8k0q

The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 at symmetric pre-cleavage state

Method: ELECTRON MICROSCOPY D_max: 238.4 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	8k0q
沉积日期 deposition_date	2023-07-10
最后修订 last_revision	2024-05-15
结构标题 title	The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 at symmetric pre-cleavage state
关键词 keywords	ORF-less Group IIC intron, ribozymes, RNA; RNA
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	67.83 Å
回转半径 Rg (电子) rg_electron	67.99 Å
零角强度 I(0) i0	5562790000.00
分子量 molecular_weight	357240.0 kDa
排除体积 excluded_volume	332860 Å³
包络体积 envelope_volume	706000 Å³
水化壳体积 shell_volume	87664 Å³
包络直径 envelope_diameter	237.0 Å
壳层 Rg shell_rg	65.95 Å
包络 Rg envelope_rg	66.15 Å
形状 Rg shape_rg	67.96 Å
总 Rg total_rg	68.01 Å
总原子数 total_atoms	23586
残基数 n_residues	1100
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	238.4 Å
Rg (实空间) rg_real	67.95 Å
Rg 误差 (实空间) rg_real_error	3.52 Å
I(0) (实空间) i0_real	5.5630e+09
I(0) 误差 (实空间) i0_real_error	1.4850e+08
Rg (倒空间) rg_reciprocal	67.25 Å
I(0) (倒空间) i0_reciprocal	5555000000.0000
解质量估计 total_estimate	0.8554
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	62.2 Å
偏度 Skewness skewness	0.274
峰度 Kurtosis kurtosis	-0.688
角度范围 angular_range	— – 0.1150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	100900000.0000
实空间数据点数 n_real_points	24
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.886; Smooth: 0.751

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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	RNA (542-MER)
分子量 formula_weight	205134.9 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	A,C
原子数 atom_count	23586

GUGCGCUCGGCAUGGGUGCAAUCUCUAGGGUGAAAGUCCCGAACUGCGAAGGCAGAAGUAGCAGUUAGCUUAACGCAAGGGUGUCCGUGGUGACGCGGAAUCUGAAGGAAGCGGGCGGCAAACUUCCGGUCUGAGGAACACGAACUUCAUAUAAGGCUAGGUAUCAUUGGAUGAGUUUGCAAGACAAAACAAAGUCCUUUCUGCCGAAGGUGAUACAGAGUAAAUGAAGCAGAUAGAUGGAAGGAAAGAUUGUACUCUUACCCGAGGAGGUCUGAUGGAUACGUGAAGUGCGCUUCAUAACCUACUUAGUGAUAAGUAACUGAACCAUCAGAAGUCAGCAGAGGUCAUAGUACGAAUCGGUCUAGAACGAUUCGGAAGGACUGAACAAUCAAGAGAAAAUAGCCCUUGGCAUUCAGUACGUCAUGAUGAACACAGAAAACAUGGUACCUCCCAAGAGAAAGGAAACGGUGAAUCCCGUGGGAAUCUUUUGGAGGGUGGAGUGACGACUGGCAUAAGAAGAUCAGCUAUUUACGGAAGGAAGCUUGCGUCAUUAUCUUGAUUGAACCGCCGUAUACGGAACCGUACGUACGGUGGUGUGAGAGGACGGAGGUUAAUCACCUCCUCCUACUCGAU

来源 Source

来源生物 organism	Anoxybacillus pushchinoensis
NCBI 分类编号 ncbi_taxonomy_id	150248
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	DNA
分子量 formula_weight	2672.8 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	E,F

TGTCTTTCC

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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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	3.14 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	153769

fit	/app/data/saxs_computation/k0/8k0q/8k0q.fit
pddf	/app/data/pr_computation/k0/8k0q/8k0q.pr.out
profile	/app/data/saxs_computation/k0/8k0q/8k0q.dat

The Anoxybacillus pushchinoensis ORF-less Group IIC Intron HYER1 at symmetric pre-cleavage state

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 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)