1oyd
Structural Basis of Multiple Binding Capacity of the AcrB multidrug Efflux Pump
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 | 1oyd |
| 沉积日期 deposition_date | 2003-04-03 |
| 结构标题 title | Structural Basis of Multiple Binding Capacity of the AcrB multidrug Efflux Pump |
| 关键词 keywords | MEMBRANE PROTEIN; MEMBRANE PROTEIN |
| 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 | 36.82 Å |
| 回转半径 Rg (电子) rg_electron | 36.91 Å |
| 零角强度 I(0) i0 | 167410000.00 |
| 分子量 molecular_weight | 109100.0 kDa |
| 排除体积 excluded_volume | 138810 ų |
| 包络体积 envelope_volume | 185710 ų |
| 水化壳体积 shell_volume | 44413 ų |
| 包络直径 envelope_diameter | 133.2 Å |
| 壳层 Rg shell_rg | 40.05 Å |
| 包络 Rg envelope_rg | 37.06 Å |
| 形状 Rg shape_rg | 36.91 Å |
| 总 Rg total_rg | 37.17 Å |
| 总原子数 total_atoms | 7673 |
| 残基数 n_residues | 1006 |
| 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 | 126.9 Å |
| Rg (实空间) rg_real | 37.18 Å |
| Rg 误差 (实空间) rg_real_error | 1.21 Å |
| I(0) (实空间) i0_real | 1.6740e+08 |
| I(0) 误差 (实空间) i0_real_error | 2.8700e+06 |
| Rg (倒空间) rg_reciprocal | 36.96 Å |
| I(0) (倒空间) i0_reciprocal | 167400000.0000 |
| 解质量估计 total_estimate | 0.8094 |
| 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 | 35.4 Å |
| 偏度 Skewness skewness | 0.605 |
| 峰度 Kurtosis kurtosis | -0.117 |
| 角度范围 angular_range | — – 0.2150 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 27360000.0000 |
| 实空间数据点数 n_real_points | 44 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.721; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.799; Smooth: 0.557 |
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) 16 domains
SCOP 2.08 (8 domains)
| 结构域编号 domain_id | d1oyda1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains |
| 家族 Family family | d.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains |
| 结构域编号 domain_id | d1oyda2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains |
| 家族 Family family | d.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains |
| 结构域编号 domain_id | d1oyda3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains |
| 家族 Family family | d.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains |
| 结构域编号 domain_id | d1oyda4 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.58 — Ferredoxin-like |
| 超家族 Superfamily superfamily | d.58.44 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains |
| 家族 Family family | d.58.44.1 — Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains |
| 结构域编号 domain_id | d1oyda5 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.225 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains |
| 超家族 Superfamily superfamily | d.225.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains |
| 家族 Family family | d.225.1.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains |
| 结构域编号 domain_id | d1oyda6 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.225 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains |
| 超家族 Superfamily superfamily | d.225.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains |
| 家族 Family family | d.225.1.1 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains |
| 结构域编号 domain_id | d1oyda7 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.35 — Multidrug efflux transporter AcrB transmembrane domain |
| 超家族 Superfamily superfamily | f.35.1 — Multidrug efflux transporter AcrB transmembrane domain |
| 家族 Family family | f.35.1.1 — Multidrug efflux transporter AcrB transmembrane domain |
| 结构域编号 domain_id | d1oyda8 |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.35 — Multidrug efflux transporter AcrB transmembrane domain |
| 超家族 Superfamily superfamily | f.35.1 — Multidrug efflux transporter AcrB transmembrane domain |
| 家族 Family family | f.35.1.1 — Multidrug efflux transporter AcrB transmembrane domain |
CATH v4.4 (8 domains)
| 结构域编号 domain_id | 1oydA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1640 — Multidrug efflux transporter AcrB transmembrane fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — Multidrug efflux transporter AcrB transmembrane domain |
| 结构域编号 domain_id | 1oydA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 1430 — Multidrug efflux transporter AcrB pore domain |
| 结构域编号 domain_id | 1oydA03 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 1320 — Multidrug efflux transporter AcrB pore domain like |
| 结构域编号 domain_id | 1oydA04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains |
| 同源超家族 H-superfamily homologous superfamily | 10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains |
| 结构域编号 domain_id | 1oydA05 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1640 — Multidrug efflux transporter AcrB transmembrane fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — Multidrug efflux transporter AcrB transmembrane domain |
| 结构域编号 domain_id | 1oydA06 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 1430 — Multidrug efflux transporter AcrB pore domain |
| 结构域编号 domain_id | 1oydA07 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 70 — Alpha-Beta Plaits |
| 同源超家族 H-superfamily homologous superfamily | 1440 — Multidrug efflux transporter AcrB pore domain |
| 结构域编号 domain_id | 1oydA08 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 2090 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains |
| 同源超家族 H-superfamily homologous superfamily | 10 — Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains |