1p3d
Crystal Structure of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) in Complex with UMA and ANP.
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 | 1p3d |
| 沉积日期 deposition_date | 2003-04-17 |
| 结构标题 title | Crystal Structure of UDP-N-acetylmuramic acid:L-alanine ligase (MurC) in Complex with UMA and ANP. |
| 关键词 keywords | alpha/beta protein, LIGASE; LIGASE |
| 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 | 52.57 Å |
| 回转半径 Rg (电子) rg_electron | 52.75 Å |
| 零角强度 I(0) i0 | 170782000.00 |
| 分子量 molecular_weight | 104640.0 kDa |
| 排除体积 excluded_volume | 128520 ų |
| 包络体积 envelope_volume | 197520 ų |
| 水化壳体积 shell_volume | 30286 ų |
| 包络直径 envelope_diameter | 158.0 Å |
| 壳层 Rg shell_rg | 61.88 Å |
| 包络 Rg envelope_rg | 49.27 Å |
| 形状 Rg shape_rg | 52.82 Å |
| 总 Rg total_rg | 52.79 Å |
| 总原子数 total_atoms | 7235 |
| 残基数 n_residues | 895 |
| 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 | 161.2 Å |
| Rg (实空间) rg_real | 52.93 Å |
| Rg 误差 (实空间) rg_real_error | 1.90 Å |
| I(0) (实空间) i0_real | 1.7080e+08 |
| I(0) 误差 (实空间) i0_real_error | 3.4610e+06 |
| Rg (倒空间) rg_reciprocal | 52.20 Å |
| I(0) (倒空间) i0_reciprocal | 170600000.0000 |
| 解质量估计 total_estimate | 0.5819 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 26.9 Å |
| 偏度 Skewness skewness | 0.104 |
| 峰度 Kurtosis kurtosis | -1.523 |
| 角度范围 angular_range | — – 0.1500 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 5037000.0000 |
| 实空间数据点数 n_real_points | 31 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.002; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.111; Smooth: 0.445 |
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) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1p3da1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.5 — MurCD N-terminal domain |
| 超家族 Superfamily superfamily | c.5.1 — MurCD N-terminal domain |
| 家族 Family family | c.5.1.1 — MurCD N-terminal domain |
| 结构域编号 domain_id | d1p3da2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.59 — MurD-like peptide ligases, peptide-binding domain |
| 超家族 Superfamily superfamily | c.59.1 — MurD-like peptide ligases, peptide-binding domain |
| 家族 Family family | c.59.1.1 — MurCDEF C-terminal domain |
| 结构域编号 domain_id | d1p3da3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.72 — Ribokinase-like |
| 超家族 Superfamily superfamily | c.72.2 — MurD-like peptide ligases, catalytic domain |
| 家族 Family family | c.72.2.1 — MurCDEF |
| 结构域编号 domain_id | d1p3db1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.5 — MurCD N-terminal domain |
| 超家族 Superfamily superfamily | c.5.1 — MurCD N-terminal domain |
| 家族 Family family | c.5.1.1 — MurCD N-terminal domain |
| 结构域编号 domain_id | d1p3db2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.59 — MurD-like peptide ligases, peptide-binding domain |
| 超家族 Superfamily superfamily | c.59.1 — MurD-like peptide ligases, peptide-binding domain |
| 家族 Family family | c.59.1.1 — MurCDEF C-terminal domain |
| 结构域编号 domain_id | d1p3db3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.72 — Ribokinase-like |
| 超家族 Superfamily superfamily | c.72.2 — MurD-like peptide ligases, catalytic domain |
| 家族 Family family | c.72.2.1 — MurCDEF |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 1p3dA01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1p3dA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Mur-like, catalytic domain |
| 结构域编号 domain_id | 1p3dA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 190 — Protein-Tyrosine Phosphatase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Mur ligase, C-terminal domain |
| 结构域编号 domain_id | 1p3dB01 |
| 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 | 720 — NAD(P)-binding Rossmann-like Domain |
| 结构域编号 domain_id | 1p3dB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1190 — UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase |
| 同源超家族 H-superfamily homologous superfamily | 10 — Mur-like, catalytic domain |
| 结构域编号 domain_id | 1p3dB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 90 — Alpha-Beta Complex |
| 拓扑 Topology topology | 190 — Protein-Tyrosine Phosphatase; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 20 — Mur ligase, C-terminal domain |