1gg4
CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDPMURNAC-TRIPEPTIDE D-ALANYL-D-ALANINE-ADDING ENZYME (MURF) AT 2.3 ANGSTROM RESOLUTION
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 | 1gg4 |
| 沉积日期 deposition_date | 2000-07-12 |
| 结构标题 title | CRYSTAL STRUCTURE OF ESCHERICHIA COLI UDPMURNAC-TRIPEPTIDE D-ALANYL-D-ALANINE-ADDING ENZYME (MURF) AT 2.3 ANGSTROM RESOLUTION |
| 关键词 keywords | alpha/beta sheet, 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 | 36.26 Å |
| 回转半径 Rg (电子) rg_electron | 36.18 Å |
| 零角强度 I(0) i0 | 136832000.00 |
| 分子量 molecular_weight | 93126.0 kDa |
| 排除体积 excluded_volume | 116000 ų |
| 包络体积 envelope_volume | 150810 ų |
| 水化壳体积 shell_volume | 36965 ų |
| 包络直径 envelope_diameter | 120.9 Å |
| 壳层 Rg shell_rg | 39.77 Å |
| 包络 Rg envelope_rg | 36.01 Å |
| 形状 Rg shape_rg | 36.18 Å |
| 总 Rg total_rg | 36.39 Å |
| 总原子数 total_atoms | 6484 |
| 残基数 n_residues | 860 |
| 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 | 119.8 Å |
| Rg (实空间) rg_real | 36.34 Å |
| Rg 误差 (实空间) rg_real_error | 1.10 Å |
| I(0) (实空间) i0_real | 1.3680e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.6300e+06 |
| Rg (倒空间) rg_reciprocal | 36.29 Å |
| I(0) (倒空间) i0_reciprocal | 136800000.0000 |
| 解质量估计 total_estimate | 0.8781 |
| 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 | 46.3 Å |
| 偏度 Skewness skewness | 0.298 |
| 峰度 Kurtosis kurtosis | -0.514 |
| 角度范围 angular_range | — – 0.2200 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 13370000.0000 |
| 实空间数据点数 n_real_points | 45 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.909; Smooth: 0.795 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d1gg4a1 |
| 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 | d1gg4a3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.98 — MurF and HprK N-domain-like |
| 超家族 Superfamily superfamily | c.98.1 — MurE/MurF N-terminal domain |
| 家族 Family family | c.98.1.1 — MurE/MurF N-terminal domain |
| 结构域编号 domain_id | d1gg4a4 |
| 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 | d1gg4b1 |
| 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 | d1gg4b3 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.98 — MurF and HprK N-domain-like |
| 超家族 Superfamily superfamily | c.98.1 — MurE/MurF N-terminal domain |
| 家族 Family family | c.98.1.1 — MurE/MurF N-terminal domain |
| 结构域编号 domain_id | d1gg4b4 |
| 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 | 1gg4A01 |
| 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 | 1gg4A02 |
| 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 | 1gg4A03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — MurE/MurF, N-terminal domain |
| 结构域编号 domain_id | 1gg4B01 |
| 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 | 1gg4B02 |
| 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 | 1gg4B03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 1390 — Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 10 — MurE/MurF, N-terminal domain |