2dgl
Crystal structure of Escherichia coli GadB in complex with bromide
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 | 2dgl |
| 沉积日期 deposition_date | 2006-03-14 |
| 结构标题 title | Crystal structure of Escherichia coli GadB in complex with bromide |
| 关键词 keywords | GadB complexed with bromide, 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 | 41.91 Å |
| 回转半径 Rg (电子) rg_electron | 41.42 Å |
| 零角强度 I(0) i0 | 1418870000.00 |
| 分子量 molecular_weight | 309020.0 kDa |
| 排除体积 excluded_volume | 384550 ų |
| 包络体积 envelope_volume | 466560 ų |
| 水化壳体积 shell_volume | 88689 ų |
| 包络直径 envelope_diameter | 131.3 Å |
| 壳层 Rg shell_rg | 50.21 Å |
| 包络 Rg envelope_rg | 41.28 Å |
| 形状 Rg shape_rg | 41.43 Å |
| 总 Rg total_rg | 41.73 Å |
| 总原子数 total_atoms | 21635 |
| 残基数 n_residues | 2704 |
| 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 | 131.0 Å |
| Rg (实空间) rg_real | 41.73 Å |
| Rg 误差 (实空间) rg_real_error | 0.63 Å |
| I(0) (实空间) i0_real | 1.4190e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.3700e+07 |
| Rg (倒空间) rg_reciprocal | 41.91 Å |
| I(0) (倒空间) i0_reciprocal | 1419000000.0000 |
| 解质量估计 total_estimate | 0.8899 |
| 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 | 51.7 Å |
| 偏度 Skewness skewness | 0.188 |
| 峰度 Kurtosis kurtosis | -0.484 |
| 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 | 326300000.0000 |
| 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: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.839 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (5)
6. 折叠分类 (SCOP + CATH) 24 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d2dgla_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.67 — PLP-dependent transferase-like |
| 超家族 Superfamily superfamily | c.67.1 — PLP-dependent transferases |
| 家族 Family family | c.67.1.6 — Pyridoxal-dependent decarboxylase |
| 结构域编号 domain_id | d2dglb_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.67 — PLP-dependent transferase-like |
| 超家族 Superfamily superfamily | c.67.1 — PLP-dependent transferases |
| 家族 Family family | c.67.1.6 — Pyridoxal-dependent decarboxylase |
| 结构域编号 domain_id | d2dglc_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.67 — PLP-dependent transferase-like |
| 超家族 Superfamily superfamily | c.67.1 — PLP-dependent transferases |
| 家族 Family family | c.67.1.6 — Pyridoxal-dependent decarboxylase |
| 结构域编号 domain_id | d2dgld_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.67 — PLP-dependent transferase-like |
| 超家族 Superfamily superfamily | c.67.1 — PLP-dependent transferases |
| 家族 Family family | c.67.1.6 — Pyridoxal-dependent decarboxylase |
| 结构域编号 domain_id | d2dgle_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.67 — PLP-dependent transferase-like |
| 超家族 Superfamily superfamily | c.67.1 — PLP-dependent transferases |
| 家族 Family family | c.67.1.6 — Pyridoxal-dependent decarboxylase |
| 结构域编号 domain_id | d2dglf_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.67 — PLP-dependent transferase-like |
| 超家族 Superfamily superfamily | c.67.1 — PLP-dependent transferases |
| 家族 Family family | c.67.1.6 — Pyridoxal-dependent decarboxylase |
CATH v4.4 (18 domains)
| 结构域编号 domain_id | 2dglA01 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B |
| 同源超家族 H-superfamily homologous superfamily | 50 — |
| 结构域编号 domain_id | 2dglA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 640 — Aspartate Aminotransferase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain) |
| 结构域编号 domain_id | 2dglA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1150 — Aspartate Aminotransferase, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 160 — |
| 结构域编号 domain_id | 2dglB01 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B |
| 同源超家族 H-superfamily homologous superfamily | 50 — |
| 结构域编号 domain_id | 2dglB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 640 — Aspartate Aminotransferase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain) |
| 结构域编号 domain_id | 2dglB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1150 — Aspartate Aminotransferase, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 160 — |
| 结构域编号 domain_id | 2dglC01 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B |
| 同源超家族 H-superfamily homologous superfamily | 50 — |
| 结构域编号 domain_id | 2dglC02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 640 — Aspartate Aminotransferase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain) |
| 结构域编号 domain_id | 2dglC03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1150 — Aspartate Aminotransferase, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 160 — |
| 结构域编号 domain_id | 2dglD01 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B |
| 同源超家族 H-superfamily homologous superfamily | 50 — |
| 结构域编号 domain_id | 2dglD02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 640 — Aspartate Aminotransferase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain) |
| 结构域编号 domain_id | 2dglD03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1150 — Aspartate Aminotransferase, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 160 — |
| 结构域编号 domain_id | 2dglE01 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B |
| 同源超家族 H-superfamily homologous superfamily | 50 — |
| 结构域编号 domain_id | 2dglE02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 640 — Aspartate Aminotransferase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain) |
| 结构域编号 domain_id | 2dglE03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1150 — Aspartate Aminotransferase, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 160 — |
| 结构域编号 domain_id | 2dglF01 |
| 类 Class class | 4 — Few Secondary Structures |
| 架构 Architecture architecture | 10 — Irregular |
| 拓扑 Topology topology | 280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B |
| 同源超家族 H-superfamily homologous superfamily | 50 — |
| 结构域编号 domain_id | 2dglF02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 640 — Aspartate Aminotransferase; domain 2 |
| 同源超家族 H-superfamily homologous superfamily | 10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain) |
| 结构域编号 domain_id | 2dglF03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 1150 — Aspartate Aminotransferase, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 160 — |