2jir
;A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand ;
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 | 2jir |
| 沉积日期 deposition_date | 2007-06-28 |
| 结构标题 title | ;A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand ; |
| 关键词 keywords | ;NITRATE ASSIMILATION, NITROGENOUS ACCEPTOR, IRON, TRANSPORT, MOLYBDENUM, PERIPLASMIC, DISULFIDE BOND, ELECTRON TRANSPORT, IRON-SULFUR, IRON- SULFUR, METAL-BINDING, DISSIMILATORY NITRATE REDUCTASE, MOLYBDOPTERIN COFACTOR, SULFIDO LIGAND, 4FE-4S CLUSTER, OXIDOREDUCTASE, ELECTRON PARAMAGNETIC RESONANCE ;; 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 | 25.45 Å |
| 回转半径 Rg (电子) rg_electron | 24.62 Å |
| 零角强度 I(0) i0 | 116634000.00 |
| 分子量 molecular_weight | 81991.0 kDa |
| 排除体积 excluded_volume | 101180 ų |
| 包络体积 envelope_volume | 113410 ų |
| 水化壳体积 shell_volume | 36165 ų |
| 包络直径 envelope_diameter | 81.2 Å |
| 壳层 Rg shell_rg | 33.71 Å |
| 包络 Rg envelope_rg | 25.12 Å |
| 形状 Rg shape_rg | 24.67 Å |
| 总 Rg total_rg | 25.33 Å |
| 总原子数 total_atoms | 5730 |
| 残基数 n_residues | 720 |
| 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 | 79.5 Å |
| Rg (实空间) rg_real | 25.31 Å |
| Rg 误差 (实空间) rg_real_error | 0.41 Å |
| I(0) (实空间) i0_real | 1.1660e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.6430e+06 |
| Rg (倒空间) rg_reciprocal | 25.36 Å |
| I(0) (倒空间) i0_reciprocal | 116600000.0000 |
| 解质量估计 total_estimate | 0.7399 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 30.8 Å |
| 偏度 Skewness skewness | 0.195 |
| 峰度 Kurtosis kurtosis | -0.444 |
| 角度范围 angular_range | — – 0.3100 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 34420000.0000 |
| 实空间数据点数 n_real_points | 63 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 0.315; Positv: 1.000; Valcen: 0.986; Smooth: 0.982 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (7)
6. 折叠分类 (SCOP + CATH) 6 domains
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d2jira1 |
| 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 | d2jira2 |
| 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 |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 2jirA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 20 — Single Sheet |
| 拓扑 Topology topology | 25 — N-terminal domain of TfIIb |
| 同源超家族 H-superfamily homologous superfamily | 90 — ADC-like domains |
| 结构域编号 domain_id | 2jirA02 |
| 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 | 2jirA03 |
| 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 | 2jirA04 |
| 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 — |