1ogy
Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides
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 | 1ogy |
| 沉积日期 deposition_date | 2003-05-19 |
| 结构标题 title | Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides |
| 关键词 keywords | NITRATE REDUCTASE, 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 | 60.15 Å |
| 回转半径 Rg (电子) rg_electron | 59.71 Å |
| 零角强度 I(0) i0 | 10737200000.00 |
| 分子量 molecular_weight | 845340.0 kDa |
| 排除体积 excluded_volume | 1041500 ų |
| 包络体积 envelope_volume | 1326900 ų |
| 水化壳体积 shell_volume | 171060 ų |
| 包络直径 envelope_diameter | 188.8 Å |
| 壳层 Rg shell_rg | 71.03 Å |
| 包络 Rg envelope_rg | 58.67 Å |
| 形状 Rg shape_rg | 59.79 Å |
| 总 Rg total_rg | 59.59 Å |
| 总原子数 total_atoms | 59336 |
| 残基数 n_residues | 7336 |
| 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 | 188.0 Å |
| Rg (实空间) rg_real | 59.63 Å |
| Rg 误差 (实空间) rg_real_error | 1.05 Å |
| I(0) (实空间) i0_real | 1.0740e+10 |
| I(0) 误差 (实空间) i0_real_error | 1.8770e+08 |
| Rg (倒空间) rg_reciprocal | 60.57 Å |
| I(0) (倒空间) i0_reciprocal | 10750000000.0000 |
| 解质量估计 total_estimate | 0.8690 |
| 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 | 79.5 Å |
| 偏度 Skewness skewness | -0.020 |
| 峰度 Kurtosis kurtosis | -0.495 |
| 角度范围 angular_range | — – 0.1300 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 743500000.0000 |
| 实空间数据点数 n_real_points | 27 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.852 |
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) 56 domains
SCOP 2.08 (24 domains)
| 结构域编号 domain_id | d1ogya1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.52 — Double psi beta-barrel |
| 超家族 Superfamily superfamily | b.52.2 — ADC-like |
| 家族 Family family | b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain |
| 结构域编号 domain_id | d1ogya2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 超家族 Superfamily superfamily | c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 家族 Family family | c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 结构域编号 domain_id | d1ogyb_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.138 — Multiheme cytochromes |
| 超家族 Superfamily superfamily | a.138.1 — Multiheme cytochromes |
| 家族 Family family | a.138.1.3 — Di-heme elbow motif |
| 结构域编号 domain_id | d1ogyc1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.52 — Double psi beta-barrel |
| 超家族 Superfamily superfamily | b.52.2 — ADC-like |
| 家族 Family family | b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain |
| 结构域编号 domain_id | d1ogyc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 超家族 Superfamily superfamily | c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 家族 Family family | c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 结构域编号 domain_id | d1ogyd_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.138 — Multiheme cytochromes |
| 超家族 Superfamily superfamily | a.138.1 — Multiheme cytochromes |
| 家族 Family family | a.138.1.3 — Di-heme elbow motif |
| 结构域编号 domain_id | d1ogye1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.52 — Double psi beta-barrel |
| 超家族 Superfamily superfamily | b.52.2 — ADC-like |
| 家族 Family family | b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain |
| 结构域编号 domain_id | d1ogye2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 超家族 Superfamily superfamily | c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 家族 Family family | c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 结构域编号 domain_id | d1ogyf_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.138 — Multiheme cytochromes |
| 超家族 Superfamily superfamily | a.138.1 — Multiheme cytochromes |
| 家族 Family family | a.138.1.3 — Di-heme elbow motif |
| 结构域编号 domain_id | d1ogyg1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.52 — Double psi beta-barrel |
| 超家族 Superfamily superfamily | b.52.2 — ADC-like |
| 家族 Family family | b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain |
| 结构域编号 domain_id | d1ogyg2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 超家族 Superfamily superfamily | c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 家族 Family family | c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 结构域编号 domain_id | d1ogyh_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.138 — Multiheme cytochromes |
| 超家族 Superfamily superfamily | a.138.1 — Multiheme cytochromes |
| 家族 Family family | a.138.1.3 — Di-heme elbow motif |
| 结构域编号 domain_id | d1ogyi1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.52 — Double psi beta-barrel |
| 超家族 Superfamily superfamily | b.52.2 — ADC-like |
| 家族 Family family | b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain |
| 结构域编号 domain_id | d1ogyi2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 超家族 Superfamily superfamily | c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 家族 Family family | c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 结构域编号 domain_id | d1ogyj_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.138 — Multiheme cytochromes |
| 超家族 Superfamily superfamily | a.138.1 — Multiheme cytochromes |
| 家族 Family family | a.138.1.3 — Di-heme elbow motif |
| 结构域编号 domain_id | d1ogyk1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.52 — Double psi beta-barrel |
| 超家族 Superfamily superfamily | b.52.2 — ADC-like |
| 家族 Family family | b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain |
| 结构域编号 domain_id | d1ogyk2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 超家族 Superfamily superfamily | c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 家族 Family family | c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 结构域编号 domain_id | d1ogyl_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.138 — Multiheme cytochromes |
| 超家族 Superfamily superfamily | a.138.1 — Multiheme cytochromes |
| 家族 Family family | a.138.1.3 — Di-heme elbow motif |
| 结构域编号 domain_id | d1ogym1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.52 — Double psi beta-barrel |
| 超家族 Superfamily superfamily | b.52.2 — ADC-like |
| 家族 Family family | b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain |
