9c6k

Cryo-EM structure of the TPP riboswitch embedded in an RNA scaffold bound to thiamine pyrophosphate

Method: ELECTRON MICROSCOPY D_max: 71.5 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9c6k
沉积日期 deposition_date	2024-06-07
结构标题 title	Cryo-EM structure of the TPP riboswitch embedded in an RNA scaffold bound to thiamine pyrophosphate
关键词 keywords	RNA, Riboswitch, Ligand; RNA
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	20.03 Å
回转半径 Rg (电子) rg_electron	19.68 Å
零角强度 I(0) i0	34893900.00
分子量 molecular_weight	26563.0 kDa
排除体积 excluded_volume	24804 Å³
包络体积 envelope_volume	35539 Å³
水化壳体积 shell_volume	16174 Å³
包络直径 envelope_diameter	73.9 Å
壳层 Rg shell_rg	24.93 Å
包络 Rg envelope_rg	19.77 Å
形状 Rg shape_rg	19.61 Å
总 Rg total_rg	20.22 Å
总原子数 total_atoms	1745
残基数 n_residues	80
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	71.5 Å
Rg (实空间) rg_real	20.07 Å
Rg 误差 (实空间) rg_real_error	0.67 Å
I(0) (实空间) i0_real	3.4890e+07
I(0) 误差 (实空间) i0_real_error	4.8460e+05
Rg (倒空间) rg_reciprocal	20.07 Å
I(0) (倒空间) i0_reciprocal	34890000.0000
解质量估计 total_estimate	0.8574
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	21.5 Å
偏度 Skewness skewness	0.412
峰度 Kurtosis kurtosis	-0.251
角度范围 angular_range	— – 0.3950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3019000.0000
实空间数据点数 n_real_points	71
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.757; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.887; Smooth: 0.988

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	TPP riboswitch embedded in an RNA scaffold bound to thiamine pyrophosphate
分子量 formula_weight	161102.5 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	X
原子数 atom_count	1745

UUAUGUGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGGGAGGUCUGGAAACAGAAGUCAGCAGAAGUCAUAGUACCCUCAGUACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUGCUGAGGGGAAGGACGGAACAAGUAUGGCGUUCGCGCCUAAGCUUGAACCACCGUAUACCGAACGGUACGUACGGUGGUGUGAGAGGAGUUCGCUCUACUCUAUUAG

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

Entity 2 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	6

Entity 3 non-polymer

描述 description	THIAMINE DIPHOSPHATE
分子量 formula_weight	425.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

▶

7. 引用文献 (1)

▶

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	2.94 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	655558

fit	/app/data/saxs_computation/c6/9c6k/9c6k.fit
pddf	/app/data/pr_computation/c6/9c6k/9c6k.pr.out
profile	/app/data/saxs_computation/c6/9c6k/9c6k.dat