2gvn
L-asparaginase from Erwinia carotovora in complex with aspartic acid
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 | 2gvn |
| 沉积日期 deposition_date | 2006-05-03 |
| 结构标题 title | L-asparaginase from Erwinia carotovora in complex with aspartic acid |
| 关键词 keywords | L-asparaginase, Erwinia carotovora, 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 | 47.57 Å |
| 回转半径 Rg (电子) rg_electron | 47.84 Å |
| 零角强度 I(0) i0 | 1069130000.00 |
| 分子量 molecular_weight | 275390.0 kDa |
| 排除体积 excluded_volume | 346680 ų |
| 包络体积 envelope_volume | 425540 ų |
| 水化壳体积 shell_volume | 74013 ų |
| 包络直径 envelope_diameter | 164.3 Å |
| 壳层 Rg shell_rg | 51.46 Å |
| 包络 Rg envelope_rg | 47.38 Å |
| 形状 Rg shape_rg | 47.82 Å |
| 总 Rg total_rg | 48.03 Å |
| 总原子数 total_atoms | 19368 |
| 残基数 n_residues | 2600 |
| 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 | 159.8 Å |
| Rg (实空间) rg_real | 47.90 Å |
| Rg 误差 (实空间) rg_real_error | 1.50 Å |
| I(0) (实空间) i0_real | 1.0690e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.0940e+07 |
| Rg (倒空间) rg_reciprocal | 47.57 Å |
| I(0) (倒空间) i0_reciprocal | 1069000000.0000 |
| 解质量估计 total_estimate | 0.8145 |
| 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 | 43.6 Å |
| 偏度 Skewness skewness | 0.442 |
| 峰度 Kurtosis kurtosis | -0.588 |
| 角度范围 angular_range | — – 0.1650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 322900000.0000 |
| 实空间数据点数 n_real_points | 34 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.694; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.557 |
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) 24 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d2gvna_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.88 — Glutaminase/Asparaginase |
| 超家族 Superfamily superfamily | c.88.1 — Glutaminase/Asparaginase |
| 家族 Family family | c.88.1.1 — Glutaminase/Asparaginase |
| 结构域编号 domain_id | d2gvnb_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.88 — Glutaminase/Asparaginase |
| 超家族 Superfamily superfamily | c.88.1 — Glutaminase/Asparaginase |
| 家族 Family family | c.88.1.1 — Glutaminase/Asparaginase |
| 结构域编号 domain_id | d2gvnc_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.88 — Glutaminase/Asparaginase |
| 超家族 Superfamily superfamily | c.88.1 — Glutaminase/Asparaginase |
| 家族 Family family | c.88.1.1 — Glutaminase/Asparaginase |
| 结构域编号 domain_id | d2gvnd_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.88 — Glutaminase/Asparaginase |
| 超家族 Superfamily superfamily | c.88.1 — Glutaminase/Asparaginase |
| 家族 Family family | c.88.1.1 — Glutaminase/Asparaginase |
| 结构域编号 domain_id | d2gvne_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.88 — Glutaminase/Asparaginase |
| 超家族 Superfamily superfamily | c.88.1 — Glutaminase/Asparaginase |
| 家族 Family family | c.88.1.1 — Glutaminase/Asparaginase |
| 结构域编号 domain_id | d2gvnf_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.88 — Glutaminase/Asparaginase |
| 超家族 Superfamily superfamily | c.88.1 — Glutaminase/Asparaginase |
| 家族 Family family | c.88.1.1 — Glutaminase/Asparaginase |
| 结构域编号 domain_id | d2gvng_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.88 — Glutaminase/Asparaginase |
| 超家族 Superfamily superfamily | c.88.1 — Glutaminase/Asparaginase |
| 家族 Family family | c.88.1.1 — Glutaminase/Asparaginase |
| 结构域编号 domain_id | d2gvnh_ |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.88 — Glutaminase/Asparaginase |
| 超家族 Superfamily superfamily | c.88.1 — Glutaminase/Asparaginase |
| 家族 Family family | c.88.1.1 — Glutaminase/Asparaginase |
CATH v4.4 (16 domains)
| 结构域编号 domain_id | 2gvnA01 |
| 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 | 1170 — L-asparaginase, N-terminal domain |
| 结构域编号 domain_id | 2gvnA02 |
| 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 | 40 — |
| 结构域编号 domain_id | 2gvnB01 |
| 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 | 1170 — L-asparaginase, N-terminal domain |
| 结构域编号 domain_id | 2gvnB02 |
| 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 | 40 — |
| 结构域编号 domain_id | 2gvnC01 |
| 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 | 1170 — L-asparaginase, N-terminal domain |
| 结构域编号 domain_id | 2gvnC02 |
| 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 | 40 — |
| 结构域编号 domain_id | 2gvnD01 |
| 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 | 1170 — L-asparaginase, N-terminal domain |
| 结构域编号 domain_id | 2gvnD02 |
| 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 | 40 — |
| 结构域编号 domain_id | 2gvnE01 |
| 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 | 1170 — L-asparaginase, N-terminal domain |
| 结构域编号 domain_id | 2gvnE02 |
| 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 | 40 — |
| 结构域编号 domain_id | 2gvnF01 |
| 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 | 1170 — L-asparaginase, N-terminal domain |
| 结构域编号 domain_id | 2gvnF02 |
| 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 | 40 — |
| 结构域编号 domain_id | 2gvnG01 |
| 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 | 1170 — L-asparaginase, N-terminal domain |
| 结构域编号 domain_id | 2gvnG02 |
| 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 | 40 — |
| 结构域编号 domain_id | 2gvnH01 |
| 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 | 1170 — L-asparaginase, N-terminal domain |
| 结构域编号 domain_id | 2gvnH02 |
| 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 | 40 — |