1wog
Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily
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 | 1wog |
| 沉积日期 deposition_date | 2004-08-18 |
| 结构标题 title | Crystal Structure of Agmatinase Reveals Structural Conservation and Inhibition Mechanism of the Ureohydrolase Superfamily |
| 关键词 keywords | alpha/beta fold, 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 | 34.20 Å |
| 回转半径 Rg (电子) rg_electron | 33.00 Å |
| 零角强度 I(0) i0 | 587495000.00 |
| 分子量 molecular_weight | 195800.0 kDa |
| 排除体积 excluded_volume | 244770 ų |
| 包络体积 envelope_volume | 283470 ų |
| 水化壳体积 shell_volume | 66044 ų |
| 包络直径 envelope_diameter | 101.7 Å |
| 壳层 Rg shell_rg | 43.39 Å |
| 包络 Rg envelope_rg | 32.88 Å |
| 形状 Rg shape_rg | 33.02 Å |
| 总 Rg total_rg | 33.63 Å |
| 总原子数 total_atoms | 13782 |
| 残基数 n_residues | 1818 |
| 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 | 100.8 Å |
| Rg (实空间) rg_real | 33.93 Å |
| Rg 误差 (实空间) rg_real_error | 0.40 Å |
| I(0) (实空间) i0_real | 5.8750e+08 |
| I(0) 误差 (实空间) i0_real_error | 8.9300e+06 |
| Rg (倒空间) rg_reciprocal | 34.10 Å |
| I(0) (倒空间) i0_reciprocal | 587600000.0000 |
| 解质量估计 total_estimate | 0.8993 |
| 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 | 46.0 Å |
| 偏度 Skewness skewness | 0.005 |
| 峰度 Kurtosis kurtosis | -0.561 |
| 角度范围 angular_range | — – 0.2300 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 1021000000.0000 |
| 实空间数据点数 n_real_points | 47 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.942 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (4)
6. 折叠分类 (SCOP + CATH) 18 domains
SCOP 2.08 (12 domains)
| 结构域编号 domain_id | d1woga1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.42 — Arginase/deacetylase |
| 超家族 Superfamily superfamily | c.42.1 — Arginase/deacetylase |
| 家族 Family family | c.42.1.1 — Arginase-like amidino hydrolases |
| 结构域编号 domain_id | d1woga2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1wogb1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.42 — Arginase/deacetylase |
| 超家族 Superfamily superfamily | c.42.1 — Arginase/deacetylase |
| 家族 Family family | c.42.1.1 — Arginase-like amidino hydrolases |
| 结构域编号 domain_id | d1wogb2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1wogc1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.42 — Arginase/deacetylase |
| 超家族 Superfamily superfamily | c.42.1 — Arginase/deacetylase |
| 家族 Family family | c.42.1.1 — Arginase-like amidino hydrolases |
| 结构域编号 domain_id | d1wogc2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1wogd1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.42 — Arginase/deacetylase |
| 超家族 Superfamily superfamily | c.42.1 — Arginase/deacetylase |
| 家族 Family family | c.42.1.1 — Arginase-like amidino hydrolases |
| 结构域编号 domain_id | d1wogd2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1woge1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.42 — Arginase/deacetylase |
| 超家族 Superfamily superfamily | c.42.1 — Arginase/deacetylase |
| 家族 Family family | c.42.1.1 — Arginase-like amidino hydrolases |
| 结构域编号 domain_id | d1woge2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
| 结构域编号 domain_id | d1wogf1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.42 — Arginase/deacetylase |
| 超家族 Superfamily superfamily | c.42.1 — Arginase/deacetylase |
| 家族 Family family | c.42.1.1 — Arginase-like amidino hydrolases |
| 结构域编号 domain_id | d1wogf2 |
| 类 Class class | l — Artifacts |
| 折叠类型 Fold fold | l.1 — Tags |
| 超家族 Superfamily superfamily | l.1.1 — Tags |
| 家族 Family family | l.1.1.1 — Tags |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1wogA00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 800 — Arginase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ureohydrolase domain |
| 结构域编号 domain_id | 1wogB00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 800 — Arginase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ureohydrolase domain |
| 结构域编号 domain_id | 1wogC00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 800 — Arginase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ureohydrolase domain |
| 结构域编号 domain_id | 1wogD00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 800 — Arginase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ureohydrolase domain |
| 结构域编号 domain_id | 1wogE00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 800 — Arginase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ureohydrolase domain |
| 结构域编号 domain_id | 1wogF00 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 800 — Arginase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Ureohydrolase domain |