1yc9
The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 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 | 1yc9 |
| 沉积日期 deposition_date | 2004-12-22 |
| 结构标题 title | The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 resolution |
| 关键词 keywords | Vibrio cholerae, outer membrane protein, multidrug resistance, 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 | 36.58 Å |
| 回转半径 Rg (电子) rg_electron | 37.99 Å |
| 零角强度 I(0) i0 | 34048600.00 |
| 分子量 molecular_weight | 44911.0 kDa |
| 排除体积 excluded_volume | 55563 ų |
| 包络体积 envelope_volume | 85241 ų |
| 水化壳体积 shell_volume | 21948 ų |
| 包络直径 envelope_diameter | 139.0 Å |
| 壳层 Rg shell_rg | 36.28 Å |
| 包络 Rg envelope_rg | 39.18 Å |
| 形状 Rg shape_rg | 38.14 Å |
| 总 Rg total_rg | 37.38 Å |
| 总原子数 total_atoms | 3147 |
| 残基数 n_residues | 411 |
| 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 | 131.6 Å |
| Rg (实空间) rg_real | 37.49 Å |
| Rg 误差 (实空间) rg_real_error | 1.80 Å |
| I(0) (实空间) i0_real | 3.4050e+07 |
| I(0) 误差 (实空间) i0_real_error | 6.0340e+05 |
| Rg (倒空间) rg_reciprocal | 36.93 Å |
| I(0) (倒空间) i0_reciprocal | 34030000.0000 |
| 解质量估计 total_estimate | 0.6899 |
| 解质量评级 solution_quality | REASONABLE a REASONABLE solution |
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 24.5 Å |
| 偏度 Skewness skewness | 0.719 |
| 峰度 Kurtosis kurtosis | -0.090 |
| 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 | 1597000.0000 |
| 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: 0.511; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.134; Smooth: 0.298 |
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) 3 domains
SCOP 2.08 (1 domains)
| 结构域编号 domain_id | d1yc9a_ |
| 类 Class class | f — Membrane and cell surface proteins and peptides |
| 折叠类型 Fold fold | f.5 — Outer membrane efflux proteins (OEP) |
| 超家族 Superfamily superfamily | f.5.1 — Outer membrane efflux proteins (OEP) |
| 家族 Family family | f.5.1.0 — automated matches |
CATH v4.4 (2 domains)
| 结构域编号 domain_id | 1yc9A01 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 1600 — Outer membrane efflux proteins (OEP) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Outer membrane efflux proteins (OEP) |
| 结构域编号 domain_id | 1yc9A02 |
| 类 Class class | 2 — Mainly Beta |
| 架构 Architecture architecture | 20 — Single Sheet |
| 拓扑 Topology topology | 200 — Outer membrane efflux proteins (OEP) |
| 同源超家族 H-superfamily homologous superfamily | 10 — Outer membrane efflux proteins (OEP) |