2ji9
X-ray structure of Oxalyl-CoA decarboxylase in complex with 3-deaza- ThDP
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 | 2ji9 |
| 沉积日期 deposition_date | 2007-02-26 |
| 结构标题 title | X-ray structure of Oxalyl-CoA decarboxylase in complex with 3-deaza- ThDP |
| 关键词 keywords | ;OXALATE DEGRADATION, THIAMINE PYROPHOSPHATE, LYASE, FLAVOPROTEIN, DECARBOXYLASE, COFACTOR ANALOGUE INHIBITOR COMPLEX, NON- OXIDATIVE DECARBOXYLASE, THIAMIN DIPHOSPHATE-DEPENDENT ;; LYASE |
| 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 | 30.81 Å |
| 回转半径 Rg (电子) rg_electron | 30.35 Å |
| 零角强度 I(0) i0 | 228914000.00 |
| 分子量 molecular_weight | 119090.0 kDa |
| 排除体积 excluded_volume | 148290 ų |
| 包络体积 envelope_volume | 175360 ų |
| 水化壳体积 shell_volume | 46636 ų |
| 包络直径 envelope_diameter | 111.8 Å |
| 壳层 Rg shell_rg | 38.68 Å |
| 包络 Rg envelope_rg | 30.86 Å |
| 形状 Rg shape_rg | 30.35 Å |
| 总 Rg total_rg | 30.98 Å |
| 总原子数 total_atoms | 8314 |
| 残基数 n_residues | 1094 |
| 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 | 103.7 Å |
| Rg (实空间) rg_real | 30.76 Å |
| Rg 误差 (实空间) rg_real_error | 0.79 Å |
| I(0) (实空间) i0_real | 2.2890e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.7420e+06 |
| Rg (倒空间) rg_reciprocal | 30.78 Å |
| I(0) (倒空间) i0_reciprocal | 228900000.0000 |
| 解质量估计 total_estimate | 0.6663 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 38.6 Å |
| 偏度 Skewness skewness | 0.383 |
| 峰度 Kurtosis kurtosis | -0.102 |
| 角度范围 angular_range | — – 0.2550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 103600000.0000 |
| 实空间数据点数 n_real_points | 52 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.789; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.994; Smooth: 0.951 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (6)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d2ji9a1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.31 — DHS-like NAD/FAD-binding domain |
| 超家族 Superfamily superfamily | c.31.1 — DHS-like NAD/FAD-binding domain |
| 家族 Family family | c.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain |
| 结构域编号 domain_id | d2ji9a2 |
| 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.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module |
| 结构域编号 domain_id | d2ji9a3 |
| 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.36.1.9 — Pyruvate oxidase and decarboxylase PP module |
| 结构域编号 domain_id | d2ji9b1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.31 — DHS-like NAD/FAD-binding domain |
| 超家族 Superfamily superfamily | c.31.1 — DHS-like NAD/FAD-binding domain |
| 家族 Family family | c.31.1.3 — Pyruvate oxidase and decarboxylase, middle domain |
| 结构域编号 domain_id | d2ji9b2 |
| 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.36.1.5 — Pyruvate oxidase and decarboxylase Pyr module |
| 结构域编号 domain_id | d2ji9b3 |
| 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.36.1.9 — Pyruvate oxidase and decarboxylase PP module |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2ji9A01 |
| 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 | 2ji9A02 |
| 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 | 1220 — TPP-binding domain |
| 结构域编号 domain_id | 2ji9A03 |
| 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 | 2ji9B01 |
| 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 | 2ji9B02 |
| 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 | 1220 — TPP-binding domain |
| 结构域编号 domain_id | 2ji9B03 |
| 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 |