1sql
Crystal structure of 7,8-dihydroneopterin aldolase in complex with guanine
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 | 1sql |
| 沉积日期 deposition_date | 2004-03-19 |
| 结构标题 title | Crystal structure of 7,8-dihydroneopterin aldolase in complex with guanine |
| 关键词 keywords | tetrahydrofolate biosynthesis, aldolase classes, retroaldol reaction, purin binding, Schiff base, LYASE; LYASE |
| 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 | 46.91 Å |
| 回转半径 Rg (电子) rg_electron | 46.60 Å |
| 零角强度 I(0) i0 | 632615000.00 |
| 分子量 molecular_weight | 218960.0 kDa |
| 排除体积 excluded_volume | 278700 ų |
| 包络体积 envelope_volume | 367120 ų |
| 水化壳体积 shell_volume | 65629 ų |
| 包络直径 envelope_diameter | 152.0 Å |
| 壳层 Rg shell_rg | 51.09 Å |
| 包络 Rg envelope_rg | 45.57 Å |
| 形状 Rg shape_rg | 46.60 Å |
| 总 Rg total_rg | 46.78 Å |
| 总原子数 total_atoms | 15471 |
| 残基数 n_residues | 1939 |
| 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 | 146.6 Å |
| Rg (实空间) rg_real | 47.11 Å |
| Rg 误差 (实空间) rg_real_error | 1.16 Å |
| I(0) (实空间) i0_real | 6.3260e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.1420e+07 |
| Rg (倒空间) rg_reciprocal | 46.91 Å |
| I(0) (倒空间) i0_reciprocal | 632500000.0000 |
| 解质量估计 total_estimate | 0.8150 |
| 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 | 47.4 Å |
| 偏度 Skewness skewness | 0.374 |
| 峰度 Kurtosis kurtosis | -0.663 |
| 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 | 201500000.0000 |
| 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: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.207 |
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) 32 domains
SCOP 2.08 (16 domains)
| 结构域编号 domain_id | d1sqla_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqlb_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqlc_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqld_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqle_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqlf_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqlg_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqlh_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqli_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqlj_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqlk_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqll_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqlm_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqln_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqlo_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
| 结构域编号 domain_id | d1sqlp_ |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.96 — T-fold |
| 超家族 Superfamily superfamily | d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like |
| 家族 Family family | d.96.1.3 — DHN aldolase/epimerase |
CATH v4.4 (16 domains)
| 结构域编号 domain_id | 1sqlA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlC00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlD00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlE00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlF00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlG00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlH00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlI00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlJ00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlK00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlL00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlM00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlN00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlO00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |
| 结构域编号 domain_id | 1sqlP00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1130 — GTP Cyclohydrolase I, domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain |