8tvu

In situ cryo-EM structure of bacteriophage P22 portal protein: head-to-tail protein complex at 3.0A resolution

Method: ELECTRON MICROSCOPY D_max: 216.4 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	8tvu
沉积日期 deposition_date	2023-08-18
结构标题 title	In situ cryo-EM structure of bacteriophage P22 portal protein: head-to-tail protein complex at 3.0A resolution
关键词 keywords	;phage, bacteriophage, portal protein, head-to-tail protein, gene product 1 (gp1), gene product 4 (gp4, STRUCTURAL PROTEIN, VIRAL PROTEIN ;; 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	69.24 Å
回转半径 Rg (电子) rg_electron	68.55 Å
零角强度 I(0) i0	15297200000.00
分子量 molecular_weight	1034300.0 kDa
排除体积 excluded_volume	1286400 Å³
包络体积 envelope_volume	1939600 Å³
水化壳体积 shell_volume	224110 Å³
包络直径 envelope_diameter	235.5 Å
壳层 Rg shell_rg	79.10 Å
包络 Rg envelope_rg	66.17 Å
形状 Rg shape_rg	68.53 Å
总 Rg total_rg	68.75 Å
总原子数 total_atoms	72840
残基数 n_residues	9120
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	216.4 Å
Rg (实空间) rg_real	68.93 Å
Rg 误差 (实空间) rg_real_error	1.09 Å
I(0) (实空间) i0_real	1.5290e+10
I(0) 误差 (实空间) i0_real_error	2.9930e+08
Rg (倒空间) rg_reciprocal	70.19 Å
I(0) (倒空间) i0_reciprocal	15330000000.0000
解质量估计 total_estimate	0.8605
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	94.1 Å
偏度 Skewness skewness	0.095
峰度 Kurtosis kurtosis	-0.188
角度范围 angular_range	— – 0.1150 Å⁻¹
当前正则化参数 α current_alpha	0.0015
最高正则化参数 α highest_alpha	1219000000.0000
实空间数据点数 n_real_points	24
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.815

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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 (2)

Entity 1 polymer

描述 description	Portal protein
分子量 formula_weight	82829.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,D,F,H,J,L,N,P,R,T,W
原子数 atom_count	72840

MADNENRLESILSRFDADWTASDEARREAKNDLFFSRVSQWDDWLSQYTTLQYRGQFDVVRPVVRKLVSEMRQNPIDVLYRPKDGARPDAADVLMGMYRTDMRHNTAKIAVNIAVREQIEAGVGAWRLVTDYEDQSPTSNNQVIRREPIHSACSHVIWDSNSKLMDKSDARHCTVIHSMSQNGWEDFAEKYDLDADDIPSFQNPNDWVFPWLTQDTIQIAEFYEVVEKKETAFIYQDPVTGEPVSYFKRDIKDVIDDLADSGFIKIAERQIKRRRVYKSIITCTAVLKDKQLIAGEHIPIVPVFGEWGFVEDKEVYEGVVRLTKDGQRLRNMIMSFNADIVARTPKKKPFFWPEQIAGFEHMYDGNDDYPYYLLNRTDENSGDLPTQPLAYYENPEVPQANAYMLEAATSAVKEVATLGVDTEAVNGGQVAFDTVNQLNMRADLETYVFQDNLATAMRRDGEIYQSIVNDIYDVPRNVTITLEDGSEKDVQLMAEVVDLATGEKQVLNDIRGRYECYTDVGPSFQSMKQQNRAEILELLGKTPQGTPEYQLLLLQYFTLLDGKGVEMMRDYANKQLIQMGVKKPETPEEQQWLVEAQQAKQGQQDPAMVQAQGVLLQGQAELAKAQNQTLSLQIDAAKVEAQNQLNAARIAEIFNNMDLSKQSEFREFLKTVASFQQDRSEDARANAELLLKGDEQTHKQRMDIANILQSQRQNQPSGSVAETPQ

Entity 2 polymer

描述 description	Peptidoglycan hydrolase gp4
分子量 formula_weight	18045.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	a,C,E,G,I,K,M,O,Q,S,V,X

MQIKTKGDLVRAALRKLGVASDATLTDVEPQSMQDAVDDLEAMMAEWYQDGKGIITGYVFSDDENPPAEGDDHGLRSSAVSAVFHNLACRIAPDYALEATAKIIATAKYGKELLYKQTAISRAKRAPYPSRMPTGSGNSFANLNEWHYFPGEQNADSTTPHDEGNG

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7. 引用文献 (1)

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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	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	3.00 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	38151

fit	/app/data/saxs_computation/tv/8tvu/8tvu.fit
pddf	/app/data/pr_computation/tv/8tvu/8tvu.pr.out
profile	/app/data/saxs_computation/tv/8tvu/8tvu.dat

In situ cryo-EM structure of bacteriophage P22 portal protein: head-to-tail protein complex at 3.0A 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

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

晶胞参数 Unit Cell

对称性 Symmetry

冷冻电镜 EM 3D

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)