SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
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| 条目编号 entry_id | 1jo3 |
| 沉积日期 deposition_date | 2001-07-26 |
| 结构标题 title | Gramicidin B in Sodium Dodecyl Sulfate Micelles (NMR) |
| 关键词 keywords | GRAMICIDIN, ANTIFUNGAL, ANTIBACTERIAL, MEMBRANE ION CHANNEL, LINEAR GRAMICIDIN, SDS MICELLES, ANTIBIOTIC; ANTIBIOTIC |
| 实验方法 method | SOLUTION NMR |
| 回转半径 Rg (Guinier) rg_guinier | 10.39 Å |
| 回转半径 Rg (电子) rg_electron | 9.48 Å |
| 零角强度 I(0) i0 | 221136.00 |
| 分子量 molecular_weight | 3701.0 kDa |
| 排除体积 excluded_volume | 5112 ų |
| 包络体积 envelope_volume | 5225 ų |
| 水化壳体积 shell_volume | 5262 ų |
| 包络直径 envelope_diameter | 31.6 Å |
| 壳层 Rg shell_rg | 13.88 Å |
| 包络 Rg envelope_rg | 9.79 Å |
| 形状 Rg shape_rg | 9.52 Å |
| 总 Rg total_rg | 11.30 Å |
| 总原子数 total_atoms | 544 |
| 残基数 n_residues | 16 |
| 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 |
| 最大尺寸 Dmax dmax | 35.3 Å |
| Rg (实空间) rg_real | 10.49 Å |
| Rg 误差 (实空间) rg_real_error | 0.38 Å |
| I(0) (实空间) i0_real | 2.2110e+05 |
| I(0) 误差 (实空间) i0_real_error | 2.6170e+03 |
| Rg (倒空间) rg_reciprocal | 10.48 Å |
| I(0) (倒空间) i0_reciprocal | 221100.0000 |
| 解质量估计 total_estimate | 0.8457 |
| 解质量评级 solution_quality |
GOOD
a GOOD solution
|
| P(r) 峰数 n_peaks | 2 |
| 主峰位置 r_peak_primary | 9.4 Å |
| 偏度 Skewness skewness | 0.484 |
| 峰度 Kurtosis kurtosis | -0.357 |
| 角度范围 angular_range | — – 0.5000 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 23660.0000 |
| 实空间数据点数 n_real_points | 80 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria |
AN1: 0.000;
Oscil: 0.814;
Stabil: 1.000;
Sysdev: 1.000;
Positv: 1.000;
Valcen: 0.608;
Smooth: 0.940
|
晶胞参数 Unit Cell
| 晶胞边长 a length_a | 1.000 Å |
| 晶胞边长 b length_b | 1.000 Å |
| 晶胞边长 c length_c | 1.000 Å |
| 晶胞夹角 α angle_alpha | 90.00 ° |
| 晶胞夹角 β angle_beta | 90.00 ° |
| 晶胞夹角 γ angle_gamma | 90.00 ° |
| 晶胞分子数 Z z_pdb | 1 |
对称性 Symmetry
| 空间群 space_group | P 1 |
| 空间群编号 int_tables_number | 1 |
| 晶系 crystal_system | — |
Entity 1
polymer
| 描述 description | GRAMICIDIN B |
| 分子量 formula_weight | 1843.3 kDa |
| 来源方法 src_method | nat |
| 拷贝数 entity_count | 2 |
聚合体 Polymer
| 聚合体类型 type | polypeptide(L) |
| 链编号 strand_id | A,B |
| 原子数 atom_count | 544 |
VGALAVVVWLFLWLWX
SCOP 2.08 (2 domains)
| 结构域编号 domain_id | d1jo3a_ |
| 类 Class class | j — Peptides |
| 折叠类型 Fold fold | j.1 — Membrane ion channel-forming peptide antibiotics containing D-aminoacids |
| 超家族 Superfamily superfamily | j.1.1 — Membrane ion channel-forming peptide antibiotics containing D-aminoacids |
| 家族 Family family | j.1.1.1 — Gramicidin |
| 结构域编号 domain_id | d1jo3b_ |
| 类 Class class | j — Peptides |
| 折叠类型 Fold fold | j.1 — Membrane ion channel-forming peptide antibiotics containing D-aminoacids |
| 超家族 Superfamily superfamily | j.1.1 — Membrane ion channel-forming peptide antibiotics containing D-aminoacids |
| 家族 Family family | j.1.1.1 — Gramicidin |
Structures of Gramicidins A, B, and C Incorporated Into Sodium Dodecyl Sulfate Micelles.
Biochemistry (2001)
Files (7)
- pr_distribution /app/data/pr_computation/jo/1jo3/pr_distribution.json
- pr_output /app/data/pr_computation/jo/1jo3/1jo3.pr.out
- pr_plot /app/data/visualization/pr_computation/jo/1jo3/1jo3_pr_distribution.png
- saxs_curve_dat /app/data/saxs_computation/jo/1jo3/1jo3.dat
- saxs_fit /app/data/saxs_computation/jo/1jo3/1jo3.fit
- saxs_log /app/data/saxs_computation/jo/1jo3/1jo3.log
- saxs_plot /app/data/visualization/saxs_computation/jo/1jo3/1jo3_saxs_profile.png
Curves (3)
| fit |
/app/data/saxs_computation/jo/1jo3/1jo3.fit |
| pddf |
/app/data/pr_computation/jo/1jo3/1jo3.pr.out |
| profile |
/app/data/saxs_computation/jo/1jo3/1jo3.dat |