1p80
Crystal structure of the D181Q variant of catalase HPII from E. coli
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 | 1p80 |
| 沉积日期 deposition_date | 2003-05-06 |
| 结构标题 title | Crystal structure of the D181Q variant of catalase HPII from E. coli |
| 关键词 keywords | catalase, beta barrel, channel, 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 | 41.71 Å |
| 回转半径 Rg (电子) rg_electron | 41.43 Å |
| 零角强度 I(0) i0 | 1559300000.00 |
| 分子量 molecular_weight | 327340.0 kDa |
| 排除体积 excluded_volume | 408930 ų |
| 包络体积 envelope_volume | 481550 ų |
| 水化壳体积 shell_volume | 90430 ų |
| 包络直径 envelope_diameter | 146.4 Å |
| 壳层 Rg shell_rg | 50.79 Å |
| 包络 Rg envelope_rg | 41.82 Å |
| 形状 Rg shape_rg | 41.36 Å |
| 总 Rg total_rg | 42.01 Å |
| 总原子数 total_atoms | 23160 |
| 残基数 n_residues | 2908 |
| 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 | 136.8 Å |
| Rg (实空间) rg_real | 41.64 Å |
| Rg 误差 (实空间) rg_real_error | 0.91 Å |
| I(0) (实空间) i0_real | 1.5590e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.6050e+07 |
| Rg (倒空间) rg_reciprocal | 41.71 Å |
| I(0) (倒空间) i0_reciprocal | 1559000000.0000 |
| 解质量估计 total_estimate | 0.6343 |
| 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 | 50.4 Å |
| 偏度 Skewness skewness | 0.368 |
| 峰度 Kurtosis kurtosis | -0.178 |
| 角度范围 angular_range | — – 0.1900 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 642200000.0000 |
| 实空间数据点数 n_real_points | 39 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.817; Stabil: 0.998; Sysdev: 0.008; Positv: 1.000; Valcen: 0.980; Smooth: 0.793 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (3)
6. 折叠分类 (SCOP + CATH) 20 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d1p80a1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.16 — Class I glutamine amidotransferase-like |
| 家族 Family family | c.23.16.3 — Catalase, C-terminal domain |
| 结构域编号 domain_id | d1p80a2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.5 — Heme-dependent catalase-like |
| 超家族 Superfamily superfamily | e.5.1 — Heme-dependent catalase-like |
| 家族 Family family | e.5.1.1 — Heme-dependent catalases |
| 结构域编号 domain_id | d1p80b1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.16 — Class I glutamine amidotransferase-like |
| 家族 Family family | c.23.16.3 — Catalase, C-terminal domain |
| 结构域编号 domain_id | d1p80b2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.5 — Heme-dependent catalase-like |
| 超家族 Superfamily superfamily | e.5.1 — Heme-dependent catalase-like |
| 家族 Family family | e.5.1.1 — Heme-dependent catalases |
| 结构域编号 domain_id | d1p80c1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.16 — Class I glutamine amidotransferase-like |
| 家族 Family family | c.23.16.3 — Catalase, C-terminal domain |
| 结构域编号 domain_id | d1p80c2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.5 — Heme-dependent catalase-like |
| 超家族 Superfamily superfamily | e.5.1 — Heme-dependent catalase-like |
| 家族 Family family | e.5.1.1 — Heme-dependent catalases |
| 结构域编号 domain_id | d1p80d1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.23 — Flavodoxin-like |
| 超家族 Superfamily superfamily | c.23.16 — Class I glutamine amidotransferase-like |
| 家族 Family family | c.23.16.3 — Catalase, C-terminal domain |
| 结构域编号 domain_id | d1p80d2 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.5 — Heme-dependent catalase-like |
| 超家族 Superfamily superfamily | e.5.1 — Heme-dependent catalase-like |
| 家族 Family family | e.5.1.1 — Heme-dependent catalases |
CATH v4.4 (12 domains)
| 结构域编号 domain_id | 1p80A01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 180 — Catalase HpII, Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Catalase core domain |
| 结构域编号 domain_id | 1p80A02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1370 — Hemocyanin, N-terminal domain |
| 同源超家族 H-superfamily homologous superfamily | 20 — Catalase, four-helical domain |
| 结构域编号 domain_id | 1p80A03 |
| 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 | 880 — Class I glutamine amidotransferase (GATase) domain |
| 结构域编号 domain_id | 1p80B01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 180 — Catalase HpII, Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Catalase core domain |
| 结构域编号 domain_id | 1p80B02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1370 — Hemocyanin, N-terminal domain |
| 同源超家族 H-superfamily homologous superfamily | 20 — Catalase, four-helical domain |
| 结构域编号 domain_id | 1p80B03 |
| 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 | 880 — Class I glutamine amidotransferase (GATase) domain |
| 结构域编号 domain_id | 1p80C01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 180 — Catalase HpII, Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Catalase core domain |
| 结构域编号 domain_id | 1p80C02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1370 — Hemocyanin, N-terminal domain |
| 同源超家族 H-superfamily homologous superfamily | 20 — Catalase, four-helical domain |
| 结构域编号 domain_id | 1p80C03 |
| 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 | 880 — Class I glutamine amidotransferase (GATase) domain |
| 结构域编号 domain_id | 1p80D01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 40 — Beta Barrel |
| 拓扑 Topology topology | 180 — Catalase HpII, Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Catalase core domain |
| 结构域编号 domain_id | 1p80D02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1370 — Hemocyanin, N-terminal domain |
| 同源超家族 H-superfamily homologous superfamily | 20 — Catalase, four-helical domain |
| 结构域编号 domain_id | 1p80D03 |
| 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 | 880 — Class I glutamine amidotransferase (GATase) domain |