SAXSdb — 8vb2

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8vb2
沉积日期 deposition_date	2023-12-11
最后修订 last_revision	2024-10-23
结构标题 title	C4 pre-infection ejectosome of the mature bacteriophage PhiM1 particle
关键词 keywords	ejectosome, internal core, internal proteins, core, mature phage, 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	76.25 Å
回转半径 Rg (电子) rg_electron	75.69 Å
零角强度 I(0) i0	25483500000.00
分子量 molecular_weight	1309300.0 kDa
排除体积 excluded_volume	1618600 Å³
包络体积 envelope_volume	2762900 Å³
水化壳体积 shell_volume	282310 Å³
包络直径 envelope_diameter	219.0 Å
壳层 Rg shell_rg	89.60 Å
包络 Rg envelope_rg	72.65 Å
形状 Rg shape_rg	75.72 Å
总 Rg total_rg	75.71 Å
总原子数 total_atoms	92008
残基数 n_residues	12164
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	283.6 Å
Rg (实空间) rg_real	79.29 Å
Rg 误差 (实空间) rg_real_error	1.75 Å
I(0) (实空间) i0_real	2.5460e+10
I(0) 误差 (实空间) i0_real_error	5.3500e+08
Rg (倒空间) rg_reciprocal	77.82 Å
I(0) (倒空间) i0_reciprocal	25590000000.0000
解质量估计 total_estimate	0.8738
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	99.2 Å
偏度 Skewness skewness	0.450
峰度 Kurtosis kurtosis	0.627
角度范围 angular_range	— – 0.1000 Å⁻¹
当前正则化参数 α current_alpha	0.9623
最高正则化参数 α highest_alpha	4309000000.0000
实空间数据点数 n_real_points	21
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.595; Stabil: 0.895; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.948

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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	Tetrameric ejection protein (gp48)
分子量 formula_weight	135391.5 kDa
来源方法 src_method	nat
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	92008

MIHLRPDSTAYARSAAVSANPAVGGYVTPDNTVLEGQNPSALVQAMQKPVASVTDSFKATLSESIGAKALRGVEYASIPTEAGFEPSKALGDSVSQYTADELEFLSDARSSAELAQRRSQVQDTRNNYDAMGQNMLTTVAASMLDVDMVIGGGVGALSKVSRATRLAVGLSANAALLGTASYGGTITPLDVVGTSVGIAMSAIPGIRKVAKAEQVQQGAVRGGVNAAEDAAGTVVPPKDVTVPPVREVPEVQPIKTVADEDYPKIDIDTYSNKEHIEVGRTGGAKTGSLKTTVQNAVLAVTALGDDLPEGVRALGRALGASLEADADVPVVFRSRTGANAQARSAVITEAETGATRAEIFNPAVGGTLSDHVRGMSTYEKTILLHEAAHAKTGRSIRAVESGAVSDGVVYEAVQRIKEIQWYVKANVELPPLGKGAKYNVDYGLSDTHEFISQLFNSEHFRDALRSVKMPGSDGTLLSNLMKRVVTLFTGKAPEGNAFDATLQAFDNLLSQPTTPADVFLNAPKATPDLQSKVLQAPNVIEMNNKVMGALNRNFSLYERLKSFGYKASTLADQLVVDATGTEANSAAHHARAAHLASNVSIVQVDDAFRQALSADWPLVQRLRHPVLYREAQRDLSQKVYQQLAENHDRFLKGQSIQPSNDPRVNSMVDAFVNSNWAKDELARVKGAGINGADAVRESPYYLPRQHSGNKLNDFMRNNRQVTKDDIVGMYTEQFSRMFQQNGITPETARKLGAKMFDNMQDQAAHVQGYRQSIAGMSYDDIENTLEALGASDPTITAFLDAVKGSGEQANKVRNLRGRAEFDMTAQYTTKSGDMISPSMFVNNDVMGLMEGYSRRMSGRVGLAKAGFPDLRDAVKAIDEAAAEAQDPAAALHAFDNTMNQILGYPTGEDVPDILRSASIIGGALNLANSGIYQLADMSLMLQQFGITKTLKAFGSTAFGRNAMDVAKSAEFGSRLQDVIEARHVLSGKYRSVLTHLEDNRDIGSLGVAHRYVQQMGQGTRFVNGMEFIRRGQAKLVSGLIADTVDDAIAGNASAVTAMERFGLNQQLLDELRKATAANPDMRKWPDSVRMDIEAVTHNMADSIVLENRLGEIPAWMQFSSVGKVILPYMTFVAGAWNKILRRTAKLDGATGVAIALAYQMPLVTLSSATSIAISGKPVTPESVAQRALVQVPMMSWAGFAVDFWANGASNNLAALALVDRMHAAMSSIASGETNPESLIKAVPFLSILPGMRLMGASLADDDE

