8j60

Structural and mechanistic insight into ribosomal ITS2 RNA processing by nuclease-kinase machinery

Method: ELECTRON MICROSCOPY D_max: 137.5 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	8j60
沉积日期 deposition_date	2023-04-24
结构标题 title	Structural and mechanistic insight into ribosomal ITS2 RNA processing by nuclease-kinase machinery
关键词 keywords	endoribonuclease; ribosome biosynthesis; Las1; Grc3, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	40.56 Å
回转半径 Rg (电子) rg_electron	40.34 Å
零角强度 I(0) i0	275828000.00
分子量 molecular_weight	138120.0 kDa
排除体积 excluded_volume	173780 Å³
包络体积 envelope_volume	236110 Å³
水化壳体积 shell_volume	50180 Å³
包络直径 envelope_diameter	144.8 Å
壳层 Rg shell_rg	44.23 Å
包络 Rg envelope_rg	40.35 Å
形状 Rg shape_rg	40.39 Å
总 Rg total_rg	40.38 Å
总原子数 total_atoms	9757
残基数 n_residues	1306
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	137.5 Å
Rg (实空间) rg_real	40.77 Å
Rg 误差 (实空间) rg_real_error	1.13 Å
I(0) (实空间) i0_real	2.7580e+08
I(0) 误差 (实空间) i0_real_error	4.3750e+06
Rg (倒空间) rg_reciprocal	40.57 Å
I(0) (倒空间) i0_reciprocal	275800000.0000
解质量估计 total_estimate	0.8426
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	38.8 Å
偏度 Skewness skewness	0.458
峰度 Kurtosis kurtosis	-0.496
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	48030000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.801; Smooth: 0.808

▶

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

▶

5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	;Polynucleotide 5'-hydroxyl-kinase GRC3 ;
分子量 formula_weight	69612.9 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,A
原子数 atom_count	9757

MHKSAFQALQGDIPTYEVNSSDEQDSDQDEEDVEQPSEPMHRLVSAPAASIHIEESKYISSNFSFDDDNTIYGHDYVIFGLKSNQNLIVKGQFVLEIQRGAIDINGVIYHSGVEPMKFINPSSSSIPLIQATQVLNSSLLENKESQENQHLFTPGYKSVIKLTNLDTHLESIGRVCPLFKNLFWQFDNFFAEDSLRLLDQYELAFSDYTFYPITKPDNTVSVIKHKNWMDVIKSLTELYSNDQSIKVIVIGGKNSGKSTFLRLLVQHMLSPTLQQLPINFMDLDPGQPEYSGTDCISLSKISEVQHGNHLSLTSTDSTQCHYVGFNSPKDQPTRYNLLVEQLVRSYESDGELKHESLLINTPGWIKGYGLELTRTLIERVKPTHVIYLNSGTLGVDIDIPKGTNLIPLQGSFNHSGSRYSSSQLRLLKTMAYFHKIDDFKFDFQPLLFSPPIQVSYGVSTGISALTHLKETGIGMDHLERSIEATIVGIFKVKRDHLEECELFNKGQLPLLPYKEFIKLSTEFFRLALVHSIDQEKKIMNLYIPQFRTLDLTKEAIIMVRGNTDLPIWEIASNEIVKRFKRQLPYITFEKGSSLEKKWKVRKNVQRRGQM

来源 Source

来源生物 organism	Cyberlindnera jadinii
NCBI 分类编号 ncbi_taxonomy_id	4903
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 polymer

描述 description	LAS1 protein
分子量 formula_weight	49413.6 kDa
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D

MNSHPRLTPWKSSDEVVYLKGLFFPADREQISRDELYRQYEEAISLVEMYSSRTRVSHILQSTAHLFSALMMLESFEGGLDDTVRLTASMTIIRFVNGLLDPNQQSQFAIPLHLLAKKIDLPSLFVEFRHSATHDALPSLEMCKTCVDRAIDWVWDHYWDGVLSIVEPQVETDDLEESLIKELKDLFKQYRRIRRQNITKLYKFGDSTPEGKEYWTCIAGIKDHADMANFYNVMIERIVSNKLKWEHLRALFEPMMNHFIHLKGWDFPLGLIDSMLSKNYEYSKFRGIDDTERAYLNDQEFKCAQKWIRWLAIEQIDRYDDVLVSKMIDTLGKTNHELNVELLEKLQSRFSADPVIKDKIQAKLTLIQRLSTDTKTKRMNNLEDIMSDLESLKKRAKVTPTLHIKSFESHPNWTPKPFGVI

来源 Source

来源生物 organism	Cyberlindnera jadinii
NCBI 分类编号 ncbi_taxonomy_id	4903
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

▶

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	3.39 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	523843

fit	/app/data/saxs_computation/j6/8j60/8j60.fit
pddf	/app/data/pr_computation/j6/8j60/8j60.pr.out
profile	/app/data/saxs_computation/j6/8j60/8j60.dat

Structural and mechanistic insight into ribosomal ITS2 RNA processing by nuclease-kinase machinery

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

来源 Source

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)