1vlr
Crystal structure of mRNA decapping enzyme (DcpS) from Mus musculus at 1.83 A resolution
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 | 1vlr |
| 沉积日期 deposition_date | 2004-08-10 |
| 结构标题 title | Crystal structure of mRNA decapping enzyme (DcpS) from Mus musculus at 1.83 A resolution |
| 关键词 keywords | ;16740816, mRNA decapping enzyme (DcpS), STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, Joint Center for Structural Genomics, RNA BINDING PROTEIN ;; RNA BINDING PROTEIN |
| 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 | 27.20 Å |
| 回转半径 Rg (电子) rg_electron | 26.00 Å |
| 零角强度 I(0) i0 | 71697500.00 |
| 分子量 molecular_weight | 67844.0 kDa |
| 排除体积 excluded_volume | 85780 ų |
| 包络体积 envelope_volume | 105850 ų |
| 水化壳体积 shell_volume | 33383 ų |
| 包络直径 envelope_diameter | 83.0 Å |
| 壳层 Rg shell_rg | 33.69 Å |
| 包络 Rg envelope_rg | 25.56 Å |
| 形状 Rg shape_rg | 25.99 Å |
| 总 Rg total_rg | 26.88 Å |
| 总原子数 total_atoms | 4802 |
| 残基数 n_residues | 582 |
| 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 | 78.2 Å |
| Rg (实空间) rg_real | 27.00 Å |
| Rg 误差 (实空间) rg_real_error | 0.35 Å |
| I(0) (实空间) i0_real | 7.1700e+07 |
| I(0) 误差 (实空间) i0_real_error | 8.8340e+05 |
| Rg (倒空间) rg_reciprocal | 27.06 Å |
| I(0) (倒空间) i0_reciprocal | 71700000.0000 |
| 解质量估计 total_estimate | 0.9158 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 36.4 Å |
| 偏度 Skewness skewness | 0.057 |
| 峰度 Kurtosis kurtosis | -0.616 |
| 角度范围 angular_range | — – 0.2900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 12610000.0000 |
| 实空间数据点数 n_real_points | 59 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.986; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.950 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 10 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1vlra1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.13 — HIT-like |
| 超家族 Superfamily superfamily | d.13.1 — HIT-like |
| 家族 Family family | d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain |
| 结构域编号 domain_id | d1vlra2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.246 — mRNA decapping enzyme DcpS N-terminal domain |
| 超家族 Superfamily superfamily | d.246.1 — mRNA decapping enzyme DcpS N-terminal domain |
| 家族 Family family | d.246.1.1 — mRNA decapping enzyme DcpS N-terminal domain |
| 结构域编号 domain_id | d1vlrb1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.13 — HIT-like |
| 超家族 Superfamily superfamily | d.13.1 — HIT-like |
| 家族 Family family | d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain |
| 结构域编号 domain_id | d1vlrb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.246 — mRNA decapping enzyme DcpS N-terminal domain |
| 超家族 Superfamily superfamily | d.246.1 — mRNA decapping enzyme DcpS N-terminal domain |
| 家族 Family family | d.246.1.1 — mRNA decapping enzyme DcpS N-terminal domain |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1vlrA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 200 — Phosphorylase Kinase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 40 — Scavenger mRNA decapping enzyme, N-terminal domain |
| 结构域编号 domain_id | 1vlrA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 2240 — mRNA decapping enzyme DcpS N-terminal fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — mRNA decapping enzyme DcpS N-terminal domain |
| 结构域编号 domain_id | 1vlrA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 428 — HIT family, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 10 — HIT-like |
| 结构域编号 domain_id | 1vlrB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 200 — Phosphorylase Kinase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 40 — Scavenger mRNA decapping enzyme, N-terminal domain |
| 结构域编号 domain_id | 1vlrB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 2240 — mRNA decapping enzyme DcpS N-terminal fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — mRNA decapping enzyme DcpS N-terminal domain |
| 结构域编号 domain_id | 1vlrB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 428 — HIT family, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 10 — HIT-like |