1z1b
;Crystal structure of a lambda integrase dimer bound to a COC' core site ;
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 | 1z1b |
| 沉积日期 deposition_date | 2005-03-03 |
| 结构标题 title | ;Crystal structure of a lambda integrase dimer bound to a COC' core site ; |
| 关键词 keywords | PROTEIN-DNA COMPLEX, DNA BINDING PROTEIN-DNA COMPLEX; DNA BINDING PROTEIN/DNA |
| 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 | 39.17 Å |
| 回转半径 Rg (电子) rg_electron | 38.31 Å |
| 零角强度 I(0) i0 | 273286000.00 |
| 分子量 molecular_weight | 110710.0 kDa |
| 排除体积 excluded_volume | 129030 ų |
| 包络体积 envelope_volume | 207830 ų |
| 水化壳体积 shell_volume | 47065 ų |
| 包络直径 envelope_diameter | 128.9 Å |
| 壳层 Rg shell_rg | 42.60 Å |
| 包络 Rg envelope_rg | 37.08 Å |
| 形状 Rg shape_rg | 38.28 Å |
| 总 Rg total_rg | 38.66 Å |
| 总原子数 total_atoms | 7653 |
| 残基数 n_residues | 805 |
| 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 | 125.0 Å |
| Rg (实空间) rg_real | 39.01 Å |
| Rg 误差 (实空间) rg_real_error | 0.94 Å |
| I(0) (实空间) i0_real | 2.7330e+08 |
| I(0) 误差 (实空间) i0_real_error | 4.7620e+06 |
| Rg (倒空间) rg_reciprocal | 39.11 Å |
| I(0) (倒空间) i0_reciprocal | 273300000.0000 |
| 解质量估计 total_estimate | 0.9038 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 53.1 Å |
| 偏度 Skewness skewness | 0.102 |
| 峰度 Kurtosis kurtosis | -0.598 |
| 角度范围 angular_range | — – 0.2000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 10450000.0000 |
| 实空间数据点数 n_real_points | 41 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.908 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 10 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1z1ba1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.10 — DNA-binding domain |
| 超家族 Superfamily superfamily | d.10.1 — DNA-binding domain |
| 家族 Family family | d.10.1.4 — lambda integrase N-terminal domain |
| 结构域编号 domain_id | d1z1ba2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.163 — DNA breaking-rejoining enzymes |
| 超家族 Superfamily superfamily | d.163.1 — DNA breaking-rejoining enzymes |
| 家族 Family family | d.163.1.1 — Lambda integrase-like, catalytic core |
| 结构域编号 domain_id | d1z1bb1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.10 — DNA-binding domain |
| 超家族 Superfamily superfamily | d.10.1 — DNA-binding domain |
| 家族 Family family | d.10.1.4 — lambda integrase N-terminal domain |
| 结构域编号 domain_id | d1z1bb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.163 — DNA breaking-rejoining enzymes |
| 超家族 Superfamily superfamily | d.163.1 — DNA breaking-rejoining enzymes |
| 家族 Family family | d.163.1.1 — Lambda integrase-like, catalytic core |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1z1bA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 160 — Double Stranded RNA Binding Domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — Classic Zinc Finger |
| 结构域编号 domain_id | 1z1bA02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 130 — Tyrosine recombinase, N-terminal domain |
| 结构域编号 domain_id | 1z1bA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 443 — hpI Integrase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Intergrase catalytic core |
| 结构域编号 domain_id | 1z1bB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 160 — Double Stranded RNA Binding Domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — Classic Zinc Finger |
| 结构域编号 domain_id | 1z1bB02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 150 — DNA polymerase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 130 — Tyrosine recombinase, N-terminal domain |
| 结构域编号 domain_id | 1z1bB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 443 — hpI Integrase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Intergrase catalytic core |