8gtd

Cryo-EM model of the marine siphophage vB_DshS-R4C portal-adaptor complex

Method: ELECTRON MICROSCOPY D_max: 163.3 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	8gtd
沉积日期 deposition_date	2022-09-08
结构标题 title	Cryo-EM model of the marine siphophage vB_DshS-R4C portal-adaptor complex
关键词 keywords	Marine bacteriophage, Cryo-EM, Siphophage, Portal protein, Adaptor protein, Head-to-tail interface, VIRUS; VIRUS
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	60.55 Å
回转半径 Rg (电子) rg_electron	59.85 Å
零角强度 I(0) i0	6378210000.00
分子量 molecular_weight	414670.0 kDa
排除体积 excluded_volume	407670 Å³
包络体积 envelope_volume	1256400 Å³
水化壳体积 shell_volume	167390 Å³
包络直径 envelope_diameter	172.5 Å
壳层 Rg shell_rg	69.12 Å
包络 Rg envelope_rg	56.72 Å
形状 Rg shape_rg	59.85 Å
总 Rg total_rg	60.01 Å
总原子数 total_atoms	29580
残基数 n_residues	7392
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	163.3 Å
Rg (实空间) rg_real	60.01 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	6.3780e+09
I(0) 误差 (实空间) i0_real_error	9.7300e+07
Rg (倒空间) rg_reciprocal	60.99 Å
I(0) (倒空间) i0_reciprocal	6388000000.0000
解质量估计 total_estimate	0.8446
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	81.6 Å
偏度 Skewness skewness	-0.005
峰度 Kurtosis kurtosis	-0.560
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1391000000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.992; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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 (2)

Entity 1 polymer

描述 description	Portal protein
分子量 formula_weight	60353.9 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,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	29580

MRFWPFSKTTNAATRAEPMVTRPDTAPRVRSYRAAKSDRIAGGFGVFPTTPRDELRREIRGLVGHSRHAAQNFDYARAYEMLTRRHVIGFNGIRLQMDVRDPGGKKDVAAGAQIESAWARWGKMKNSPTPCGRLSWWGVECQVATGIAREGGSFVRIHQGTNRGRFGFQVEPIPFDLLDLDLTGPTPGGGFVGIAREGGSFVRIHQGTNRGRFGFQVEPIPFDLLDLDLTGPTPGGGFVESGVEFDATDRVVAYHMWSAAMSEGHRPGARRRLRIPAAQMLYVLVPEEIGQALGVPRSATALRLMNLSEKFQESALTAANYGASNMVFFERAADNGVVTGPEDDAQIPIDQIEAGTLTELPPGVKAVSHNPAYPDAAVGPFLRQMGTSQAAGLGVSYETLTADLSGANFSSLRAGKGEEREEWRMLQRAVFEGLHDRVFSRWLPLAMLSGEVRLPLAKLDKFDAATWRPRGWPSVNPKDDATAHEKDLKNGVRTRTEICAERGRDFADVVAEAAAERQMMRDAGLDPDAPLRTSPPETPPDPGEEIEGKDT

Entity 2 polymer

描述 description	Head-to-tail joining protein
分子量 formula_weight	19249.6 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	M,N,O,P,Q,R,S,T,U,V,W,X

MTVSIHPPATLVAGDSWAWEAGAVFEDHPDPWAASYVLRPEAGGDPVTVSGGLEVLAPVFRLPASVTADLPPGEWTWFAVAVDATTDARAVLAQGRVTVIPDPLAGTEDRRTPARRILAAIEATLEGRATKDADTYSIEGRSITRTPLPDLLRLRAVYAEQVARETGRSPYRQRRVSF

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7. 引用文献 (1)

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分辨率 resolution	4.70 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	5844

fit	/app/data/saxs_computation/gt/8gtd/8gtd.fit
pddf	/app/data/pr_computation/gt/8gtd/8gtd.pr.out
profile	/app/data/saxs_computation/gt/8gtd/8gtd.dat

Cryo-EM model of the marine siphophage vB_DshS-R4C portal-adaptor complex

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 (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)