1wda
Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with benzoyl-L-arginine amide
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 | 1wda |
| 沉积日期 deposition_date | 2004-05-12 |
| 结构标题 title | Crystal structure of human peptidylarginine deiminase type4 (PAD4) in complex with benzoyl-L-arginine amide |
| 关键词 keywords | Post-translational enzyme, 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 | 32.86 Å |
| 回转半径 Rg (电子) rg_electron | 33.55 Å |
| 零角强度 I(0) i0 | 78879200.00 |
| 分子量 molecular_weight | 71150.0 kDa |
| 排除体积 excluded_volume | 89233 ų |
| 包络体积 envelope_volume | 113170 ų |
| 水化壳体积 shell_volume | 31059 ų |
| 包络直径 envelope_diameter | 134.1 Å |
| 壳层 Rg shell_rg | 35.90 Å |
| 包络 Rg envelope_rg | 34.73 Å |
| 形状 Rg shape_rg | 33.55 Å |
| 总 Rg total_rg | 33.74 Å |
| 总原子数 total_atoms | 4986 |
| 残基数 n_residues | 628 |
| 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 | 126.4 Å |
| Rg (实空间) rg_real | 33.61 Å |
| Rg 误差 (实空间) rg_real_error | 1.68 Å |
| I(0) (实空间) i0_real | 7.8880e+07 |
| I(0) 误差 (实空间) i0_real_error | 1.4280e+06 |
| Rg (倒空间) rg_reciprocal | 33.29 Å |
| I(0) (倒空间) i0_reciprocal | 78860000.0000 |
| 解质量估计 total_estimate | 0.4279 |
| 解质量评级 solution_quality | SUSPICIOUS a SUSPICIOUS solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 29.0 Å |
| 偏度 Skewness skewness | 0.750 |
| 峰度 Kurtosis kurtosis | -0.040 |
| 角度范围 angular_range | — – 0.2400 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 18590000.0000 |
| 实空间数据点数 n_real_points | 49 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.304; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.213; Smooth: 0.000 |
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) 6 domains
SCOP 2.08 (3 domains)
| 结构域编号 domain_id | d1wdaa1 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f |
| 超家族 Superfamily superfamily | b.2.9 — Peptidylarginine deiminase Pad4, middle domain |
| 家族 Family family | b.2.9.1 — Peptidylarginine deiminase Pad4, middle domain |
| 结构域编号 domain_id | d1wdaa2 |
| 类 Class class | b — All beta proteins |
| 折叠类型 Fold fold | b.6 — Cupredoxin-like |
| 超家族 Superfamily superfamily | b.6.1 — Cupredoxins |
| 家族 Family family | b.6.1.6 — Peptidylarginine deiminase Pad4, N-terminal domain |
| 结构域编号 domain_id | d1wdaa3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.126 — Pentein, beta/alpha-propeller |
| 超家族 Superfamily superfamily | d.126.1 — Pentein |
| 家族 Family family | d.126.1.5 — Peptidylarginine deiminase Pad4, catalytic C-terminal domain |
CATH v4.4 (3 domains)
| 结构域编号 domain_id | 1wdaA01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1860 — Protein-arginine deiminase, N-terminal domain |
| 结构域编号 domain_id | 1wdaA02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 1700 — Protein-arginine deiminase, central domain |
| 结构域编号 domain_id | 1wdaA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 75 — 5-stranded Propeller |
| 拓扑 Topology topology | 10 — L-arginine/glycine Amidinotransferase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — L-arginine/glycine Amidinotransferase; Chain A |