1kek
Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase
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 | 1kek |
| 沉积日期 deposition_date | 2001-11-16 |
| 结构标题 title | Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase |
| 关键词 keywords | homodimer, 7 domains, OXIDOREDUCTASE; 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 | 39.04 Å |
| 回转半径 Rg (电子) rg_electron | 38.62 Å |
| 零角强度 I(0) i0 | 1107070000.00 |
| 分子量 molecular_weight | 270350.0 kDa |
| 排除体积 excluded_volume | 336480 ų |
| 包络体积 envelope_volume | 403390 ų |
| 水化壳体积 shell_volume | 81027 ų |
| 包络直径 envelope_diameter | 134.6 Å |
| 壳层 Rg shell_rg | 47.88 Å |
| 包络 Rg envelope_rg | 39.23 Å |
| 形状 Rg shape_rg | 38.60 Å |
| 总 Rg total_rg | 39.11 Å |
| 总原子数 total_atoms | 18882 |
| 残基数 n_residues | 2462 |
| 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 | 124.1 Å |
| Rg (实空间) rg_real | 38.87 Å |
| Rg 误差 (实空间) rg_real_error | 0.73 Å |
| I(0) (实空间) i0_real | 1.1070e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.8400e+07 |
| Rg (倒空间) rg_reciprocal | 38.98 Å |
| I(0) (倒空间) i0_reciprocal | 1107000000.0000 |
| 解质量估计 total_estimate | 0.8756 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 46.5 Å |
| 偏度 Skewness skewness | 0.297 |
| 峰度 Kurtosis kurtosis | -0.243 |
| 角度范围 angular_range | — – 0.2000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 303100000.0000 |
| 实空间数据点数 n_real_points | 41 |
| 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: 0.984; Smooth: 0.775 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (7)
6. 折叠分类 (SCOP + CATH) 24 domains
SCOP 2.08 (10 domains)
| 结构域编号 domain_id | d1keka1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.36 — Thiamin diphosphate-binding fold (THDP-binding) |
| 超家族 Superfamily superfamily | c.36.1 — Thiamin diphosphate-binding fold (THDP-binding) |
| 家族 Family family | c.36.1.8 — PFOR Pyr module |
| 结构域编号 domain_id | d1keka2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.36 — Thiamin diphosphate-binding fold (THDP-binding) |
| 超家族 Superfamily superfamily | c.36.1 — Thiamin diphosphate-binding fold (THDP-binding) |
| 家族 Family family | c.36.1.12 — PFOR PP module |
| 结构域编号 domain_id | d1keka3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.48 — TK C-terminal domain-like |
| 超家族 Superfamily superfamily | c.48.1 — TK C-terminal domain-like |
| 家族 Family family | c.48.1.3 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain II |
| 结构域编号 domain_id | d1keka4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.64 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III |
| 超家族 Superfamily superfamily | c.64.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III |
| 家族 Family family | c.64.1.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III |
| 结构域编号 domain_id | d1keka5 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.1 — 4Fe-4S ferredoxins |
| 家族 Family family | d.58.1.5 — Ferredoxin domains from multidomain proteins |
| 结构域编号 domain_id | d1kekb1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.36 — Thiamin diphosphate-binding fold (THDP-binding) |
| 超家族 Superfamily superfamily | c.36.1 — Thiamin diphosphate-binding fold (THDP-binding) |
| 家族 Family family | c.36.1.8 — PFOR Pyr module |
| 结构域编号 domain_id | d1kekb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.36 — Thiamin diphosphate-binding fold (THDP-binding) |
| 超家族 Superfamily superfamily | c.36.1 — Thiamin diphosphate-binding fold (THDP-binding) |
| 家族 Family family | c.36.1.12 — PFOR PP module |
| 结构域编号 domain_id | d1kekb3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.48 — TK C-terminal domain-like |
| 超家族 Superfamily superfamily | c.48.1 — TK C-terminal domain-like |
| 家族 Family family | c.48.1.3 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain II |
| 结构域编号 domain_id | d1kekb4 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.64 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III |
| 超家族 Superfamily superfamily | c.64.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III |
| 家族 Family family | c.64.1.1 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III |
| 结构域编号 domain_id | d1kekb5 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.1 — 4Fe-4S ferredoxins |
| 家族 Family family | d.58.1.5 — Ferredoxin domains from multidomain proteins |
CATH v4.4 (14 domains)
| 结构域编号 domain_id | 1kekA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains |
| 结构域编号 domain_id | 1kekA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 920 — |
| 结构域编号 domain_id | 1kekA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 920 — Pyruvate-ferredoxin Oxidoreductase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III |
| 结构域编号 domain_id | 1kekA04 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 780 — Pyruvate-ferredoxin Oxidoreductase; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Pyruvate-flavodoxin oxidoreductase, EKR domain |
| 结构域编号 domain_id | 1kekA05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1kekA06 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains |
| 结构域编号 domain_id | 1kekA07 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 790 — Pyruvate-ferredoxin Oxidoreductase; domain 7 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Pyruvate-ferredoxin Oxidoreductase; domain 7 |
| 结构域编号 domain_id | 1kekB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains |
| 结构域编号 domain_id | 1kekB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 920 — |
| 结构域编号 domain_id | 1kekB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 920 — Pyruvate-ferredoxin Oxidoreductase; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Pyruvate-ferredoxin oxidoreductase, PFOR, domain III |
| 结构域编号 domain_id | 1kekB04 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 780 — Pyruvate-ferredoxin Oxidoreductase; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Pyruvate-flavodoxin oxidoreductase, EKR domain |
| 结构域编号 domain_id | 1kekB05 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1kekB06 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains |
| 结构域编号 domain_id | 1kekB07 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 790 — Pyruvate-ferredoxin Oxidoreductase; domain 7 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Pyruvate-ferredoxin Oxidoreductase; domain 7 |