1w5d
Crystal structure of PBP4a from Bacillus subtilis
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 | 1w5d |
| 沉积日期 deposition_date | 2004-08-06 |
| 结构标题 title | Crystal structure of PBP4a from Bacillus subtilis |
| 关键词 keywords | ;PENICILLIN-BINDING PROTEIN, D-ALA-D-ALA-CARBOXYPEPTIDASE, PEPTIDOGLYCAN, BACILLUS SUBTILIS, BETA-LACTAM, HYDROLASE, PEPTIDOGLYCAN SYNTHESIS ;; 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 | 24.87 Å |
| 回转半径 Rg (电子) rg_electron | 24.06 Å |
| 零角强度 I(0) i0 | 41083200.00 |
| 分子量 molecular_weight | 49355.0 kDa |
| 排除体积 excluded_volume | 61752 ų |
| 包络体积 envelope_volume | 73024 ų |
| 水化壳体积 shell_volume | 25921 ų |
| 包络直径 envelope_diameter | 86.5 Å |
| 壳层 Rg shell_rg | 30.80 Å |
| 包络 Rg envelope_rg | 24.28 Å |
| 形状 Rg shape_rg | 24.04 Å |
| 总 Rg total_rg | 24.90 Å |
| 总原子数 total_atoms | 3465 |
| 残基数 n_residues | 458 |
| 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 | 82.4 Å |
| Rg (实空间) rg_real | 24.86 Å |
| Rg 误差 (实空间) rg_real_error | 0.67 Å |
| I(0) (实空间) i0_real | 4.1080e+07 |
| I(0) 误差 (实空间) i0_real_error | 6.3880e+05 |
| Rg (倒空间) rg_reciprocal | 24.87 Å |
| I(0) (倒空间) i0_reciprocal | 41080000.0000 |
| 解质量估计 total_estimate | 0.8126 |
| 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 | 28.8 Å |
| 偏度 Skewness skewness | 0.336 |
| 峰度 Kurtosis kurtosis | -0.381 |
| 角度范围 angular_range | — – 0.3200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 7581000.0000 |
| 实空间数据点数 n_real_points | 64 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.866; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.000 |
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) 3 domains
SCOP 2.08 (1 domains)
| 结构域编号 domain_id | d1w5da1 |
| 类 Class class | e — Multi-domain proteins (alpha and beta) |
| 折叠类型 Fold fold | e.3 — beta-lactamase/transpeptidase-like |
| 超家族 Superfamily superfamily | e.3.1 — beta-lactamase/transpeptidase-like |
| 家族 Family family | e.3.1.3 — Dac-like |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1w5dA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 710 — Beta-lactamase |
| 同源超家族 H-superfamily homologous superfamily | 10 — DD-peptidase/beta-lactamase superfamily |
| 结构域编号 domain_id | 1w5dA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 50 — 3-Layer(bba) Sandwich |
| 拓扑 Topology topology | 80 — D-tyrosyl-trna(Tyr) Deacylase; Chain: A; |
| 同源超家族 H-superfamily homologous superfamily | 20 — D-Ala-D-Ala carboxypeptidase C, peptidase S13 |