2iga
;Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations. ;
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 | 2iga |
| 沉积日期 deposition_date | 2006-09-22 |
| 结构标题 title | ;Structure of Homoprotocatechuate 2,3-Dioxygenase from B. fuscum in complex with reactive intermediates formed via in crystallo reaction with 4-nitrocatechol at low oxygen concentrations. ; |
| 关键词 keywords | ;oxygenase, extradiol, Fe(II), homoprotocatechuate, alkylperoxo intermediate, substrate-semiquinone, open-ring product, 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 | 33.40 Å |
| 回转半径 Rg (电子) rg_electron | 32.56 Å |
| 零角强度 I(0) i0 | 441049000.00 |
| 分子量 molecular_weight | 165530.0 kDa |
| 排除体积 excluded_volume | 204860 ų |
| 包络体积 envelope_volume | 236990 ų |
| 水化壳体积 shell_volume | 57139 ų |
| 包络直径 envelope_diameter | 106.5 Å |
| 壳层 Rg shell_rg | 41.86 Å |
| 包络 Rg envelope_rg | 32.80 Å |
| 形状 Rg shape_rg | 32.55 Å |
| 总 Rg total_rg | 33.22 Å |
| 总原子数 total_atoms | 11689 |
| 残基数 n_residues | 1436 |
| 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 | 104.4 Å |
| Rg (实空间) rg_real | 33.24 Å |
| Rg 误差 (实空间) rg_real_error | 0.72 Å |
| I(0) (实空间) i0_real | 4.4100e+08 |
| I(0) 误差 (实空间) i0_real_error | 7.5110e+06 |
| Rg (倒空间) rg_reciprocal | 33.34 Å |
| I(0) (倒空间) i0_reciprocal | 441100000.0000 |
| 解质量估计 total_estimate | 0.8263 |
| 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 | 42.2 Å |
| 偏度 Skewness skewness | 0.156 |
| 峰度 Kurtosis kurtosis | -0.512 |
| 角度范围 angular_range | — – 0.2350 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 154300000.0000 |
| 实空间数据点数 n_real_points | 48 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (10)
6. 折叠分类 (SCOP + CATH) 20 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d2igaa1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 超家族 Superfamily superfamily | d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 家族 Family family | d.32.1.3 — Extradiol dioxygenases |
| 结构域编号 domain_id | d2igaa2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 超家族 Superfamily superfamily | d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 家族 Family family | d.32.1.3 — Extradiol dioxygenases |
| 结构域编号 domain_id | d2igab1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 超家族 Superfamily superfamily | d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 家族 Family family | d.32.1.3 — Extradiol dioxygenases |
| 结构域编号 domain_id | d2igab2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 超家族 Superfamily superfamily | d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 家族 Family family | d.32.1.3 — Extradiol dioxygenases |
| 结构域编号 domain_id | d2igac1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 超家族 Superfamily superfamily | d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 家族 Family family | d.32.1.3 — Extradiol dioxygenases |
| 结构域编号 domain_id | d2igac2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 超家族 Superfamily superfamily | d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 家族 Family family | d.32.1.3 — Extradiol dioxygenases |
| 结构域编号 domain_id | d2igad1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 超家族 Superfamily superfamily | d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 家族 Family family | d.32.1.3 — Extradiol dioxygenases |
| 结构域编号 domain_id | d2igad2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 超家族 Superfamily superfamily | d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase |
| 家族 Family family | d.32.1.3 — Extradiol dioxygenases |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 2igaA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 |
| 结构域编号 domain_id | 2igaA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 |
| 结构域编号 domain_id | 2igaA03 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 1270 — homoprotocatechuate 2,3-dioxygenase fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — homoprotocatechuate 2,3-dioxygenase domains |
| 结构域编号 domain_id | 2igaB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 |
| 结构域编号 domain_id | 2igaB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 |
| 结构域编号 domain_id | 2igaB03 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 1270 — homoprotocatechuate 2,3-dioxygenase fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — homoprotocatechuate 2,3-dioxygenase domains |
| 结构域编号 domain_id | 2igaC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 |
| 结构域编号 domain_id | 2igaC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 |
| 结构域编号 domain_id | 2igaC03 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 1270 — homoprotocatechuate 2,3-dioxygenase fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — homoprotocatechuate 2,3-dioxygenase domains |
| 结构域编号 domain_id | 2igaD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 |
| 结构域编号 domain_id | 2igaD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 |
| 结构域编号 domain_id | 2igaD03 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 1270 — homoprotocatechuate 2,3-dioxygenase fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — homoprotocatechuate 2,3-dioxygenase domains |