1xvf
soluble methane monooxygenase hydroxylase: chloropropanol soaked structure
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 | 1xvf |
| 沉积日期 deposition_date | 2004-10-27 |
| 结构标题 title | soluble methane monooxygenase hydroxylase: chloropropanol soaked structure |
| 关键词 keywords | methane, diiron, four-helix bundle, cavities, 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 | 41.32 Å |
| 回转半径 Rg (电子) rg_electron | 40.93 Å |
| 零角强度 I(0) i0 | 879282000.00 |
| 分子量 molecular_weight | 245320.0 kDa |
| 排除体积 excluded_volume | 306100 ų |
| 包络体积 envelope_volume | 356930 ų |
| 水化壳体积 shell_volume | 69155 ų |
| 包络直径 envelope_diameter | 134.5 Å |
| 壳层 Rg shell_rg | 48.81 Å |
| 包络 Rg envelope_rg | 40.92 Å |
| 形状 Rg shape_rg | 40.92 Å |
| 总 Rg total_rg | 41.29 Å |
| 总原子数 total_atoms | 17350 |
| 残基数 n_residues | 2128 |
| 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 | 128.1 Å |
| Rg (实空间) rg_real | 41.28 Å |
| Rg 误差 (实空间) rg_real_error | 0.97 Å |
| I(0) (实空间) i0_real | 8.7930e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.4860e+07 |
| Rg (倒空间) rg_reciprocal | 41.32 Å |
| I(0) (倒空间) i0_reciprocal | 879300000.0000 |
| 解质量估计 total_estimate | 0.8695 |
| 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 | 43.8 Å |
| 偏度 Skewness skewness | 0.276 |
| 峰度 Kurtosis kurtosis | -0.591 |
| 角度范围 angular_range | — – 0.1900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 422500000.0000 |
| 实空间数据点数 n_real_points | 39 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.442 |
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) 14 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1xvfa_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.25 — Ferritin-like |
| 超家族 Superfamily superfamily | a.25.1 — Ferritin-like |
| 家族 Family family | a.25.1.2 — Ribonucleotide reductase-like |
| 结构域编号 domain_id | d1xvfb_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.25 — Ferritin-like |
| 超家族 Superfamily superfamily | a.25.1 — Ferritin-like |
| 家族 Family family | a.25.1.2 — Ribonucleotide reductase-like |
| 结构域编号 domain_id | d1xvfc_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.25 — Ferritin-like |
| 超家族 Superfamily superfamily | a.25.1 — Ferritin-like |
| 家族 Family family | a.25.1.2 — Ribonucleotide reductase-like |
| 结构域编号 domain_id | d1xvfd_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.25 — Ferritin-like |
| 超家族 Superfamily superfamily | a.25.1 — Ferritin-like |
| 家族 Family family | a.25.1.2 — Ribonucleotide reductase-like |
| 结构域编号 domain_id | d1xvfe_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.23 — Open three-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.23.3 — Methane monooxygenase hydrolase, gamma subunit |
| 家族 Family family | a.23.3.1 — Methane monooxygenase hydrolase, gamma subunit |
| 结构域编号 domain_id | d1xvff_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.23 — Open three-helical up-and-down bundle |
| 超家族 Superfamily superfamily | a.23.3 — Methane monooxygenase hydrolase, gamma subunit |
| 家族 Family family | a.23.3.1 — Methane monooxygenase hydrolase, gamma subunit |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1xvfA00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 620 — Ribonucleotide Reductase, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Ribonucleotide Reductase, subunit A |
| 结构域编号 domain_id | 1xvfB00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 620 — Ribonucleotide Reductase, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Ribonucleotide Reductase, subunit A |
| 结构域编号 domain_id | 1xvfC00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 620 — Ribonucleotide Reductase, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Ribonucleotide Reductase, subunit A |
| 结构域编号 domain_id | 1xvfD00 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 620 — Ribonucleotide Reductase, subunit A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Ribonucleotide Reductase, subunit A |
| 结构域编号 domain_id | 1xvfE01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1280 — Monooxygenase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methane monooxygenase, gamma chain, domain 1 |
| 结构域编号 domain_id | 1xvfE02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1280 — Monooxygenase |
| 同源超家族 H-superfamily homologous superfamily | 30 — Methane monooxygenase, gamma chain, domain 2 |
| 结构域编号 domain_id | 1xvfF01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1280 — Monooxygenase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Methane monooxygenase, gamma chain, domain 1 |
| 结构域编号 domain_id | 1xvfF02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1280 — Monooxygenase |
| 同源超家族 H-superfamily homologous superfamily | 30 — Methane monooxygenase, gamma chain, domain 2 |