9b40

Pseudomonas phage Pa193 5-fold vertex (capsid, decorating, and scaffolding proteins)

Method: ELECTRON MICROSCOPY D_max: 226.5 Å Quality: GOOD

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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9b40
沉积日期 deposition_date	2024-03-20
最后修订 last_revision	2024-10-16
结构标题 title	Pseudomonas phage Pa193 5-fold vertex (capsid, decorating, and scaffolding proteins)
关键词 keywords	;phage, bacteriophage, gene product 24 (gp24), STRUCTURAL PROTEIN, VIRAL PROTEIN, gene product 25 (gp25), scaffolding protein, decorating protein, major capsid protein, gene product 26 (gp26) ;; VIRAL 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	73.05 Å
回转半径 Rg (电子) rg_electron	73.56 Å
零角强度 I(0) i0	3003690000.00
分子量 molecular_weight	466960.0 kDa
排除体积 excluded_volume	585520 Å³
包络体积 envelope_volume	898630 Å³
水化壳体积 shell_volume	103130 Å³
包络直径 envelope_diameter	290.6 Å
壳层 Rg shell_rg	67.46 Å
包络 Rg envelope_rg	74.86 Å
形状 Rg shape_rg	73.56 Å
总 Rg total_rg	73.46 Å
总原子数 total_atoms	32946
残基数 n_residues	4325
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	226.5 Å
Rg (实空间) rg_real	73.12 Å
Rg 误差 (实空间) rg_real_error	1.53 Å
I(0) (实空间) i0_real	2.9970e+09
I(0) 误差 (实空间) i0_real_error	5.9850e+07
Rg (倒空间) rg_reciprocal	71.31 Å
I(0) (倒空间) i0_reciprocal	2991000000.0000
解质量估计 total_estimate	0.8350
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	64.7 Å
偏度 Skewness skewness	0.447
峰度 Kurtosis kurtosis	-0.513
角度范围 angular_range	— – 0.1050 Å⁻¹
当前正则化参数 α current_alpha	0.0569
最高正则化参数 α highest_alpha	109900000.0000
实空间数据点数 n_real_points	22
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.950; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.014

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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 (3)

Entity 1 polymer

描述 description	gp26 Major capsid
分子量 formula_weight	41610.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	11

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,N,O,P,Q,R,S
原子数 atom_count	32946

MSQISKTHSRLAGRNAKPFDLKNITNDAVASLSRIGLVFDHAVVQDQIKALAKAGAFRSGSAMDSNFTAPVTTPSIPTPIQFLQTWLPGFVKVMTAARKIDEIIGIDTVGSWEDQEIVQGIVEPAGTAVEYGDHTNIPLTSWNANFERRTIVRGELGMMVGTLEEGRASAIRLNSAETKRQQAAIGLEIFRNAIGFYGWQSGLGNRTYGFLNDPNLPAFQTPPSQGWSTADWAGIIGDIREAVRQLRIQSQDQIDPKAEKITLALATSKVDYLSVTTPYGISVSDWIEQTYPKMRIVSAPELSGVQMKAQEPEDALVLFVEDVNAAVDGSTDGGSVFSQLVQSKFITLGVEKRAKSYVEDFSNGTAGALCKRPWAVVRYLGI

Entity 2 polymer

描述 description	gp25 Decorating protein
分子量 formula_weight	21677.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	K,L,M

MFQKQVYRQYTPGFPGDLIEDGPKRARPGRIMSLSAVNPAATATGPNRISRAFGYAGDVSALGEGQPKTIAARASEVVIGGANFFGVLGHPKHYALFGSAGDSLAPSYDLPDGAEGEFFDMATGLVVEIFNGAATALDLDYGDLVAYVPNNLPTADNALGLPAGALVGFKAGSMPTGLVQIPNARIVNAISLPAQSAGNLVAGVTIVQLTQ

Entity 3 polymer

描述 description	gp24 Scaffolding protein
分子量 formula_weight	51908.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	5

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G,F,H,I,J

MAKSKRKIDENGYMTIEGCPISSYGVFQYSAGQLGLPGDPMRIVNVYRPESAVSDPEYIESLKNLPLIDEHEMLSGFDDDDDSVAPEDKGVEGIITSNAYYEAPWARGDIRIYSRNMQNQLERGKEDLSLGYSCRYTEQPGIWNGTPYEVVQDKMRGNHIALVKEGRVPGARVLDGLCFDHLSFDFRPSDEGNEMSLKKAKQKPPVQRVGQAADSAVEELRALWPKLSASVQKFLGEEAQEPEHQEGAAAPAEPTDSEHMTEHPTLEGAQKDNEEHEEAPSVVDPAVAAAESERQESAASEMSGEGEVAELISQVKAILARLEGTAAEGADEEHGEGKDVVEGLEEQSSLSGSQTASDDGGEGKDNSEELPEMAQKNAQDAAIRGLYRDIAAKDRLYKRLSSVVGAFDHRAMDSAEVAVYGVKKLNINCAKGQEALALDMYLKGVEASRGAASRQSKAQDSAGSAPQCAELDSYLKGE

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7. 引用文献 (1)

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分辨率 resolution	2.90 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	8278

fit	/app/data/saxs_computation/b4/9b40/9b40.fit
pddf	/app/data/pr_computation/b4/9b40/9b40.pr.out
profile	/app/data/saxs_computation/b4/9b40/9b40.dat

Pseudomonas phage Pa193 5-fold vertex (capsid, decorating, and scaffolding proteins)

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

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)