2afh
Crystal Structure of Nucleotide-Free Av2-Av1 Complex
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 | 2afh |
| 沉积日期 deposition_date | 2005-07-25 |
| 结构标题 title | Crystal Structure of Nucleotide-Free Av2-Av1 Complex |
| 关键词 keywords | Nitrogen fixation, Iron-sulfur, Metal-binding, Molybdenum, 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 | 44.78 Å |
| 回转半径 Rg (电子) rg_electron | 44.59 Å |
| 零角强度 I(0) i0 | 1294690000.00 |
| 分子量 molecular_weight | 295380.0 kDa |
| 排除体积 excluded_volume | 367780 ų |
| 包络体积 envelope_volume | 441610 ų |
| 水化壳体积 shell_volume | 81348 ų |
| 包络直径 envelope_diameter | 159.6 Å |
| 壳层 Rg shell_rg | 49.97 Å |
| 包络 Rg envelope_rg | 44.78 Å |
| 形状 Rg shape_rg | 44.59 Å |
| 总 Rg total_rg | 44.80 Å |
| 总原子数 total_atoms | 20567 |
| 残基数 n_residues | 2572 |
| 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 | 152.4 Å |
| Rg (实空间) rg_real | 44.89 Å |
| Rg 误差 (实空间) rg_real_error | 1.62 Å |
| I(0) (实空间) i0_real | 1.2950e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.6720e+07 |
| Rg (倒空间) rg_reciprocal | 44.78 Å |
| I(0) (倒空间) i0_reciprocal | 1295000000.0000 |
| 解质量估计 total_estimate | 0.8615 |
| 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 | 47.9 Å |
| 偏度 Skewness skewness | 0.426 |
| 峰度 Kurtosis kurtosis | -0.323 |
| 角度范围 angular_range | — – 0.1750 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 350300000.0000 |
| 实空间数据点数 n_real_points | 36 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.763 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (16)
6. 折叠分类 (SCOP + CATH) 22 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d2afha_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.92 — Chelatase-like |
| 超家族 Superfamily superfamily | c.92.2 — 'Helical backbone' metal receptor |
| 家族 Family family | c.92.2.3 — Nitrogenase iron-molybdenum protein |
| 结构域编号 domain_id | d2afhb_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.92 — Chelatase-like |
| 超家族 Superfamily superfamily | c.92.2 — 'Helical backbone' metal receptor |
| 家族 Family family | c.92.2.3 — Nitrogenase iron-molybdenum protein |
| 结构域编号 domain_id | d2afhc_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.92 — Chelatase-like |
| 超家族 Superfamily superfamily | c.92.2 — 'Helical backbone' metal receptor |
| 家族 Family family | c.92.2.3 — Nitrogenase iron-molybdenum protein |
| 结构域编号 domain_id | d2afhd_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.92 — Chelatase-like |
| 超家族 Superfamily superfamily | c.92.2 — 'Helical backbone' metal receptor |
| 家族 Family family | c.92.2.3 — Nitrogenase iron-molybdenum protein |
| 结构域编号 domain_id | d2afhe_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.10 — Nitrogenase iron protein-like |
| 结构域编号 domain_id | d2afhf_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.37 — P-loop containing nucleoside triphosphate hydrolases |
| 超家族 Superfamily superfamily | c.37.1 — P-loop containing nucleoside triphosphate hydrolases |
| 家族 Family family | c.37.1.10 — Nitrogenase iron protein-like |
CATH v4.4 (16 domains)
| 结构域编号 domain_id | 2afhA01 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhA02 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhA03 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhB01 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhB02 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 89 — Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 |
| 结构域编号 domain_id | 2afhB04 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhC01 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhC02 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhC03 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhD01 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhD02 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhD03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 89 — Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 |
| 结构域编号 domain_id | 2afhD04 |
| 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 | 1980 — Nitrogenase molybdenum iron protein domain |
| 结构域编号 domain_id | 2afhE00 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |
| 结构域编号 domain_id | 2afhF00 |
| 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 | 300 — P-loop containing nucleotide triphosphate hydrolases |