1m1y
Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein
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 | 1m1y |
| 沉积日期 deposition_date | 2002-06-20 |
| 结构标题 title | Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein |
| 关键词 keywords | nitrogenase, nitrogen fixation, chemical crosslink, protein interaction, 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 | 64.65 Å |
| 回转半径 Rg (电子) rg_electron | 64.30 Å |
| 零角强度 I(0) i0 | 7260600000.00 |
| 分子量 molecular_weight | 710470.0 kDa |
| 排除体积 excluded_volume | 883600 ų |
| 包络体积 envelope_volume | 1213700 ų |
| 水化壳体积 shell_volume | 153430 ų |
| 包络直径 envelope_diameter | 227.3 Å |
| 壳层 Rg shell_rg | 68.13 Å |
| 包络 Rg envelope_rg | 63.13 Å |
| 形状 Rg shape_rg | 64.29 Å |
| 总 Rg total_rg | 64.41 Å |
| 总原子数 total_atoms | 49464 |
| 残基数 n_residues | 6296 |
| 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 | 219.2 Å |
| Rg (实空间) rg_real | 64.45 Å |
| Rg 误差 (实空间) rg_real_error | 2.24 Å |
| I(0) (实空间) i0_real | 7.2610e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.6840e+08 |
| Rg (倒空间) rg_reciprocal | 64.78 Å |
| I(0) (倒空间) i0_reciprocal | 7264000000.0000 |
| 解质量估计 total_estimate | 0.8627 |
| 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 | 82.2 Å |
| 偏度 Skewness skewness | 0.237 |
| 峰度 Kurtosis kurtosis | -0.357 |
| 角度范围 angular_range | — – 0.1200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 263200000.0000 |
| 实空间数据点数 n_real_points | 25 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.776 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (8)
6. 折叠分类 (SCOP + CATH) 52 domains
SCOP 2.08 (16 domains)
| 结构域编号 domain_id | d1m1ya_ |
| 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 | d1m1yb_ |
| 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 | d1m1yc_ |
| 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 | d1m1yd_ |
| 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 | d1m1ye_ |
| 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 | d1m1yf_ |
| 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 | d1m1yg_ |
| 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 | d1m1yh_ |
| 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 | d1m1yi_ |
| 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 | d1m1yj_ |
| 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 | d1m1yk_ |
| 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 | d1m1yl_ |
| 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 | d1m1ym_ |
| 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 | d1m1yn_ |
| 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 | d1m1yo_ |
| 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 | d1m1yp_ |
| 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 (36 domains)
| 结构域编号 domain_id | 1m1yA01 |
| 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 | 1m1yA02 |
| 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 | 1m1yA03 |
| 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 | 1m1yB01 |
| 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 | 1m1yB02 |
| 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 | 1m1yB03 |
| 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 | 1m1yB04 |
| 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 | 1m1yC01 |
| 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 | 1m1yC02 |
| 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 | 1m1yC03 |
| 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 | 1m1yD01 |
| 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 | 1m1yD02 |
| 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 | 1m1yD03 |
| 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 | 1m1yD04 |
| 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 | 1m1yE00 |
| 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 | 1m1yF00 |
| 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 | 1m1yG00 |
| 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 | 1m1yH00 |
| 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 | 1m1yI01 |
| 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 | 1m1yI02 |
| 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 | 1m1yI03 |
| 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 | 1m1yJ01 |
| 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 | 1m1yJ02 |
| 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 | 1m1yJ03 |
| 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 | 1m1yJ04 |
| 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 | 1m1yK01 |
| 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 | 1m1yK02 |
| 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 | 1m1yK03 |
| 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 | 1m1yL01 |
| 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 | 1m1yL02 |
| 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 | 1m1yL03 |
| 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 | 1m1yL04 |
| 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 | 1m1yM00 |
| 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 | 1m1yN00 |
| 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 | 1m1yO00 |
| 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 | 1m1yP00 |
| 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 |