 (实空间) i0_real_error | 6.0180e+05 |
| Rg (倒空间) rg_reciprocal | 24.73 Å |
| I(0) (倒空间) i0_reciprocal | 40060000.0000 |
| 解质量估计 total_estimate | 0.7724 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 24.6 Å |
| 偏度 Skewness skewness | 0.429 |
| 峰度 Kurtosis kurtosis | -0.214 |
| 角度范围 angular_range | — – 0.3200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 9571000.0000 |
| 实空间数据点数 n_real_points | 64 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.720; Stabil: 0.989; Sysdev: 1.000; Positv: 1.000; Valcen: 0.910; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d2jaza_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.28 — Acyl carrier protein-like |
| 超家族 Superfamily superfamily | a.28.2 — Colicin E immunity proteins |
| 家族 Family family | a.28.2.1 — Colicin E immunity proteins |
| 结构域编号 domain_id | d2jazb1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.4 — His-Me finger endonucleases |
| 超家族 Superfamily superfamily | d.4.1 — His-Me finger endonucleases |
| 家族 Family family | d.4.1.1 — HNH-motif |
| 结构域编号 domain_id | d2jazc_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.28 — Acyl carrier protein-like |
| 超家族 Superfamily superfamily | a.28.2 — Colicin E immunity proteins |
| 家族 Family family | a.28.2.1 — Colicin E immunity proteins |
| 结构域编号 domain_id | d2jazd_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.4 — His-Me finger endonucleases |
| 超家族 Superfamily superfamily | d.4.1 — His-Me finger endonucleases |
| 家族 Family family | d.4.1.1 — HNH-motif |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2jazA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Colicin E immunity protein |
| 结构域编号 domain_id | 2jazB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Colicin/pyocin, DNase domain |
| 结构域编号 domain_id | 2jazC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Colicin E immunity protein |
| 结构域编号 domain_id | 2jazD00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 540 — Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain |
| 同源超家族 H-superfamily homologous superfamily | 10 — Colicin/pyocin, DNase domain |