1yf2
;Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications ;
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 | 1yf2 |
| 沉积日期 deposition_date | 2004-12-30 |
| 结构标题 title | ;Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications ; |
| 关键词 keywords | ;Type I restriction modification enzyme, S-subunit, Structural genomics, PSI, Protein Structure Initiative, Berkeley Structural Genomics Center, BSGC, HYDROLASE REGULATOR ;; HYDROLASE REGULATOR |
| 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 | 37.03 Å |
| 回转半径 Rg (电子) rg_electron | 36.25 Å |
| 零角强度 I(0) i0 | 128786000.00 |
| 分子量 molecular_weight | 96958.0 kDa |
| 排除体积 excluded_volume | 124240 ų |
| 包络体积 envelope_volume | 173050 ų |
| 水化壳体积 shell_volume | 40718 ų |
| 包络直径 envelope_diameter | 124.1 Å |
| 壳层 Rg shell_rg | 41.53 Å |
| 包络 Rg envelope_rg | 35.31 Å |
| 形状 Rg shape_rg | 36.26 Å |
| 总 Rg total_rg | 36.65 Å |
| 总原子数 total_atoms | 6828 |
| 残基数 n_residues | 850 |
| 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 | 117.7 Å |
| Rg (实空间) rg_real | 36.91 Å |
| Rg 误差 (实空间) rg_real_error | 1.06 Å |
| I(0) (实空间) i0_real | 1.2880e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.1090e+06 |
| Rg (倒空间) rg_reciprocal | 36.99 Å |
| I(0) (倒空间) i0_reciprocal | 128800000.0000 |
| 解质量估计 total_estimate | 0.6180 |
| 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 | 54.7 Å |
| 偏度 Skewness skewness | 0.140 |
| 峰度 Kurtosis kurtosis | -0.285 |
| 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 | 14800000.0000 |
| 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: 0.734; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.999; Smooth: 0.686 |
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 (4 domains)
| 结构域编号 domain_id | d1yf2a1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.287 — DNA methylase specificity domain |
| 超家族 Superfamily superfamily | d.287.1 — DNA methylase specificity domain |
| 家族 Family family | d.287.1.2 — Type I restriction modification DNA specificity domain |
| 结构域编号 domain_id | d1yf2a2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.287 — DNA methylase specificity domain |
| 超家族 Superfamily superfamily | d.287.1 — DNA methylase specificity domain |
| 家族 Family family | d.287.1.2 — Type I restriction modification DNA specificity domain |
| 结构域编号 domain_id | d1yf2b1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.287 — DNA methylase specificity domain |
| 超家族 Superfamily superfamily | d.287.1 — DNA methylase specificity domain |
| 家族 Family family | d.287.1.2 — Type I restriction modification DNA specificity domain |
| 结构域编号 domain_id | d1yf2b2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.287 — DNA methylase specificity domain |
| 超家族 Superfamily superfamily | d.287.1 — DNA methylase specificity domain |
| 家族 Family family | d.287.1.2 — Type I restriction modification DNA specificity domain |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1yf2A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 20 — DNA methylase specificity domains |
| 结构域编号 domain_id | 1yf2A02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 1120 — Bipartite methylase S protein |
| 结构域编号 domain_id | 1yf2A03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 20 — DNA methylase specificity domains |
| 结构域编号 domain_id | 1yf2B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 20 — DNA methylase specificity domains |
| 结构域编号 domain_id | 1yf2B02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 287 — Helix Hairpins |
| 同源超家族 H-superfamily homologous superfamily | 1120 — Bipartite methylase S protein |
| 结构域编号 domain_id | 1yf2B03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 220 — Adenine-n6-DNA-methyltransferase TaqI; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 20 — DNA methylase specificity domains |