1pj5
Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with acetate
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 | 1pj5 |
| 沉积日期 deposition_date | 2003-06-01 |
| 结构标题 title | Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with acetate |
| 关键词 keywords | Channelling, FAD binding, folate binding, amine oxidase, 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 | 28.98 Å |
| 回转半径 Rg (电子) rg_electron | 28.03 Å |
| 零角强度 I(0) i0 | 131619000.00 |
| 分子量 molecular_weight | 90161.0 kDa |
| 排除体积 excluded_volume | 112580 ų |
| 包络体积 envelope_volume | 134640 ų |
| 水化壳体积 shell_volume | 39372 ų |
| 包络直径 envelope_diameter | 97.4 Å |
| 壳层 Rg shell_rg | 36.16 Å |
| 包络 Rg envelope_rg | 27.85 Å |
| 形状 Rg shape_rg | 28.02 Å |
| 总 Rg total_rg | 28.82 Å |
| 总原子数 total_atoms | 6357 |
| 残基数 n_residues | 827 |
| 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 | 91.2 Å |
| Rg (实空间) rg_real | 28.89 Å |
| Rg 误差 (实空间) rg_real_error | 0.72 Å |
| I(0) (实空间) i0_real | 1.3160e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.0180e+06 |
| Rg (倒空间) rg_reciprocal | 28.93 Å |
| I(0) (倒空间) i0_reciprocal | 131600000.0000 |
| 解质量估计 total_estimate | 0.9025 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 34.8 Å |
| 偏度 Skewness skewness | 0.247 |
| 峰度 Kurtosis kurtosis | -0.432 |
| 角度范围 angular_range | — – 0.2750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 32500000.0000 |
| 实空间数据点数 n_real_points | 56 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.969 |
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) 9 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1pj5a1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.44 — Elongation factor/aminomethyltransferase common domain |
| 超家族 Superfamily superfamily | b.44.2 — Aminomethyltransferase beta-barrel domain |
| 家族 Family family | b.44.2.1 — Aminomethyltransferase beta-barrel domain |
| 结构域编号 domain_id | d1pj5a2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.3 — FAD/NAD(P)-binding domain |
| 超家族 Superfamily superfamily | c.3.1 — FAD/NAD(P)-binding domain |
| 家族 Family family | c.3.1.2 — FAD-linked reductases, N-terminal domain |
| 结构域编号 domain_id | d1pj5a3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.16 — FAD-linked reductases, C-terminal domain |
| 超家族 Superfamily superfamily | d.16.1 — FAD-linked reductases, C-terminal domain |
| 家族 Family family | d.16.1.5 — L-aminoacid/polyamine oxidase |
| 结构域编号 domain_id | d1pj5a4 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.250 — Folate-binding domain |
| 超家族 Superfamily superfamily | d.250.1 — Folate-binding domain |
| 家族 Family family | d.250.1.1 — Aminomethyltransferase folate-binding domain |
CATH v4.4 (5 domains)
| 结构域编号 domain_id | 1pj5A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 50 — FAD/NAD(P)-binding domain |
| 同源超家族 H-superfamily homologous superfamily | 60 — FAD/NAD(P)-binding domain |
| 结构域编号 domain_id | 1pj5A02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 9 — D-Amino Acid Oxidase; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — D-Amino Acid Oxidase, subunit A, domain 2 |
| 结构域编号 domain_id | 1pj5A03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1360 — Gyrase A; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 120 — Probable tRNA modification gtpase trme; domain 1 |
| 结构域编号 domain_id | 1pj5A04 |
| 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 | 1400 — Aminomethyltransferase beta-barrel domains |
| 结构域编号 domain_id | 1pj5A05 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 30 — Elongation Factor Tu (Ef-tu); domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 110 — Aminomethyltransferase beta-barrel domains |