8vxa

Structure of HamB-DNA complex, conformation 1, from the Escherichia coli Hachiman defense system

Method: ELECTRON MICROSCOPY D_max: 106.0 Å Quality: EXCELLENT

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	8vxa
沉积日期 deposition_date	2024-02-03
结构标题 title	Structure of HamB-DNA complex, conformation 1, from the Escherichia coli Hachiman defense system
关键词 keywords	Helicase-DNA complex, antiphage defense system, IMMUNE SYSTEM, IMMUNE SYSTEM-DNA complex; IMMUNE SYSTEM/DNA
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	33.65 Å
回转半径 Rg (电子) rg_electron	32.52 Å
零角强度 I(0) i0	299930000.00
分子量 molecular_weight	134230.0 kDa
排除体积 excluded_volume	165970 Å³
包络体积 envelope_volume	209400 Å³
水化壳体积 shell_volume	51889 Å³
包络直径 envelope_diameter	110.8 Å
壳层 Rg shell_rg	40.88 Å
包络 Rg envelope_rg	32.50 Å
形状 Rg shape_rg	32.50 Å
总 Rg total_rg	33.17 Å
总原子数 total_atoms	9431
残基数 n_residues	1163
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	106.0 Å
Rg (实空间) rg_real	33.50 Å
Rg 误差 (实空间) rg_real_error	0.56 Å
I(0) (实空间) i0_real	2.9990e+08
I(0) 误差 (实空间) i0_real_error	4.5800e+06
Rg (倒空间) rg_reciprocal	33.60 Å
I(0) (倒空间) i0_reciprocal	300000000.0000
解质量估计 total_estimate	0.9006
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	42.8 Å
偏度 Skewness skewness	0.157
峰度 Kurtosis kurtosis	-0.494
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0002
最高正则化参数 α highest_alpha	64920000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.952

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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	DNA (40-MER)
分子量 formula_weight	12154.8 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	B,C
原子数 atom_count	9431

TCGTCACCAGTACAAACTACAACGCCTGTAGCATTCCACA

Entity 2 polymer

描述 description	HamB
分子量 formula_weight	130898.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

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

MPATADEIIEAIKEASAVGFRGRLIARGQARSVIWRDGDLPPDAPEFSALLSQDLQGYAYALIDLGLRLRELNGDDAYARIAFEQAGTALESAIAKGKRDSRDTDFHFVMAAASYHLAHLSARAYSLLAMVGQDDNFSPIERALTQLIRRDLRTLRDNALGFRLRGDGSDVKITEILQARLNLPQDENGDSESEEDILFDGLDLALTDAYMSAISLYLLAVERGESRLLSRAIEKLRISLSICAQFNMLPQWWLNFITIHLLSDLWSDTFHERLPLVPVGGDAAEWPALRELFIALLQRRPRAEIDLWPSQREAAGRSVNDNDDLVVSLPTSAGKTRIAELCILRCLAGGKRVVFITPLRALSAQTEATLSRTFGPLGKTISMLYGSIGVSGMDEDAIRQRDIVVATPEKLDFALRNDPSIINDVGLFIFDEGHMIGADEREVRYEVQIQRLLRRQDADTRRIVCLSAILPDGEQLDDFAGWLRRDKPGGPIKNNWRPTRLQFGEVIWSAPAGRLNLSVGYEAAWVSRFIVSRQPPKVKLPNKKQRTKMFPSDNKELCLATAWRLIEDGQTVLIYCPLRRSVEPFAETIVDLHQRGLLPSLFDAAPDILDTAISLGEEWLGAHSPILACLRLGVALHHGALPTAYRKEIERLLRDGVLKVTISSPTLAQGLNLSATAIVMHSLHRNRELIKVSEFRNVIGRAGRAYVDVEGLVIYPIFDKVNKRQTNWHTLTSDTGAREMESGLIQLVCVLLIRMHTRLGGDLKALTEYVTNNAVAWEFPEIMTESPQERDIAQAIWEKQLSTLDTAILSLLGENDIPDDQIETALDDILQSSLWQRSLQRYRDENERILLKSGLLSRSRYIWQRSTAAGRRGYFLSGVGLTTGLRLDAIAAKANQLLIDANAAIMGGDAEEAIAAITALAEEVFTFYPFIPDPLPGDWRGILRSWLLGEPMTNVANTQASETLQFVENGLVYRLPWAMEAIRVRATANGDLIGDTDTTLDDYELGFAVAAVETGTLSRSSSLLIQAGFSSRLAAIKVVTDTTADFQSGQELRRWLNSEEVISHTDNHDWPTPETRVMWLEFLGSLSPKGSQVWSRHRYNGMVDWRDTPAVIGTPLQLYTVDGIHHVLADDGTPLGSINGRINTNRRGLLRVEVDDENGRAMFDYLGPDDFIST

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21

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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	2.79 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	239111

fit	/app/data/saxs_computation/vx/8vxa/8vxa.fit
pddf	/app/data/pr_computation/vx/8vxa/8vxa.pr.out
profile	/app/data/saxs_computation/vx/8vxa/8vxa.dat

Structure of HamB-DNA complex, conformation 1, from the Escherichia coli Hachiman defense system

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

来源 Source

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)