2i8c
Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies
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 | 2i8c |
| 沉积日期 deposition_date | 2006-09-01 |
| 结构标题 title | Allosteric inhibition of Staphylococcus aureus D-alanine:D-alanine ligase revealed by crystallographic studies |
| 关键词 keywords | d-alanine:d-alanine ligase, ADP complex, Staphylococcus aureus, LYASE; LYASE |
| 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 | 26.78 Å |
| 回转半径 Rg (电子) rg_electron | 25.59 Å |
| 零角强度 I(0) i0 | 102952000.00 |
| 分子量 molecular_weight | 79003.0 kDa |
| 排除体积 excluded_volume | 98693 ų |
| 包络体积 envelope_volume | 120760 ų |
| 水化壳体积 shell_volume | 37636 ų |
| 包络直径 envelope_diameter | 86.1 Å |
| 壳层 Rg shell_rg | 34.37 Å |
| 包络 Rg envelope_rg | 25.65 Å |
| 形状 Rg shape_rg | 25.61 Å |
| 总 Rg total_rg | 26.47 Å |
| 总原子数 total_atoms | 5561 |
| 残基数 n_residues | 692 |
| 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 | 80.3 Å |
| Rg (实空间) rg_real | 26.58 Å |
| Rg 误差 (实空间) rg_real_error | 0.41 Å |
| I(0) (实空间) i0_real | 1.0300e+08 |
| I(0) 误差 (实空间) i0_real_error | 1.1760e+06 |
| Rg (倒空间) rg_reciprocal | 26.64 Å |
| I(0) (倒空间) i0_reciprocal | 103000000.0000 |
| 解质量估计 total_estimate | 0.9056 |
| 解质量评级 solution_quality | EXCELLENT a EXCELLENT solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 35.4 Å |
| 偏度 Skewness skewness | 0.111 |
| 峰度 Kurtosis kurtosis | -0.493 |
| 角度范围 angular_range | — – 0.2950 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 47770000.0000 |
| 实空间数据点数 n_real_points | 60 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.937; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.984 |
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) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d2i8ca1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.30 — PreATP-grasp domain |
| 超家族 Superfamily superfamily | c.30.1 — PreATP-grasp domain |
| 家族 Family family | c.30.1.0 — automated matches |
| 结构域编号 domain_id | d2i8ca2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.142 — ATP-grasp |
| 超家族 Superfamily superfamily | d.142.1 — Glutathione synthetase ATP-binding domain-like |
| 家族 Family family | d.142.1.0 — automated matches |
| 结构域编号 domain_id | d2i8ca3 |
| 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 | d2i8cb1 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.30 — PreATP-grasp domain |
| 超家族 Superfamily superfamily | c.30.1 — PreATP-grasp domain |
| 家族 Family family | c.30.1.0 — automated matches |
| 结构域编号 domain_id | d2i8cb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.142 — ATP-grasp |
| 超家族 Superfamily superfamily | d.142.1 — Glutathione synthetase ATP-binding domain-like |
| 家族 Family family | d.142.1.0 — automated matches |
| 结构域编号 domain_id | d2i8cb3 |
| 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 | 2i8cA01 |
| 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 | 20 — |
| 结构域编号 domain_id | 2i8cA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 470 — D-amino Acid Aminotransferase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP-grasp fold, B domain |
| 结构域编号 domain_id | 2i8cA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP-grasp fold, A domain |
| 结构域编号 domain_id | 2i8cB01 |
| 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 | 20 — |
| 结构域编号 domain_id | 2i8cB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 470 — D-amino Acid Aminotransferase; Chain A, domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP-grasp fold, B domain |
| 结构域编号 domain_id | 2i8cB03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 1490 — Dna Ligase; domain 1 |
| 同源超家族 H-superfamily homologous superfamily | 20 — ATP-grasp fold, A domain |