1f3w
RECOMBINANT RABBIT MUSCLE PYRUVATE KINASE
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 | 1f3w |
| 沉积日期 deposition_date | 2000-06-06 |
| 结构标题 title | RECOMBINANT RABBIT MUSCLE PYRUVATE KINASE |
| 关键词 keywords | pyruvate kinase, recombinant, muscle isozyme, TRANSFERASE; TRANSFERASE |
| 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 | 56.40 Å |
| 回转半径 Rg (电子) rg_electron | 56.56 Å |
| 零角强度 I(0) i0 | 2951330000.00 |
| 分子量 molecular_weight | 453600.0 kDa |
| 排除体积 excluded_volume | 567200 ų |
| 包络体积 envelope_volume | 751080 ų |
| 水化壳体积 shell_volume | 109580 ų |
| 包络直径 envelope_diameter | 194.8 Å |
| 壳层 Rg shell_rg | 59.58 Å |
| 包络 Rg envelope_rg | 55.80 Å |
| 形状 Rg shape_rg | 56.58 Å |
| 总 Rg total_rg | 56.55 Å |
| 总原子数 total_atoms | 31728 |
| 残基数 n_residues | 4152 |
| 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 | 192.0 Å |
| Rg (实空间) rg_real | 56.44 Å |
| Rg 误差 (实空间) rg_real_error | 1.61 Å |
| I(0) (实空间) i0_real | 2.9510e+09 |
| I(0) 误差 (实空间) i0_real_error | 5.7630e+07 |
| Rg (倒空间) rg_reciprocal | 56.34 Å |
| I(0) (倒空间) i0_reciprocal | 2951000000.0000 |
| 解质量估计 total_estimate | 0.6488 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 61.7 Å |
| 偏度 Skewness skewness | 0.319 |
| 峰度 Kurtosis kurtosis | -0.523 |
| 角度范围 angular_range | — – 0.1400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 257400000.0000 |
| 实空间数据点数 n_real_points | 29 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 0.003; Positv: 1.000; Valcen: 0.997; Smooth: 0.816 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 48 domains
SCOP 2.08 (24 domains)
| 结构域编号 domain_id | d1f3wa1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d1f3wa2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d1f3wa3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d1f3wb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d1f3wb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d1f3wb3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d1f3wc1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d1f3wc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d1f3wc3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d1f3wd1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d1f3wd2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d1f3wd3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d1f3we1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d1f3we2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d1f3we3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d1f3wf1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d1f3wf2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d1f3wf3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d1f3wg1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d1f3wg2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d1f3wg3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | d1f3wh1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.58 — PK beta-barrel domain-like |
| 超家族 Superfamily superfamily | b.58.1 — PK beta-barrel domain-like |
| 家族 Family family | b.58.1.1 — Pyruvate kinase beta-barrel domain |
| 结构域编号 domain_id | d1f3wh2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.1 — TIM beta/alpha-barrel |
| 超家族 Superfamily superfamily | c.1.12 — Phosphoenolpyruvate/pyruvate domain |
| 家族 Family family | c.1.12.1 — Pyruvate kinase |
| 结构域编号 domain_id | d1f3wh3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.49 — Pyruvate kinase C-terminal domain-like |
| 超家族 Superfamily superfamily | c.49.1 — PK C-terminal domain-like |
| 家族 Family family | c.49.1.1 — Pyruvate kinase, C-terminal domain |
CATH v4.4 (24 domains)
| 结构域编号 domain_id | 1f3wA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 1f3wA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 1f3wA03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 1f3wB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 1f3wB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 1f3wB03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 1f3wC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 1f3wC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 1f3wC03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 1f3wD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 1f3wD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 1f3wD03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 1f3wE01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 1f3wE02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 1f3wE03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 1f3wF01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 1f3wF02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 1f3wF03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 1f3wG01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 1f3wG02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 1f3wG03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |
| 结构域编号 domain_id | 1f3wH01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1380 — Pyruvate Kinase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — Pyruvate kinase, C-terminal domain |
| 结构域编号 domain_id | 1f3wH02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 20 — Alpha-Beta Barrel |
| 拓扑 Topology topology | 20 — TIM Barrel |
| 同源超家族 H-superfamily homologous superfamily | 60 — Phosphoenolpyruvate-binding domains |
| 结构域编号 domain_id | 1f3wH03 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 33 — M1 Pyruvate Kinase; Domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — PK beta-barrel domain-like |