| 结构域编号 domain_id | d1ogym2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 超家族 Superfamily superfamily | c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 家族 Family family | c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 结构域编号 domain_id | d1ogyn_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.138 — Multiheme cytochromes |
| 超家族 Superfamily superfamily | a.138.1 — Multiheme cytochromes |
| 家族 Family family | a.138.1.3 — Di-heme elbow motif |
| 结构域编号 domain_id | d1ogyo1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.52 — Double psi beta-barrel |
| 超家族 Superfamily superfamily | b.52.2 — ADC-like |
| 家族 Family family | b.52.2.2 — Formate dehydrogenase/DMSO reductase, C-terminal domain |
| 结构域编号 domain_id | d1ogyo2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.81 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 超家族 Superfamily superfamily | c.81.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 家族 Family family | c.81.1.1 — Formate dehydrogenase/DMSO reductase, domains 1-3 |
| 结构域编号 domain_id | d1ogyp_ |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.138 — Multiheme cytochromes |
| 超家族 Superfamily superfamily | a.138.1 — Multiheme cytochromes |
| 家族 Family family | a.138.1.3 — Di-heme elbow motif |
CATH v4.4 (32 domains)
| 结构域编号 domain_id | 1ogyA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 200 — Phosphorylase Kinase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 210 — |
| 结构域编号 domain_id | 1ogyA02 |
| 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 | 740 — |
| 结构域编号 domain_id | 1ogyA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 228 — Dimethylsulfoxide Reductase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dimethylsulfoxide Reductase, domain 2 |
| 结构域编号 domain_id | 1ogyA04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 40 — Barwin-like endoglucanases |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1ogyC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 200 — Phosphorylase Kinase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 210 — |
| 结构域编号 domain_id | 1ogyC02 |
| 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 | 740 — |
| 结构域编号 domain_id | 1ogyC03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 228 — Dimethylsulfoxide Reductase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dimethylsulfoxide Reductase, domain 2 |
| 结构域编号 domain_id | 1ogyC04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 40 — Barwin-like endoglucanases |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1ogyE01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 200 — Phosphorylase Kinase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 210 — |
| 结构域编号 domain_id | 1ogyE02 |
| 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 | 740 — |
| 结构域编号 domain_id | 1ogyE03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 228 — Dimethylsulfoxide Reductase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dimethylsulfoxide Reductase, domain 2 |
| 结构域编号 domain_id | 1ogyE04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 40 — Barwin-like endoglucanases |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1ogyG01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 200 — Phosphorylase Kinase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 210 — |
| 结构域编号 domain_id | 1ogyG02 |
| 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 | 740 — |
| 结构域编号 domain_id | 1ogyG03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 228 — Dimethylsulfoxide Reductase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dimethylsulfoxide Reductase, domain 2 |
| 结构域编号 domain_id | 1ogyG04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 40 — Barwin-like endoglucanases |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1ogyI01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 200 — Phosphorylase Kinase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 210 — |
| 结构域编号 domain_id | 1ogyI02 |
| 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 | 740 — |
| 结构域编号 domain_id | 1ogyI03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 228 — Dimethylsulfoxide Reductase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dimethylsulfoxide Reductase, domain 2 |
| 结构域编号 domain_id | 1ogyI04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 40 — Barwin-like endoglucanases |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1ogyK01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 200 — Phosphorylase Kinase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 210 — |
| 结构域编号 domain_id | 1ogyK02 |
| 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 | 740 — |
| 结构域编号 domain_id | 1ogyK03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 228 — Dimethylsulfoxide Reductase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dimethylsulfoxide Reductase, domain 2 |
| 结构域编号 domain_id | 1ogyK04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 40 — Barwin-like endoglucanases |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1ogyM01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 200 — Phosphorylase Kinase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 210 — |
| 结构域编号 domain_id | 1ogyM02 |
| 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 | 740 — |
| 结构域编号 domain_id | 1ogyM03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 228 — Dimethylsulfoxide Reductase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dimethylsulfoxide Reductase, domain 2 |
| 结构域编号 domain_id | 1ogyM04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 40 — Barwin-like endoglucanases |
| 同源超家族 H-superfamily homologous superfamily | 20 — |
| 结构域编号 domain_id | 1ogyO01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 200 — Phosphorylase Kinase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 210 — |
| 结构域编号 domain_id | 1ogyO02 |
| 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 | 740 — |
| 结构域编号 domain_id | 1ogyO03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 228 — Dimethylsulfoxide Reductase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Dimethylsulfoxide Reductase, domain 2 |
| 结构域编号 domain_id | 1ogyO04 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 40 — Barwin-like endoglucanases |
| 同源超家族 H-superfamily homologous superfamily | 20 — |