8f6j
Cryo-EM structure of a Zinc-loaded D287A mutant of the YiiP-Fab complex
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 | 8f6j |
| 沉积日期 deposition_date | 2022-11-16 |
| 结构标题 title | Cryo-EM structure of a Zinc-loaded D287A mutant of the YiiP-Fab complex |
| 关键词 keywords | Zinc transporter, cation diffusion facilitator, membrane protein, transport protein; TRANSPORT PROTEIN |
| 实验方法 method | ELECTRON MICROSCOPY |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 48.16 Å |
| 回转半径 Rg (电子) rg_electron | 49.34 Å |
| 零角强度 I(0) i0 | 315730000.00 |
| 分子量 molecular_weight | 148770.0 kDa |
| 排除体积 excluded_volume | 187120 ų |
| 包络体积 envelope_volume | 271600 ų |
| 水化壳体积 shell_volume | 49752 ų |
| 包络直径 envelope_diameter | 158.8 Å |
| 壳层 Rg shell_rg | 46.90 Å |
| 包络 Rg envelope_rg | 49.36 Å |
| 形状 Rg shape_rg | 49.35 Å |
| 总 Rg total_rg | 49.19 Å |
| 总原子数 total_atoms | 10472 |
| 残基数 n_residues | 1366 |
| 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 | 144.4 Å |
| Rg (实空间) rg_real | 48.39 Å |
| Rg 误差 (实空间) rg_real_error | 1.35 Å |
| I(0) (实空间) i0_real | 3.1570e+08 |
| I(0) 误差 (实空间) i0_real_error | 6.2230e+06 |
| Rg (倒空间) rg_reciprocal | 48.16 Å |
| I(0) (倒空间) i0_reciprocal | 315600000.0000 |
| 解质量估计 total_estimate | 0.6117 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 39.4 Å |
| 偏度 Skewness skewness | 0.254 |
| 峰度 Kurtosis kurtosis | -0.781 |
| 角度范围 angular_range | — – 0.1650 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 16930000.0000 |
| 实空间数据点数 n_real_points | 34 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.971; Stabil: 1.000; Sysdev: 0.044; Positv: 1.000; Valcen: 0.902; Smooth: 0.001 |
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) 10 domains
CATH v4.4 (10 domains)
| 结构域编号 domain_id | 8f6jA01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1510 — Alpha-lytic protease prodomain-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cation efflux protein transmembrane domain |
| 结构域编号 domain_id | 8f6jA02 |
| 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 | 1350 — Cation efflux protein, cytoplasmic domain |
| 结构域编号 domain_id | 8f6jB01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1510 — Alpha-lytic protease prodomain-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Cation efflux protein transmembrane domain |
| 结构域编号 domain_id | 8f6jB02 |
| 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 | 1350 — Cation efflux protein, cytoplasmic domain |
| 结构域编号 domain_id | 8f6jC01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 8f6jD01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 8f6jD02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 8f6jE01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 8f6jF01 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |
| 结构域编号 domain_id | 8f6jF02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 60 — Sandwich |
| 拓扑 Topology topology | 40 — Immunoglobulin-like |
| 同源超家族 H-superfamily homologous superfamily | 10 — Immunoglobulins |