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Asymmetric structure of trimeric AcrB from Escherichia coli
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 | 2gif |
| 沉积日期 deposition_date | 2006-03-28 |
| 结构标题 title | Asymmetric structure of trimeric AcrB from Escherichia coli |
| 关键词 keywords | ;membrane protein, secondary transport, RND, antibiotic resistance, drug-efflux pump, alternating site mechanism, MEMBRANE PROTEIN-TRANSPORT PROTEIN COMPLEX ;; MEMBRANE PROTEIN/TRANSPORT 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 | 45.83 Å |
| 回转半径 Rg (电子) rg_electron | 45.18 Å |
| 零角强度 I(0) i0 | 1496110000.00 |
| 分子量 molecular_weight | 336280.0 kDa |
| 排除体积 excluded_volume | 427020 ų |
| 包络体积 envelope_volume | 567210 ų |
| 水化壳体积 shell_volume | 99186 ų |
| 包络直径 envelope_diameter | 145.6 Å |
| 壳层 Rg shell_rg | 54.04 Å |
| 包络 Rg envelope_rg | 44.42 Å |
| 形状 Rg shape_rg | 45.20 Å |
| 总 Rg total_rg | 45.47 Å |
| 总原子数 total_atoms | 23650 |
| 残基数 n_residues | 3108 |
| 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 | 142.1 Å |
| Rg (实空间) rg_real | 45.56 Å |
| Rg 误差 (实空间) rg_real_error | 0.80 Å |
| I(0) (实空间) i0_real | 1.4960e+09 |
| I(0) 误差 (实空间) i0_real_error | 2.6490e+07 |
| Rg (倒空间) rg_reciprocal | 45.83 Å |
| I(0) (倒空间) i0_reciprocal | 1497000000.0000 |
| 解质量估计 total_estimate | 0.8762 |
| 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 | 58.5 Å |
| 偏度 Skewness skewness | 0.151 |
| 峰度 Kurtosis kurtosis | -0.432 |
| 角度范围 angular_range | — – 0.1700 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 238400000.0000 |
| 实空间数据点数 n_real_points | 35 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.694 |
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) 24 domains
CATH v4.4 (24 domains)
| 结构域编号 domain_id | 2gifA01 |
| 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 | 2gifA02 |
| 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 | 2gifA03 |
| 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 | 2gifA04 |
| 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 | 2gifA05 |
| 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 | 2gifA06 |
| 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 | 2gifA07 |
| 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 | 2gifA08 |
| 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 | 2gifB01 |
| 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 | 2gifB02 |
| 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 | 2gifB03 |
| 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 | 2gifB04 |
| 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 | 2gifB05 |
| 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 | 2gifB06 |
| 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 | 2gifB07 |
| 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 | 2gifB08 |
| 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 | 2gifC01 |
| 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 | 2gifC02 |
| 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 | 2gifC03 |
| 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 | 2gifC04 |
| 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 | 2gifC05 |
| 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 | 2gifC06 |
| 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 | 2gifC07 |
| 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 | 2gifC08 |
| 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 |