1ogp
The crystal structure of plant sulfite oxidase provides insight into sulfite oxidation in plants and animals
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 | 1ogp |
| 沉积日期 deposition_date | 2003-05-08 |
| 结构标题 title | The crystal structure of plant sulfite oxidase provides insight into sulfite oxidation in plants and animals |
| 关键词 keywords | ;OXIDOREDUCTASE, MOLYBDENUM COFACTOR, MOLYBDOPTERIN, PLANT SULFITE OXIDASE, PEROXISOMES, INTRAMOLECULAR ELECTRON TRANSFER, OXIDOREDUCTAS ;; 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 | 44.07 Å |
| 回转半径 Rg (电子) rg_electron | 44.03 Å |
| 零角强度 I(0) i0 | 1024940000.00 |
| 分子量 molecular_weight | 261650.0 kDa |
| 排除体积 excluded_volume | 325630 ų |
| 包络体积 envelope_volume | 416850 ų |
| 水化壳体积 shell_volume | 78271 ų |
| 包络直径 envelope_diameter | 155.3 Å |
| 壳层 Rg shell_rg | 49.25 Å |
| 包络 Rg envelope_rg | 43.60 Å |
| 形状 Rg shape_rg | 44.02 Å |
| 总 Rg total_rg | 44.29 Å |
| 总原子数 total_atoms | 18294 |
| 残基数 n_residues | 2328 |
| 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 | 144.3 Å |
| Rg (实空间) rg_real | 44.00 Å |
| Rg 误差 (实空间) rg_real_error | 0.98 Å |
| I(0) (实空间) i0_real | 1.0250e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.7520e+07 |
| Rg (倒空间) rg_reciprocal | 44.07 Å |
| I(0) (倒空间) i0_reciprocal | 1025000000.0000 |
| 解质量估计 total_estimate | 0.8927 |
| 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 | 48.1 Å |
| 偏度 Skewness skewness | 0.244 |
| 峰度 Kurtosis kurtosis | -0.544 |
| 角度范围 angular_range | — – 0.1800 Å−1 |
| 当前正则化参数 α current_alpha | 0.0001 |
| 最高正则化参数 α highest_alpha | 202400000.0000 |
| 实空间数据点数 n_real_points | 37 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.868 |
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) 24 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1ogpa1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.18 — E set domains |
| 家族 Family family | b.1.18.6 — Molybdenum-containing oxidoreductases-like dimerisation domain |
| 结构域编号 domain_id | d1ogpa2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.176 — Oxidoreductase molybdopterin-binding domain |
| 超家族 Superfamily superfamily | d.176.1 — Oxidoreductase molybdopterin-binding domain |
| 家族 Family family | d.176.1.1 — Oxidoreductase molybdopterin-binding domain |
| 结构域编号 domain_id | d1ogpb1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.18 — E set domains |
| 家族 Family family | b.1.18.6 — Molybdenum-containing oxidoreductases-like dimerisation domain |
| 结构域编号 domain_id | d1ogpb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.176 — Oxidoreductase molybdopterin-binding domain |
| 超家族 Superfamily superfamily | d.176.1 — Oxidoreductase molybdopterin-binding domain |
| 家族 Family family | d.176.1.1 — Oxidoreductase molybdopterin-binding domain |
| 结构域编号 domain_id | d1ogpc1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.18 — E set domains |
| 家族 Family family | b.1.18.6 — Molybdenum-containing oxidoreductases-like dimerisation domain |
| 结构域编号 domain_id | d1ogpc2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.176 — Oxidoreductase molybdopterin-binding domain |
| 超家族 Superfamily superfamily | d.176.1 — Oxidoreductase molybdopterin-binding domain |
| 家族 Family family | d.176.1.1 — Oxidoreductase molybdopterin-binding domain |
| 结构域编号 domain_id | d1ogpd1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.18 — E set domains |
| 家族 Family family | b.1.18.6 — Molybdenum-containing oxidoreductases-like dimerisation domain |
| 结构域编号 domain_id | d1ogpd2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.176 — Oxidoreductase molybdopterin-binding domain |
| 超家族 Superfamily superfamily | d.176.1 — Oxidoreductase molybdopterin-binding domain |
| 家族 Family family | d.176.1.1 — Oxidoreductase molybdopterin-binding domain |
| 结构域编号 domain_id | d1ogpe1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.18 — E set domains |
| 家族 Family family | b.1.18.6 — Molybdenum-containing oxidoreductases-like dimerisation domain |
| 结构域编号 domain_id | d1ogpe2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.176 — Oxidoreductase molybdopterin-binding domain |
| 超家族 Superfamily superfamily | d.176.1 — Oxidoreductase molybdopterin-binding domain |
| 家族 Family family | d.176.1.1 — Oxidoreductase molybdopterin-binding domain |
| 结构域编号 domain_id | d1ogpf1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.1 — Immunoglobulin-like beta-sandwich |
| 超家族 Superfamily superfamily | b.1.18 — E set domains |
| 家族 Family family | b.1.18.6 — Molybdenum-containing oxidoreductases-like dimerisation domain |
| 结构域编号 domain_id | d1ogpf2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.176 — Oxidoreductase molybdopterin-binding domain |
| 超家族 Superfamily superfamily | d.176.1 — Oxidoreductase molybdopterin-binding domain |
| 家族 Family family | d.176.1.1 — Oxidoreductase molybdopterin-binding domain |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 1ogpA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 420 — Sulfite Oxidase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Oxidoreductase, molybdopterin-binding domain |
| 结构域编号 domain_id | 1ogpA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 650 — |
| 结构域编号 domain_id | 1ogpB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 420 — Sulfite Oxidase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Oxidoreductase, molybdopterin-binding domain |
| 结构域编号 domain_id | 1ogpB02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 650 — |
| 结构域编号 domain_id | 1ogpC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 420 — Sulfite Oxidase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Oxidoreductase, molybdopterin-binding domain |
| 结构域编号 domain_id | 1ogpC02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 650 — |
| 结构域编号 domain_id | 1ogpD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 420 — Sulfite Oxidase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Oxidoreductase, molybdopterin-binding domain |
| 结构域编号 domain_id | 1ogpD02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 650 — |
| 结构域编号 domain_id | 1ogpE01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 420 — Sulfite Oxidase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Oxidoreductase, molybdopterin-binding domain |
| 结构域编号 domain_id | 1ogpE02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 650 — |
| 结构域编号 domain_id | 1ogpF01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 420 — Sulfite Oxidase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Oxidoreductase, molybdopterin-binding domain |
| 结构域编号 domain_id | 1ogpF02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 650 — |