9dne

Pseudosymmetric protein nanocage GI9-F7 (local refinement)

Method: ELECTRON MICROSCOPY D_max: 194.8 Å Quality: REASONABLE

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9dne
沉积日期 deposition_date	2024-09-17
结构标题 title	Pseudosymmetric protein nanocage GI9-F7 (local refinement)
关键词 keywords	;Fusion protein, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, pseudosymmetric protein nanocages, VIRAL PROTEIN ;; VIRAL 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	62.32 Å
回转半径 Rg (电子) rg_electron	62.84 Å
零角强度 I(0) i0	326344000.00
分子量 molecular_weight	160790.0 kDa
排除体积 excluded_volume	204600 Å³
包络体积 envelope_volume	334590 Å³
水化壳体积 shell_volume	47561 Å³
包络直径 envelope_diameter	210.6 Å
壳层 Rg shell_rg	56.87 Å
包络 Rg envelope_rg	60.61 Å
形状 Rg shape_rg	62.86 Å
总 Rg total_rg	62.61 Å
总原子数 total_atoms	11436
残基数 n_residues	1827
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/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
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	194.8 Å
Rg (实空间) rg_real	63.07 Å
Rg 误差 (实空间) rg_real_error	2.39 Å
I(0) (实空间) i0_real	3.2630e+08
I(0) 误差 (实空间) i0_real_error	7.3890e+06
Rg (倒空间) rg_reciprocal	61.61 Å
I(0) (倒空间) i0_reciprocal	325500000.0000
解质量估计 total_estimate	0.7199
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	39.0 Å
偏度 Skewness skewness	0.326
峰度 Kurtosis kurtosis	-0.797
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	12210000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.568; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.652; Smooth: 0.001

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (3)

Entity 1 polymer

描述 description	Pseudosymmetric protein nanocage GI9-F7 A chain
分子量 formula_weight	24331.0 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,A,H
原子数 atom_count	11436

GSHHHHHHGSEKAAKAEEAARKMEELFKEHKIVAVLRANSVEEAKKKALAVFLGGVHLIEITFTVPDADTVIKELSFLKEMGAIIGAGTVTSVEQCREAVESGAEFIVSPHLDEEISQFCKEEGVFYMPGVMTPTELYKAMKLGHTILKLFPGEVVGPQFVEAMKGPFPNVKFVPTGGVNLDNVCEWFEAGVLAVGVGSALVEGTPVEVAEKAKAFVEKIEGCTE

来源 Source

来源生物 organism	synthetic construct
NCBI 分类编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Pseudosymmetric protein nanocage GI9-F7 C chain
分子量 formula_weight	23530.3 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,E,G

MKMEELFKEHKIVAVLRANSREEAIEIALAVFAGGVHLIEITFTVPDADEVIKRLEMLKRAGAIIGAGTVTSVEQCREAVESGAEFIVSPHLDEEISQFCKEEGVFYMPGVMTPTELVKAMKLGHTILKLFPGEVVGPQFVEAMKGPFPNVKFVPTGGVNLDNVCEWFEAGVLAVGVGSALVEGKPSEVAEKARRFVKKIRGCTEGSLEHHHHHH

来源 Source

来源生物 organism	synthetic construct
NCBI 分类编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	Pseudosymmetric protein nanocage GI9-F7 B chain
分子量 formula_weight	22115.6 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,F,I

MKMEELFKEHKIVAVLRANSVEEAISKALAVFAGGVHLIEITFTVPDADQVIKELEFLKEAGAIIGAGTVTSVEQCREAVESGAEFIVSFHLDEEISQFCKEEGVFYMPGVMTPTELVKAMKLGHTILKLVPGEVVGPQFVEAMKGPFPNVKFVPTGGVNLDNVCEWFEAGVLAVGVGSALVEGEPAEVAELAIRFVEKIRGCTE

来源 Source

来源生物 organism	synthetic construct
NCBI 分类编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

▶

7. 引用文献 (1)

▶

分辨率 resolution	4.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	795360

fit	/app/data/saxs_computation/dn/9dne/9dne.fit
pddf	/app/data/pr_computation/dn/9dne/9dne.pr.out
profile	/app/data/saxs_computation/dn/9dne/9dne.dat

Pseudosymmetric protein nanocage GI9-F7 (local refinement)

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

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 polymer

聚合体 Polymer

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)