2bq1
Ribonucleotide reductase class 1b holocomplex R1E,R2F from Salmonella typhimurium
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 | 2bq1 |
| 沉积日期 deposition_date | 2005-04-26 |
| 结构标题 title | Ribonucleotide reductase class 1b holocomplex R1E,R2F from Salmonella typhimurium |
| 关键词 keywords | ;R1, R2, R1E, R2F, IRON, CLASS 1B, HOLOCOMPLEX, ALLOSTERIC REGULATION, RIBONUCLEOTIDE REDUCTASE, ATP-BINDING, METAL-BINDING, OXIDOREDUCTASE, DNA REPLICATION, RADICAL TRANSFER, ALLOSTERIC ENZYME, ASYMMETRIC COMPLEX, NUCLEOTIDE-BINDING ;; 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 | 43.01 Å |
| 回转半径 Rg (电子) rg_electron | 42.50 Å |
| 零角强度 I(0) i0 | 706946000.00 |
| 分子量 molecular_weight | 220130.0 kDa |
| 排除体积 excluded_volume | 275670 ų |
| 包络体积 envelope_volume | 368940 ų |
| 水化壳体积 shell_volume | 70850 ų |
| 包络直径 envelope_diameter | 143.4 Å |
| 壳层 Rg shell_rg | 49.25 Å |
| 包络 Rg envelope_rg | 41.26 Å |
| 形状 Rg shape_rg | 42.51 Å |
| 总 Rg total_rg | 42.80 Å |
| 总原子数 total_atoms | 15520 |
| 残基数 n_residues | 1936 |
| 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 | 134.0 Å |
| Rg (实空间) rg_real | 42.82 Å |
| Rg 误差 (实空间) rg_real_error | 1.15 Å |
| I(0) (实空间) i0_real | 7.0690e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.3640e+07 |
| Rg (倒空间) rg_reciprocal | 43.01 Å |
| I(0) (倒空间) i0_reciprocal | 707100000.0000 |
| 解质量估计 total_estimate | 0.9015 |
| 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 | 58.0 Å |
| 偏度 Skewness skewness | 0.081 |
| 峰度 Kurtosis kurtosis | -0.640 |
| 角度范围 angular_range | — – 0.1850 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 78640000.0000 |
| 实空间数据点数 n_real_points | 38 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.876 |
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) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d2bq1e1 |
| 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 | d2bq1e2 |
| 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 | d2bq1f1 |
| 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 | d2bq1f2 |
| 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 | d2bq1i1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.25 — Ferritin-like |
| 超家族 Superfamily superfamily | a.25.1 — Ferritin-like |
| 家族 Family family | a.25.1.2 — Ribonucleotide reductase-like |
| 结构域编号 domain_id | d2bq1j1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.25 — Ferritin-like |
| 超家族 Superfamily superfamily | a.25.1 — Ferritin-like |
| 家族 Family family | a.25.1.2 — Ribonucleotide reductase-like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2bq1E02 |
| 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 | 2bq1E03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1650 — 50s Ribosomal Protein L19e, Chain O, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2bq1F02 |
| 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 | 2bq1F03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1650 — 50s Ribosomal Protein L19e, Chain O, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 2bq1I01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 620 — Ribonucleotide Reductase, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Ribonucleotide Reductase, subunit A |
| 结构域编号 domain_id | 2bq1J00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 620 — Ribonucleotide Reductase, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Ribonucleotide Reductase, subunit A |