8xtr

Comamonas testosteroni KF-1 circularly permuted group II intron 2S state

Method: ELECTRON MICROSCOPY D_max: 141.9 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	8xtr
沉积日期 deposition_date	2024-01-11
结构标题 title	Comamonas testosteroni KF-1 circularly permuted group II intron 2S state
关键词 keywords	CryoEM, Ribozyme, 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	45.96 Å
回转半径 Rg (电子) rg_electron	45.64 Å
零角强度 I(0) i0	2629990000.00
分子量 molecular_weight	242070.0 kDa
排除体积 excluded_volume	225350 Å³
包络体积 envelope_volume	442250 Å³
水化壳体积 shell_volume	80665 Å³
包络直径 envelope_diameter	151.5 Å
壳层 Rg shell_rg	50.37 Å
包络 Rg envelope_rg	44.32 Å
形状 Rg shape_rg	45.61 Å
总 Rg total_rg	45.80 Å
总原子数 total_atoms	15952
残基数 n_residues	740
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	141.9 Å
Rg (实空间) rg_real	45.80 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	2.6300e+09
I(0) 误差 (实空间) i0_real_error	4.6530e+07
Rg (倒空间) rg_reciprocal	45.96 Å
I(0) (倒空间) i0_reciprocal	2630000000.0000
解质量估计 total_estimate	0.8642
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	54.3 Å
偏度 Skewness skewness	0.251
峰度 Kurtosis kurtosis	-0.380
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	113200000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.466

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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	RNA (219-MER)
分子量 formula_weight	70556.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	A
原子数 atom_count	15952

CCGGGGCGCCACCCCGGAAGUGAUGCGAGUCGCCAACUCGCAUCACAAGCAAACGCUGUAGCCGCGUGCCUCUAAUAGGGCUGGCGCGGUUGCGAAGGGCGCUGGUGAGUGCAACUCUCACCUUCGACCCAAUCCAUCUUGCGGCUCAACCCCGCAAGAUCAUCGCCAGACCGCUGGCGGCGUACUGAGUGACAAACGAGGCAAAACCAAAUUGAAGUU

来源 Source

来源生物 organism	Comamonas testosteroni KF-1
NCBI 分类编号 ncbi_taxonomy_id	399795
宿主生物 host_organism	synthetic construct

Entity 2 polymer

描述 description	RNA (595-MER)
分子量 formula_weight	193640.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	B

GGGCGACCGUGAAACGGCGCUGGGCAGGAAAUGGCCCAGUGACCUGGUCAAUGGUGAAAGUCGGUGAAAGACCGACCGGUGGGGCGUAUCGAAAGAGCGCAACACCUGCCGCACAGGAUGGCUUCUGAGGUACCGGUGACGGUACAGAACGCGGAGGGGAAACCUGGAAGCGAGGGCACCUCGGGAAACCGGGGGUCGAUGCAUAGCUCAAACCUGUAACGGCACCAGUGGAGGGUGCUGUGCGGAGCAACGUGGAGCCACAGGCAUGAAGCCGUGGUUCGUAGUCGAUGAGACAAGCGGUGAGUAAGGGAAGGGCUGCGAACAUCGCCUCCCCGAAAUCCAAGGAAAGCCGAAAGGCUAGCCGCUUUGUUGAGACAGUGGCGCCACGUUGCGCAUUAGCCGUGACCUAAACGGGGAACCUCUUGGCCGUACCGACUCGGGUGGCACCGGUCGGGCUCGAUGGCUCAAGAGGGGGAGAUGUGAUGAUUAGGGUUUGACCCGUGAUGCGAUACGACCGAAGCAUCCGGGGAGCUGUCUGACGAAGAGUCGGCAGCAGUGGGUUUGGCGACCCGCUCCGAAAGUCGCAAGCGUUUGC

来源 Source

来源生物 organism	Comamonas testosteroni KF-1
NCBI 分类编号 ncbi_taxonomy_id	399795
宿主生物 host_organism	synthetic construct

Entity 3 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 4 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	30

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7. 引用文献 (1)

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分辨率 resolution	2.67 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	65386

fit	/app/data/saxs_computation/xt/8xtr/8xtr.fit
pddf	/app/data/pr_computation/xt/8xtr/8xtr.pr.out
profile	/app/data/saxs_computation/xt/8xtr/8xtr.dat

Comamonas testosteroni KF-1 circularly permuted group II intron 2S 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

冷冻电镜 EM 3D

5. 实体与聚合体信息 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)