2cv4
Crystal Structure of an Archaeal Peroxiredoxin from the Aerobic Hyperthermophilic Crenarchaeon Aeropyrum pernix K1
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 | 2cv4 |
| 沉积日期 deposition_date | 2005-05-31 |
| 结构标题 title | Crystal Structure of an Archaeal Peroxiredoxin from the Aerobic Hyperthermophilic Crenarchaeon Aeropyrum pernix K1 |
| 关键词 keywords | ;thioredoxin peroxidase, thioredoxin fold, reactive oxigen scavenging system, cysteine sulfonic acid, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, OXYGEN STORAGE-TRANSPORT COMPLEX ;; OXYGEN STORAGE/TRANSPORT |
| 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 | 51.15 Å |
| 回转半径 Rg (电子) rg_electron | 50.32 Å |
| 零角强度 I(0) i0 | 1072110000.00 |
| 分子量 molecular_weight | 278730.0 kDa |
| 排除体积 excluded_volume | 349680 ų |
| 包络体积 envelope_volume | 471220 ų |
| 水化壳体积 shell_volume | 73908 ų |
| 包络直径 envelope_diameter | 141.1 Å |
| 壳层 Rg shell_rg | 60.99 Å |
| 包络 Rg envelope_rg | 47.79 Å |
| 形状 Rg shape_rg | 50.35 Å |
| 总 Rg total_rg | 50.50 Å |
| 总原子数 total_atoms | 19560 |
| 残基数 n_residues | 2358 |
| 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 | 146.1 Å |
| Rg (实空间) rg_real | 50.95 Å |
| Rg 误差 (实空间) rg_real_error | 0.97 Å |
| I(0) (实空间) i0_real | 1.0720e+09 |
| I(0) 误差 (实空间) i0_real_error | 1.8270e+07 |
| Rg (倒空间) rg_reciprocal | 51.29 Å |
| I(0) (倒空间) i0_reciprocal | 1073000000.0000 |
| 解质量估计 total_estimate | 0.8229 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 3 |
| 主峰位置 r_peak_primary | 80.1 Å |
| 偏度 Skewness skewness | -0.097 |
| 峰度 Kurtosis kurtosis | -0.961 |
| 角度范围 angular_range | — – 0.1550 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 206100000.0000 |
| 实空间数据点数 n_real_points | 32 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 30 domains
SCOP 2.08 (10 domains)
| 结构域编号 domain_id | d2cv4a1 |
| 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 | d2cv4b_ |
| 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 | d2cv4c_ |
| 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 | d2cv4d_ |
| 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 | d2cv4e_ |
| 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 | d2cv4f_ |
| 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 | d2cv4g_ |
| 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 | d2cv4h_ |
| 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 | d2cv4i_ |
| 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 | d2cv4j_ |
| 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 | 2cv4A01 |
| 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 | 2cv4A02 |
| 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 | 2cv4B01 |
| 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 | 2cv4B02 |
| 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 | 2cv4C01 |
| 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 | 2cv4C02 |
| 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 | 2cv4D01 |
| 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 | 2cv4D02 |
| 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 | 2cv4E01 |
| 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 | 2cv4E02 |
| 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 | 2cv4F01 |
| 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 | 2cv4F02 |
| 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 | 2cv4G01 |
| 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 | 2cv4G02 |
| 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 | 2cv4H01 |
| 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 | 2cv4H02 |
| 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 | 2cv4I01 |
| 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 | 2cv4I02 |
| 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 | 2cv4J01 |
| 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 | 2cv4J02 |
| 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 |