SAXSdb — 8rk7

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8rk7
沉积日期 deposition_date	2023-12-23
结构标题 title	Baseplate of bacteriophage JBD30 computed in C3 symmetry
关键词 keywords	bacteriophage JBD30, virion, baseplate, distal tail protein, baseplate hub, baseplate upper protein, 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	57.74 Å
回转半径 Rg (电子) rg_electron	59.21 Å
零角强度 I(0) i0	435631000.00
分子量 molecular_weight	169570.0 kDa
排除体积 excluded_volume	211110 Å³
包络体积 envelope_volume	351100 Å³
水化壳体积 shell_volume	57433 Å³
包络直径 envelope_diameter	209.3 Å
壳层 Rg shell_rg	49.06 Å
包络 Rg envelope_rg	58.63 Å
形状 Rg shape_rg	59.22 Å
总 Rg total_rg	58.79 Å
总原子数 total_atoms	11959
残基数 n_residues	1553
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	190.7 Å
Rg (实空间) rg_real	58.68 Å
Rg 误差 (实空间) rg_real_error	2.38 Å
I(0) (实空间) i0_real	4.3560e+08
I(0) 误差 (实空间) i0_real_error	9.9010e+06
Rg (倒空间) rg_reciprocal	56.92 Å
I(0) (倒空间) i0_reciprocal	434400000.0000
解质量估计 total_estimate	0.7689
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	42.4 Å
偏度 Skewness skewness	0.633
峰度 Kurtosis kurtosis	-0.291
角度范围 angular_range	— – 0.1350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	18690000.0000
实空间数据点数 n_real_points	28
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.643; Smooth: 0.021

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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	DUF2163 domain-containing protein
分子量 formula_weight	29979.1 kDa
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	I
原子数 atom_count	11959

MSFNSRESSLADGQPVRLYQFSRGAIRWSYNSSDRDITYQNQIFRTVPGGITDNGIICSGDPQSDQFVITAPADLDVALLYKTRSPSDAIDLVVYDMHYGDAEAAVSWVGQIGDVDWPTVDSCRITCVSEDELMDQPGLTDTYCRTCTAIVGDHRCKVNLVPYRVTLTPQSVSAWVISSGVVAGYADGWFTGGYVEWQVDGDNYDRRFIEQHAGADLHILGGTEGIPAGGQLRVYPGCDGLAQTCDDKFSNLPNFRGFNAMQGKSPFDGDQVW

Entity 2 polymer

描述 description	Virion structural protein
分子量 formula_weight	62163.1 kDa
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	C

MATFPGFQVPKPVEGIVAGITPNIDALELNQDISLAAVAASTWGGAYGAHQPVEVIHSTYQAVHQSALEENYYNRLWLIPTAMELGNVVSTQIRPASVWNAYFSPRTLTAIDREAADGITLSGQASPPLGFAALEERTWTVSIGTDGPPVVNARIVWRLQGEPNLVLVITGNRIIAWTFAPDWGDSIVERLSASTNILQSESAVTQRRAMRLAPRREFDANMYAVDRERQLLDMTLFGWGARIWALPIWPDIQLLHQPLAAGSLGIPCDTAGLDFRDGGLAMLRGEDAFTYEVVEVKTVTASGLDLVRPVQAAWGTGSRLYPVRTAQLTEQPTLTRLTDTAQSARVSFLVMEPSAWPELMPATTYRGRPVLEQRPDESEDLTSSYQRLLSTLDNGSAIPRVTDVAGMALPVIGHRWIGMGRAERSAFRSLVYALRGQQKPLWVPTHADDLTLVATVSQLSTALDVRNIGYARFANGRPGRRDIRIELYDGTVYHRRILTSTELDADTERVAIDAALGRLVEPTDVARICFMALCSAASDVVEIEHVTDSEGVATAALTFKGVRDDEF

Entity 3 polymer

描述 description	Tip attachment protein J domain-containing protein
分子量 formula_weight	79898.8 kDa
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	M

MGAKPKAQTVGWRYYFDIHFALGKKVDEVCAIRASGKTAWKGSITSNGQVRINAPELFGGDKGEGGLDGTLDVLFGEEDQGVLPRLAAMLGGLVPAFRGVTTCFYSGLVTSVNPYPKKWEILRRGGNRLWDGNPWYPEKQFVWLADGQIKAMNPAHILYLVYTGRDFRGLARTRMDEASWRAAADTLYAEGFGLCFEWTRSDSFKNFCETVKSHIGAEVYPNRQTGQISIRLLRDDYNVADLPLFDEDSGLLEITQEKTGSTSLAPSQLIVKYIDQIDGAQRQIIVNNNAVAASQGRRSSEEIEFLGVPTGELAGRVGEREMRLKTTGLKRYKGVFDRRARSLNPGQPFLIRSTPRGIPETVVRVGRIEDNFLGDGKITLTVVQDQFNLPATTGVAPPPPGWTPPDRTPRAITVRRLIEAPYRELAGVIDPANLQLLDVSASYLAALAEAPTSLSQSYTLTDRVGSSGAFVDRGTGDWCPTGLLAAELPLAAGPNVVTLTNATRLEDVTVGQAAVVDDEIVRVDAVNYASGTVTLARGCADTVPAKHLAGARVWFYDTFEAVDETVYSQGVTLQARLLTNTSEGQLAPALAATDSLTLTGRQGKPYPPGQFRINGSAYPTKVYGALSVSWAKRDRIGQADQLIDTTVGNIGPEDGATVTLQVYSGTTLKRTYAGLTSSSWSYPLAEDMADGPLQDVRLVLRSVRDGIDSWQQHDITIERHGLGFRLGEELGGVSA

Entity 4 non-polymer

描述 description	FE (III) ION
分子量 formula_weight	55.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (2)

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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	4.46 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	1780

fit	/app/data/saxs_computation/rk/8rk7/8rk7.fit
pddf	/app/data/pr_computation/rk/8rk7/8rk7.pr.out
profile	/app/data/saxs_computation/rk/8rk7/8rk7.dat

Baseplate of bacteriophage JBD30 computed in C3 symmetry

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 (4)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 non-polymer

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)