1r1r
RIBONUCLEOTIDE REDUCTASE R1 PROTEIN MUTANT Y730F WITH A REDUCED ACTIVE SITE FROM ESCHERICHIA COLI
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 | 1r1r |
| 沉积日期 deposition_date | 1997-07-15 |
| 结构标题 title | RIBONUCLEOTIDE REDUCTASE R1 PROTEIN MUTANT Y730F WITH A REDUCED ACTIVE SITE FROM ESCHERICHIA COLI |
| 关键词 keywords | OXIDOREDUCTASE, DEOXYRIBONUCLEOTIDE SYNTHESIS, RADICAL CHEMISTRY, REDOX CENTER, RIBONUCLEOTIDE REDUCTASE; OXIDOREDUCTASE |
| 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 | 50.49 Å |
| 回转半径 Rg (电子) rg_electron | 50.24 Å |
| 零角强度 I(0) i0 | 925686000.00 |
| 分子量 molecular_weight | 254570.0 kDa |
| 排除体积 excluded_volume | 318800 ų |
| 包络体积 envelope_volume | 446820 ų |
| 水化壳体积 shell_volume | 72917 ų |
| 包络直径 envelope_diameter | 159.5 Å |
| 壳层 Rg shell_rg | 55.34 Å |
| 包络 Rg envelope_rg | 48.93 Å |
| 形状 Rg shape_rg | 50.26 Å |
| 总 Rg total_rg | 50.32 Å |
| 总原子数 total_atoms | 17946 |
| 残基数 n_residues | 2253 |
| 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 | 168.6 Å |
| Rg (实空间) rg_real | 50.45 Å |
| Rg 误差 (实空间) rg_real_error | 1.66 Å |
| I(0) (实空间) i0_real | 9.2570e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.9530e+07 |
| Rg (倒空间) rg_reciprocal | 50.51 Å |
| I(0) (倒空间) i0_reciprocal | 925700000.0000 |
| 解质量估计 total_estimate | 0.8838 |
| 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 | 76.1 Å |
| 偏度 Skewness skewness | 0.152 |
| 峰度 Kurtosis kurtosis | -0.752 |
| 角度范围 angular_range | — – 0.1550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 107200000.0000 |
| 实空间数据点数 n_real_points | 32 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.908 |
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) 9 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1r1ra1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.98 — R1 subunit of ribonucleotide reductase, N-terminal domain |
| 超家族 Superfamily superfamily | a.98.1 — R1 subunit of ribonucleotide reductase, N-terminal domain |
| 家族 Family family | a.98.1.1 — R1 subunit of ribonucleotide reductase, N-terminal domain |
| 结构域编号 domain_id | d1r1ra2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.7 — PFL-like glycyl radical enzymes |
| 超家族 Superfamily superfamily | c.7.1 — PFL-like glycyl radical enzymes |
| 家族 Family family | c.7.1.2 — R1 subunit of ribonucleotide reductase, C-terminal domain |
| 结构域编号 domain_id | d1r1rb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.98 — R1 subunit of ribonucleotide reductase, N-terminal domain |
| 超家族 Superfamily superfamily | a.98.1 — R1 subunit of ribonucleotide reductase, N-terminal domain |
| 家族 Family family | a.98.1.1 — R1 subunit of ribonucleotide reductase, N-terminal domain |
| 结构域编号 domain_id | d1r1rb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.7 — PFL-like glycyl radical enzymes |
| 超家族 Superfamily superfamily | c.7.1 — PFL-like glycyl radical enzymes |
| 家族 Family family | c.7.1.2 — R1 subunit of ribonucleotide reductase, C-terminal domain |
| 结构域编号 domain_id | d1r1rc1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.98 — R1 subunit of ribonucleotide reductase, N-terminal domain |
| 超家族 Superfamily superfamily | a.98.1 — R1 subunit of ribonucleotide reductase, N-terminal domain |
| 家族 Family family | a.98.1.1 — R1 subunit of ribonucleotide reductase, N-terminal domain |
| 结构域编号 domain_id | d1r1rc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.7 — PFL-like glycyl radical enzymes |
| 超家族 Superfamily superfamily | c.7.1 — PFL-like glycyl radical enzymes |
| 家族 Family family | c.7.1.2 — R1 subunit of ribonucleotide reductase, C-terminal domain |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1r1rA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1r1rB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1r1rC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain |
| 同源超家族 H-superfamily homologous superfamily | 20 — |