1r0k
Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Zymomonas mobilis
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 | 1r0k |
| 沉积日期 deposition_date | 2003-09-22 |
| 结构标题 title | Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Zymomonas mobilis |
| 关键词 keywords | reductoisomerase, NADPH dependent, Fosmidomycin, non-mevalonate pathway, zymomonas mobilis, 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 | 45.80 Å |
| 回转半径 Rg (电子) rg_electron | 46.12 Å |
| 零角强度 I(0) i0 | 396668000.00 |
| 分子量 molecular_weight | 163890.0 kDa |
| 排除体积 excluded_volume | 205510 ų |
| 包络体积 envelope_volume | 279470 ų |
| 水化壳体积 shell_volume | 53574 ų |
| 包络直径 envelope_diameter | 166.8 Å |
| 壳层 Rg shell_rg | 46.74 Å |
| 包络 Rg envelope_rg | 45.36 Å |
| 形状 Rg shape_rg | 46.10 Å |
| 总 Rg total_rg | 46.19 Å |
| 总原子数 total_atoms | 11497 |
| 残基数 n_residues | 1521 |
| 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 | 163.6 Å |
| Rg (实空间) rg_real | 46.20 Å |
| Rg 误差 (实空间) rg_real_error | 2.00 Å |
| I(0) (实空间) i0_real | 3.9670e+08 |
| I(0) 误差 (实空间) i0_real_error | 8.1520e+06 |
| Rg (倒空间) rg_reciprocal | 45.80 Å |
| I(0) (倒空间) i0_reciprocal | 396500000.0000 |
| 解质量估计 total_estimate | 0.8295 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 38.5 Å |
| 偏度 Skewness skewness | 0.493 |
| 峰度 Kurtosis kurtosis | -0.279 |
| 角度范围 angular_range | — – 0.1700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 48490000.0000 |
| 实空间数据点数 n_real_points | 35 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.722; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.879; Smooth: 0.733 |
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 (12 domains)
| 结构域编号 domain_id | d1r0ka1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.69 — Left-handed superhelix |
| 超家族 Superfamily superfamily | a.69.3 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain |
| 家族 Family family | a.69.3.1 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain |
| 结构域编号 domain_id | d1r0ka2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain |
| 结构域编号 domain_id | d1r0ka3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.81 — FwdE/GAPDH domain-like |
| 超家族 Superfamily superfamily | d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain |
| 家族 Family family | d.81.1.3 — Dihydrodipicolinate reductase-like |
| 结构域编号 domain_id | d1r0kb1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.69 — Left-handed superhelix |
| 超家族 Superfamily superfamily | a.69.3 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain |
| 家族 Family family | a.69.3.1 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain |
| 结构域编号 domain_id | d1r0kb2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain |
| 结构域编号 domain_id | d1r0kb3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.81 — FwdE/GAPDH domain-like |
| 超家族 Superfamily superfamily | d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain |
| 家族 Family family | d.81.1.3 — Dihydrodipicolinate reductase-like |
| 结构域编号 domain_id | d1r0kc1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.69 — Left-handed superhelix |
| 超家族 Superfamily superfamily | a.69.3 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain |
| 家族 Family family | a.69.3.1 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain |
| 结构域编号 domain_id | d1r0kc2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain |
| 结构域编号 domain_id | d1r0kc3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.81 — FwdE/GAPDH domain-like |
| 超家族 Superfamily superfamily | d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain |
| 家族 Family family | d.81.1.3 — Dihydrodipicolinate reductase-like |
| 结构域编号 domain_id | d1r0kd1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.69 — Left-handed superhelix |
| 超家族 Superfamily superfamily | a.69.3 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain |
| 家族 Family family | a.69.3.1 — 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain |
| 结构域编号 domain_id | d1r0kd2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.2 — NAD(P)-binding Rossmann-fold domains |
| 超家族 Superfamily superfamily | c.2.1 — NAD(P)-binding Rossmann-fold domains |
| 家族 Family family | c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain |
| 结构域编号 domain_id | d1r0kd3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.81 — FwdE/GAPDH domain-like |
| 超家族 Superfamily superfamily | d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain |
| 家族 Family family | d.81.1.3 — Dihydrodipicolinate reductase-like |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1r0kA01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r0kA03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1740 — Rna Polymerase Sigma Factor; Chain: A |
| 同源超家族 H-superfamily homologous superfamily | 10 — RNA polymerase sigma factor, region 2, helix turn helix motif |
| 结构域编号 domain_id | 1r0kB01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r0kB03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1740 — Rna Polymerase Sigma Factor; Chain: A |
| 同源超家族 H-superfamily homologous superfamily | 10 — RNA polymerase sigma factor, region 2, helix turn helix motif |
| 结构域编号 domain_id | 1r0kC01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r0kC03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1740 — Rna Polymerase Sigma Factor; Chain: A |
| 同源超家族 H-superfamily homologous superfamily | 10 — RNA polymerase sigma factor, region 2, helix turn helix motif |
| 结构域编号 domain_id | 1r0kD01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1r0kD03 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 10 — Orthogonal Bundle |
| 拓扑 Topology topology | 1740 — Rna Polymerase Sigma Factor; Chain: A |
| 同源超家族 H-superfamily homologous superfamily | 10 — RNA polymerase sigma factor, region 2, helix turn helix motif |