Entity 2 polymer

描述 description	Octameric ejection protein (gp49)
分子量 formula_weight	98011.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	8

聚合体 Polymer

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

MPVRQPTQGGVQVPGLTGYQSAGVAQPVYRAPQEEAQGVSQFWQNLLPASVKTAQAAQQTASAKGYLEGQQDSQQGREKQVRNFFTKEAYEQGYNSASVNSALASFQLGLQNTAQQYVNSGKTPEEFNVHVQQQTNQLLQEAGAQGLNLNDKDWQAWLGSVEHSRNTANASYQDLNLKRAAVLQEQSWGARGNAAIADFVTAQQSGDTEQALQNVNSFISSVTHDDSITAENKIKYTSQFVVNAFANANSTGDMQALTGYVQSLSEFKNMPTDVQTQIMGSAQQYYQQRASDESVQLYEYNSRVNSVTDYKTLNEAYPMAQYIGTVMQAVQQKKLSPGTGYGMVDAESQRRLKMQKAEQGQLAYTNGVTISDIAAGTGESLDKVKGELTKMYATIGQGYSGGGLQLMQRGLKSGAQDITGVGIEMMQQDAQSLSGIDWRNLKTDADGKPLYPAAVVGSLGNLQAAYQSALAAGNQVQANQLLSGLPDPVVYGIRQNVDARDLADVVGKRAQDIASGKVLALPANMPADVSITQADVTAGIFDLGLGKDARNRNMLGIQSWVFTSDADEKAAQARVSQVNSAMNNEYVYNQQRGSLPALVGDDLKSWLMGKVASRTVRVKDGTDNGALLVLPEVGDKQKVFGSTDNGIIESALTESVTNFKKQYPQATTVQMDYDPLTQELIFQGVNAENQLGTTRASIPAADFRNTVRGVQNTLTQNGSGTTQGNLNVPGAGFVSFNAGNSFGIQKNVVMGAVNQLVSYEGYTPSKGFSVLGVHPTTGAKLNEDKYVKQATDTPQVAADKFNMYLNDKVYPLVMPKMEQYKNLPGYIQNNIYNALVETTYHSGNSDVFDKYIQTALYGNVQEIPTFKDTPLFKDAGAGSRRNVDRYQLLGSLVTYRTNNPNLSK

Entity 3 polymer

描述 description	Ejection protein 3 (gp50)
分子量 formula_weight	21537.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	8

聚合体 Polymer

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

MIWMFAAAAAQMIQGGLQYAQDAKNQRRQNKADQKYNEAVRSASARQITEINTQRSVSRAQTAQALDAARRQGAGESSARNLQAAATDTMGASVEQNLQEVGVQLAAAEGNLMQNAELTELSLDSSVMNTVDQARNSIRELSNPLGTDWAATGSAVGQIGTSMVANKLGGQGWFGGNSGTQQPAPISQAAPPTRSNNLSTRLNV

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7. 引用文献 (1)

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分辨率 resolution	3.32 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	17729

fit	/app/data/saxs_computation/vb/8vb2/8vb2.fit
pddf	/app/data/pr_computation/vb/8vb2/8vb2.pr.out
profile	/app/data/saxs_computation/vb/8vb2/8vb2.dat

C4 pre-infection ejectosome of the mature bacteriophage PhiM1 particle

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)