1u6z
Structure of an E. coli Exopolyphosphatase: Insight into the processive hydrolysis of polyphosphate and its regulation
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 | 1u6z |
| 沉积日期 deposition_date | 2004-08-02 |
| 结构标题 title | Structure of an E. coli Exopolyphosphatase: Insight into the processive hydrolysis of polyphosphate and its regulation |
| 关键词 keywords | ;alpha/beta protein, ASKHA (Acetate and Sugar Kinases, Hsc70, Actin) superfamily, HD metal dependent phosphohydrolase superfamily, polyphosphate, twenty-nine sulfates, 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 | 33.77 Å |
| 回转半径 Rg (电子) rg_electron | 33.23 Å |
| 零角强度 I(0) i0 | 222295000.00 |
| 分子量 molecular_weight | 115600.0 kDa |
| 排除体积 excluded_volume | 143090 ų |
| 包络体积 envelope_volume | 183180 ų |
| 水化壳体积 shell_volume | 45563 ų |
| 包络直径 envelope_diameter | 116.6 Å |
| 壳层 Rg shell_rg | 40.38 Å |
| 包络 Rg envelope_rg | 32.99 Å |
| 形状 Rg shape_rg | 33.21 Å |
| 总 Rg total_rg | 33.82 Å |
| 总原子数 total_atoms | 8084 |
| 残基数 n_residues | 998 |
| 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 | 108.0 Å |
| Rg (实空间) rg_real | 33.75 Å |
| Rg 误差 (实空间) rg_real_error | 0.69 Å |
| I(0) (实空间) i0_real | 2.2230e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.0890e+06 |
| Rg (倒空间) rg_reciprocal | 33.77 Å |
| I(0) (倒空间) i0_reciprocal | 222300000.0000 |
| 解质量估计 total_estimate | 0.8994 |
| 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 | 39.0 Å |
| 偏度 Skewness skewness | 0.319 |
| 峰度 Kurtosis kurtosis | -0.430 |
| 角度范围 angular_range | — – 0.2350 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 98150000.0000 |
| 实空间数据点数 n_real_points | 48 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.924 |
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) 14 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1u6za1 |
| 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 | d1u6za2 |
| 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 | d1u6za3 |
| 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 | d1u6zb1 |
| 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 | d1u6zb2 |
| 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 | d1u6zb3 |
| 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 (8 domains)
| 结构域编号 domain_id | 1u6zA01 |
| 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 | 1u6zA02 |
| 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 | 1u6zA03 |
| 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 | 1u6zA04 |
| 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 | 1u6zB01 |
| 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 | 1u6zB02 |
| 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 | 1u6zB03 |
| 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 | 1u6zB04 |
| 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 — |