9i7w

;Extended and wrapped protein P7 dimers of dimers, the P1 layer and the RNA-dependent RNA polymerase P2 in transcribing particles of bacteriophage phi6 ;

Method: ELECTRON MICROSCOPY D_max: 205.1 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	9i7w
沉积日期 deposition_date	2025-02-03
结构标题 title	;Extended and wrapped protein P7 dimers of dimers, the P1 layer and the RNA-dependent RNA polymerase P2 in transcribing particles of bacteriophage phi6 ;
关键词 keywords	inner protein capsid, transcribing phi6 particle, localized reconstruction, 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	61.74 Å
回转半径 Rg (电子) rg_electron	62.02 Å
零角强度 I(0) i0	3620390000.00
分子量 molecular_weight	510060.0 kDa
排除体积 excluded_volume	640370 Å³
包络体积 envelope_volume	953480 Å³
水化壳体积 shell_volume	130800 Å³
包络直径 envelope_diameter	235.8 Å
壳层 Rg shell_rg	61.04 Å
包络 Rg envelope_rg	61.58 Å
形状 Rg shape_rg	62.02 Å
总 Rg total_rg	62.00 Å
总原子数 total_atoms	35915
残基数 n_residues	4612
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	205.1 Å
Rg (实空间) rg_real	61.92 Å
Rg 误差 (实空间) rg_real_error	1.39 Å
I(0) (实空间) i0_real	3.6190e+09
I(0) 误差 (实空间) i0_real_error	6.8730e+07
Rg (倒空间) rg_reciprocal	61.50 Å
I(0) (倒空间) i0_reciprocal	3617000000.0000
解质量估计 total_estimate	0.8529
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	73.8 Å
偏度 Skewness skewness	0.513
峰度 Kurtosis kurtosis	0.012
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0023
最高正则化参数 α highest_alpha	227900000.0000
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: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.565

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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	;DNA (5'-D(TPTPTPCP*C)-3') ;
分子量 formula_weight	1446.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	x
原子数 atom_count	35915

TTTCC

Entity 2 polymer

描述 description	RNA-directed RNA polymerase
分子量 formula_weight	74903.2 kDa
EC 编号 ec_number	2.7.7.48
来源方法 src_method	nat
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	U

PRRAPAFPLSDIKAQMLFANNIKAQQASKRSFKEGAIETYEGLLSVDPRFLSFKNELSRYLTDHFPANVDEYGRVYGNGVRTNFFGMRHMNGFPMIPATWPLASNLKKRADADLADGPVSERDNLLFRAAVRLMFSDLEPVPLKIRKGSSTCIPYFSNDMGTKIEIAERALEKAEEAGNLMLQGKFDDAYQLHQMGGAYYVVYRAQSTDAITLDPKTGKFVSKDRMVADFEYAVTGGEQGSLFAASKDASRLKEQYGIDVPDGFFCERRRTAMGGPFALNAPIMAVAQPVRNKIYSKYAYTFHHTTRLNKEEKVKEWSLCVATDVSDHDTFWPGWLRDLICDELLNMGYAPWWVKLFETSLKLPVYVGAPAPEQGHTLLGDPSNPDLEVGLSSGQGATDLMGTLLMSITYLVMQLDHTAPHLNSRIKDMPSACRFLDSYWQGHEEIRQISKSDDAMLGWTKGRALVGGHRLFEMLKEGKVNPSPYMKISYEHGGAFLGDILLYDSRREPGSAIFVGNINSMLNNQFSPEYGVQSGVRDRSKRKRPFPGLAWASMKDTYGACPIYSDVLEAIERCWWNAFGESYRAYREDMLKRDTLELSRYVASMARQAGLAELTPIDLEVLADPNKLQYKWTEADVSANIHEVLMHGVSVEKTERFLRSVMPR

Entity 3 polymer

描述 description	Nucleocapsid protein
分子量 formula_weight	12018.0 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	A,B,E,F,M,N,S,T

TLYLVPPLDSADKELPALASKAGVTLLEIEFLHELWPHLSGGQIVIAALNANNLAILNRHMSTLLVELPVAVMAVPGASYRSDWNMIAHALPSEDWITLSNKMLKSGLLAN

Entity 4 polymer

描述 description	Major inner protein P1
分子量 formula_weight	84783.4 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	V,W,X,Z

MFNLKVKDLNGSARGLTQAFAIGELKNQLSVGALQLPLQFTRTFSASMTSELLWEVGKGNIDPVMYARLFFQYAQAGGALSVDELVNQFTEYHQSTACNPEIWRKLTAYITGSSNRAIKADAVGKVPPTAILEQLRTLAPSEHELFHHITTDFVCHVLSPLGFILPDAAYVYRVGRTATYPNFYALVDCVRASDLRRMLTALSSVDSKMLQATFKAKGALAPALISQHLANAATTAFERSRGNFDANAVVSSVLTILGRLWSPSTPKELDPSARLRNTNGIDQLRSNLALFIAYQDMVKQRGRAEVIFSDEELSSTIIPWFIEAMSEVSPFKLRPINETTSYIGQTSAIDHMGQPSHVVVYEDWQFAKEITAFTPVKLANNSNQRFLDVEPGISDRMSATLAPIGNTFAVSAFVKNRTAVYEAVSQRGTVNSNGAEMTLGFPSVVERDYALDRDPMVAIAALRTGIVDESLEARASNDLKRSMFNYYAAVMHYAVAHNPEVVVSEHQGVAAEQGSLYLVWNVRTELRIPVGYNAIEGGSIRTPEPLEAIAYNKPIQPSEVLQAKVLDLANHTTSIHIWPWHEASTEFAYEDAYSVTIRNKRYTAEVKEFELLGLGQRRERVRILKPTVAHAIIQMWYSWFVEDDRTLAAARRTSRDDAEKLAIDGRRMQNAVTLLRKIEMIGTTGIGASAVHLAQSRIVDQMAGRGLIDDSSDLHVGINRHRIRIWAGLAVLQMMGLLSRSEAEALTKVLGDSNALGMVVATTDID

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7. 引用文献 (1)

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分辨率 resolution	4.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	18230

fit	/app/data/saxs_computation/i7/9i7w/9i7w.fit
pddf	/app/data/pr_computation/i7/9i7w/9i7w.pr.out
profile	/app/data/saxs_computation/i7/9i7w/9i7w.dat

;Extended and wrapped protein P7 dimers of dimers, the P1 layer and the RNA-dependent RNA polymerase P2 in transcribing particles of bacteriophage phi6 ;

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

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)