2e2g
Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (pre-oxidation form)
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 | 2e2g |
| 沉积日期 deposition_date | 2006-11-13 |
| 结构标题 title | Crystal structure of archaeal peroxiredoxin, thioredoxin peroxidase from Aeropyrum pernix K1 (pre-oxidation form) |
| 关键词 keywords | ;thioredoxin peroxidase, cysteine sulfenic acid, cysteine sulfinic acid, cysteine sulfonic acid, hypervalent sulfur compound, peroxidatic cysteine, 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 | 52.01 Å |
| 回转半径 Rg (电子) rg_electron | 50.96 Å |
| 零角强度 I(0) i0 | 999686000.00 |
| 分子量 molecular_weight | 273350.0 kDa |
| 排除体积 excluded_volume | 345230 ų |
| 包络体积 envelope_volume | 479340 ų |
| 水化壳体积 shell_volume | 74533 ų |
| 包络直径 envelope_diameter | 147.1 Å |
| 壳层 Rg shell_rg | 61.54 Å |
| 包络 Rg envelope_rg | 48.18 Å |
| 形状 Rg shape_rg | 50.97 Å |
| 总 Rg total_rg | 51.19 Å |
| 总原子数 total_atoms | 19336 |
| 残基数 n_residues | 2382 |
| 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 | 143.0 Å |
| Rg (实空间) rg_real | 51.79 Å |
| Rg 误差 (实空间) rg_real_error | 0.82 Å |
| I(0) (实空间) i0_real | 9.9970e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.8500e+07 |
| Rg (倒空间) rg_reciprocal | 52.17 Å |
| I(0) (倒空间) i0_reciprocal | 1000000000.0000 |
| 解质量估计 total_estimate | 0.8188 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 85.8 Å |
| 偏度 Skewness skewness | -0.115 |
| 峰度 Kurtosis kurtosis | -0.974 |
| 角度范围 angular_range | — – 0.1500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 120300000.0000 |
| 实空间数据点数 n_real_points | 31 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.871; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 30 domains
SCOP 2.08 (10 domains)
| 结构域编号 domain_id | d2e2ga_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.47 — Thioredoxin fold |
| 超家族 Superfamily superfamily | c.47.1 — Thioredoxin-like |
| 家族 Family family | c.47.1.10 — Glutathione peroxidase-like |
| 结构域编号 domain_id | d2e2gb_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.47 — Thioredoxin fold |
| 超家族 Superfamily superfamily | c.47.1 — Thioredoxin-like |
| 家族 Family family | c.47.1.10 — Glutathione peroxidase-like |
| 结构域编号 domain_id | d2e2gc_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.47 — Thioredoxin fold |
| 超家族 Superfamily superfamily | c.47.1 — Thioredoxin-like |
| 家族 Family family | c.47.1.10 — Glutathione peroxidase-like |
| 结构域编号 domain_id | d2e2gd_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.47 — Thioredoxin fold |
| 超家族 Superfamily superfamily | c.47.1 — Thioredoxin-like |
| 家族 Family family | c.47.1.10 — Glutathione peroxidase-like |
| 结构域编号 domain_id | d2e2ge_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.47 — Thioredoxin fold |
| 超家族 Superfamily superfamily | c.47.1 — Thioredoxin-like |
| 家族 Family family | c.47.1.10 — Glutathione peroxidase-like |
| 结构域编号 domain_id | d2e2gf_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.47 — Thioredoxin fold |
| 超家族 Superfamily superfamily | c.47.1 — Thioredoxin-like |
| 家族 Family family | c.47.1.10 — Glutathione peroxidase-like |
| 结构域编号 domain_id | d2e2gg_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.47 — Thioredoxin fold |
| 超家族 Superfamily superfamily | c.47.1 — Thioredoxin-like |
| 家族 Family family | c.47.1.10 — Glutathione peroxidase-like |
| 结构域编号 domain_id | d2e2gh_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.47 — Thioredoxin fold |
| 超家族 Superfamily superfamily | c.47.1 — Thioredoxin-like |
| 家族 Family family | c.47.1.10 — Glutathione peroxidase-like |
| 结构域编号 domain_id | d2e2gi_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.47 — Thioredoxin fold |
| 超家族 Superfamily superfamily | c.47.1 — Thioredoxin-like |
| 家族 Family family | c.47.1.10 — Glutathione peroxidase-like |
| 结构域编号 domain_id | d2e2gj_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.47 — Thioredoxin fold |
| 超家族 Superfamily superfamily | c.47.1 — Thioredoxin-like |
| 家族 Family family | c.47.1.10 — Glutathione peroxidase-like |
CATH v4.4 (20 domains)
| 结构域编号 domain_id | 2e2gA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 2e2gA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1020 — Antioxidant, Horf6; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Antioxidant, Horf6; Chain A, domain2 |
| 结构域编号 domain_id | 2e2gB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 2e2gB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1020 — Antioxidant, Horf6; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Antioxidant, Horf6; Chain A, domain2 |
| 结构域编号 domain_id | 2e2gC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 2e2gC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1020 — Antioxidant, Horf6; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Antioxidant, Horf6; Chain A, domain2 |
| 结构域编号 domain_id | 2e2gD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 2e2gD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1020 — Antioxidant, Horf6; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Antioxidant, Horf6; Chain A, domain2 |
| 结构域编号 domain_id | 2e2gE01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 2e2gE02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1020 — Antioxidant, Horf6; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Antioxidant, Horf6; Chain A, domain2 |
| 结构域编号 domain_id | 2e2gF01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 2e2gF02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1020 — Antioxidant, Horf6; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Antioxidant, Horf6; Chain A, domain2 |
| 结构域编号 domain_id | 2e2gG01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 2e2gG02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1020 — Antioxidant, Horf6; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Antioxidant, Horf6; Chain A, domain2 |
| 结构域编号 domain_id | 2e2gH01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 2e2gH02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1020 — Antioxidant, Horf6; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Antioxidant, Horf6; Chain A, domain2 |
| 结构域编号 domain_id | 2e2gI01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 2e2gI02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1020 — Antioxidant, Horf6; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Antioxidant, Horf6; Chain A, domain2 |
| 结构域编号 domain_id | 2e2gJ01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 30 — Glutaredoxin |
| 同源超家族 H-superfamily homologous superfamily | 10 — Glutaredoxin |
| 结构域编号 domain_id | 2e2gJ02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1020 — Antioxidant, Horf6; Chain A, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Antioxidant, Horf6; Chain A, domain2 |