SAXSdb — 9dze

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9dze
沉积日期 deposition_date	2024-10-16
结构标题 title	Computationally Designed Bifaceted Protein Nanomaterial pD5-14
关键词 keywords	nanomaterial, 4 component, bifaceted, penton, DE NOVO PROTEIN; DE NOVO PROTEIN
实验方法 method	ELECTRON MICROSCOPY

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

回转半径 Rg (Guinier) rg_guinier	— Å
回转半径 Rg (电子) rg_electron	117.10 Å
零角强度 I(0) i0	7705480000.00
分子量 molecular_weight	631190.0 kDa
排除体积 excluded_volume	737880 Å³
包络体积 envelope_volume	2819800 Å³
水化壳体积 shell_volume	208290 Å³
包络直径 envelope_diameter	285.7 Å
壳层 Rg shell_rg	125.10 Å
包络 Rg envelope_rg	98.35 Å
形状 Rg shape_rg	117.10 Å
总 Rg total_rg	117.10 Å
总原子数 total_atoms	44930
残基数 n_residues	9060
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

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

最大尺寸 Dmax dmax	265.6 Å
Rg (实空间) rg_real	116.50 Å
Rg 误差 (实空间) rg_real_error	0.38 Å
I(0) (实空间) i0_real	7.5720e+09
I(0) 误差 (实空间) i0_real_error	1.4050e+08
Rg (倒空间) rg_reciprocal	126.30 Å
I(0) (倒空间) i0_reciprocal	7937000000.0000
解质量估计 total_estimate	0.7656
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	183.9 Å
偏度 Skewness skewness	-0.421
峰度 Kurtosis kurtosis	-0.666
角度范围 angular_range	— – 0.0650 Å⁻¹
当前正则化参数 α current_alpha	0.4653
最高正则化参数 α highest_alpha	355800000.0000
实空间数据点数 n_real_points	14
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 0.984; Sysdev: 1.000; Positv: 1.000; Valcen: 0.021; Smooth: 0.000

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

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5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	pD5-14 A component
分子量 formula_weight	35302.1 kDa
来源方法 src_method	man
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J
原子数 atom_count	44930

MGSLELALKALQILVNAAYVLAEIARDRGNEELLEKAARLAEEAARQAERIARQARKEGNLELALKALQILVNAAYVLAEIARDRGNEELLEYAARLAEEAARQAIEIWAQAMEEGNQQLRTKAAHIILRAAEVLLEIARDRGNQELLEKAASLVDAVAALQQAAAAILEGDVEKAVRAAQEAVKAAKEAGDNDMLRAVAIAALRIAKEAEKQGNVEVAVKAARVAVEAAKQAGDNDVLRKVAEQALRIAKEAEKQGNVEVAVKAARVAVEAAKQAGDNDVLRKVADQALEIAKAALEQGDIDVAQKAMDVAVEALTQAGGSGGSHHHHHH

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	pD5-14 B component
分子量 formula_weight	34050.8 kDa
来源方法 src_method	man
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	K,L,M,N,O,P,Q,R,S,T

MGSPRLVLRALENMVRAAHTLAEIARDNGNEEWLERAARLAEEVARRAERLAREARKEGNLELALKALQILVNAAYVLAEIARDRGNEEELEYAARLAEEAARQAIEIAAQAMEEGNLELALKALQIIVNAAYVLAEIARDRGNEELLEKAASLAEAAAALAEAIAAILEGDVEKAVRAAQEAVKAAKEAGDNDMLRAVAIAALRIAKEAEKQGNVEVAVKAARVAVEAAKQAGDNDVLRKVAEQALRIAKEAEKQGNVEVAVKAARVAVEAAKQAGDNDVLRKVAEQALEIAKKAAEQGDVGVMQKAMDVALRAAGQAG

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	pD5-14 C component
分子量 formula_weight	56306.8 kDa
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	a,b,c,d,e

MGSKGEAVIKEFMRFKVHMEGSMNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFSWDILSPQFMYGSRAFIKHPADIPDYYKQSFPEGFKWERVMNFEDGGAVTVTQDTSLEDGTLIYKVKLRGTNFPPDGPVMQKKTMGWEASTERLYPEDGVLKGDIKMALRLKDGGRYLADFKTTYKAKKPVQMPGAYNVDRKLDITSHNEDYTVVEQYERSEGRHSTGGMDELYKGSGSGPELFLQDLRSLVEAARILARLARQRGDEHALERAARWAEQAARQAERLARQARKEGNLELALKALQILVNAAYVLAEIARDRGNEELLEYAARLAEEAARQAIEIAAQAMEEGNFELALEALEIINEAARVLARIAHHRGNQELLEKAASLTHASAALSRAIAAILEGDVEKAVRAAQEAVKAAKEAGDNDMLRAVAIAALRIAKEAEKQGNVEVAVKAARVAVEAAKQAGDNDVLRLVSERALSIAASSVKQGNYEVKEKAIRVAKEANKQAG

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 4 polymer

描述 description	pD5-14 D component
分子量 formula_weight	56573.7 kDa
来源方法 src_method	man
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	f,g,h,i,j

MGSKGEEDNMASLPATHELHIFGSINGVDFDMVGQGTGNPNDGYEELNLKSTKGDLQFSPWILVPHIGYGFHQYLPYPDGMSPFQAAMVDGSGYQVHRTMQFEDGASLTVNYRYTYEGSHIKGEAQVKGTGFPADGPVMTNSLTAADWCRSKKTYPNDKTIISTFKWSYTTGNGKRYRSTARTTYTFAKPMAANYLKNQPMYVFRKTELKHSKTELNFKEWQKAFTDVMGMDELYKGSGSGPELFLQDLRSLVEAARILARLARQRGDEHALERAARWAEQAARQAERLARQARKEGNLELALKALQILVNAAYVLAEIARDRGNEELLEYAARLAEEAARQAIEIAAQAMEEGNFELALEALEIINEAARVLARIAHHRGNQELLEKAASLTHASAALSRAIAAILEGDVEKAVRAAQEAVKAAKEAGDNDMLRAVAIAALRIAKEAEKQGNVEVAVKAARVAVEAAKQAGDNDVLKRVSETLLSIAAEATKQGNSEVMEKAIRVSEEAEKQAG

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

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7. 引用文献 (1)

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分辨率 resolution	4.30 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	209004

fit	/app/data/saxs_computation/dz/9dze/9dze.fit
pddf	/app/data/pr_computation/dz/9dze/9dze.pr.out
profile	/app/data/saxs_computation/dz/9dze/9dze.dat

Computationally Designed Bifaceted Protein Nanomaterial pD5-14

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 (4)

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

Entity 4 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)