2flo
Crystal structure of exopolyphosphatase (PPX) from E. coli O157:H7
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 | 2flo |
| 沉积日期 deposition_date | 2006-01-06 |
| 结构标题 title | Crystal structure of exopolyphosphatase (PPX) from E. coli O157:H7 |
| 关键词 keywords | ;exopolyphosphatase, PPX/GPPA, metaphosphatase, Structural Genomics, Bacterial Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, HYDROLASE ;; HYDROLASE |
| 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 | 40.86 Å |
| 回转半径 Rg (电子) rg_electron | 40.38 Å |
| 零角强度 I(0) i0 | 798739000.00 |
| 分子量 molecular_weight | 228090.0 kDa |
| 排除体积 excluded_volume | 283070 ų |
| 包络体积 envelope_volume | 370130 ų |
| 水化壳体积 shell_volume | 73703 ų |
| 包络直径 envelope_diameter | 137.3 Å |
| 壳层 Rg shell_rg | 47.97 Å |
| 包络 Rg envelope_rg | 39.78 Å |
| 形状 Rg shape_rg | 40.36 Å |
| 总 Rg total_rg | 40.81 Å |
| 总原子数 total_atoms | 15835 |
| 残基数 n_residues | 1919 |
| 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 | 130.4 Å |
| Rg (实空间) rg_real | 40.71 Å |
| Rg 误差 (实空间) rg_real_error | 0.79 Å |
| I(0) (实空间) i0_real | 7.9870e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.2310e+07 |
| Rg (倒空间) rg_reciprocal | 40.86 Å |
| I(0) (倒空间) i0_reciprocal | 798900000.0000 |
| 解质量估计 total_estimate | 0.6634 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 50.1 Å |
| 偏度 Skewness skewness | 0.208 |
| 峰度 Kurtosis kurtosis | -0.375 |
| 角度范围 angular_range | — – 0.1950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 113400000.0000 |
| 实空间数据点数 n_real_points | 40 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 0.025; Positv: 1.000; Valcen: 0.992; Smooth: 0.866 |
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) 28 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d2floa1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.211 — HD-domain/PDEase-like |
| 超家族 Superfamily superfamily | a.211.1 — HD-domain/PDEase-like |
| 家族 Family family | a.211.1.5 — Ppx associated domain |
| 结构域编号 domain_id | d2floa2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.1 — Actin-like ATPase domain |
| 家族 Family family | c.55.1.8 — Ppx/GppA phosphatase |
| 结构域编号 domain_id | d2floa3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.1 — Actin-like ATPase domain |
| 家族 Family family | c.55.1.8 — Ppx/GppA phosphatase |
| 结构域编号 domain_id | d2flob1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.211 — HD-domain/PDEase-like |
| 超家族 Superfamily superfamily | a.211.1 — HD-domain/PDEase-like |
| 家族 Family family | a.211.1.5 — Ppx associated domain |
| 结构域编号 domain_id | d2flob2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.1 — Actin-like ATPase domain |
| 家族 Family family | c.55.1.8 — Ppx/GppA phosphatase |
| 结构域编号 domain_id | d2flob3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.1 — Actin-like ATPase domain |
| 家族 Family family | c.55.1.8 — Ppx/GppA phosphatase |
| 结构域编号 domain_id | d2floc1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.211 — HD-domain/PDEase-like |
| 超家族 Superfamily superfamily | a.211.1 — HD-domain/PDEase-like |
| 家族 Family family | a.211.1.5 — Ppx associated domain |
| 结构域编号 domain_id | d2floc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.1 — Actin-like ATPase domain |
| 家族 Family family | c.55.1.8 — Ppx/GppA phosphatase |
| 结构域编号 domain_id | d2floc3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.1 — Actin-like ATPase domain |
| 家族 Family family | c.55.1.8 — Ppx/GppA phosphatase |
| 结构域编号 domain_id | d2flod1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.211 — HD-domain/PDEase-like |
| 超家族 Superfamily superfamily | a.211.1 — HD-domain/PDEase-like |
| 家族 Family family | a.211.1.5 — Ppx associated domain |
| 结构域编号 domain_id | d2flod2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.1 — Actin-like ATPase domain |
| 家族 Family family | c.55.1.8 — Ppx/GppA phosphatase |
| 结构域编号 domain_id | d2flod3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.55 — Ribonuclease H-like motif |
| 超家族 Superfamily superfamily | c.55.1 — Actin-like ATPase domain |
| 家族 Family family | c.55.1.8 — Ppx/GppA phosphatase |
CATH v4.4 (16 domains)
| 结构域编号 domain_id | 2floA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 40 — ATPase, nucleotide binding domain |
| 结构域编号 domain_id | 2floA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 150 — Exopolyphosphatase. Domain 2 |
| 结构域编号 domain_id | 2floA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3210 — Hypothetical protein af1432 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hypothetical protein af1432 |
| 结构域编号 domain_id | 2floA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 2260 — |
| 结构域编号 domain_id | 2floB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 40 — ATPase, nucleotide binding domain |
| 结构域编号 domain_id | 2floB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 150 — Exopolyphosphatase. Domain 2 |
| 结构域编号 domain_id | 2floB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3210 — Hypothetical protein af1432 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hypothetical protein af1432 |
| 结构域编号 domain_id | 2floB04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 2260 — |
| 结构域编号 domain_id | 2floC01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 40 — ATPase, nucleotide binding domain |
| 结构域编号 domain_id | 2floC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 150 — Exopolyphosphatase. Domain 2 |
| 结构域编号 domain_id | 2floC03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3210 — Hypothetical protein af1432 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hypothetical protein af1432 |
| 结构域编号 domain_id | 2floC04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 2260 — |
| 结构域编号 domain_id | 2floD01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 40 — ATPase, nucleotide binding domain |
| 结构域编号 domain_id | 2floD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 420 — Nucleotidyltransferase; domain 5 |
| 同源超家族 H-superfamily homologous superfamily | 150 — Exopolyphosphatase. Domain 2 |
| 结构域编号 domain_id | 2floD03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 3210 — Hypothetical protein af1432 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Hypothetical protein af1432 |
| 结构域编号 domain_id | 2floD04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 2260 — |