8sh5

;Crystal structure of 3'cap-independent translation enhancers (CITE) from Pea enation mosaic virus RNA 2 (PEMV2) with Fab BL3-6K170A ;

Method: X-RAY DIFFRACTION D_max: 145.0 Å Quality: REASONABLE

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	8sh5
沉积日期 deposition_date	2023-04-13
结构标题 title	;Crystal structure of 3'cap-independent translation enhancers (CITE) from Pea enation mosaic virus RNA 2 (PEMV2) with Fab BL3-6K170A ;
关键词 keywords	CITE, PEMV2, PTE, RNA, RNA-IMMUNE SYSTEM complex; RNA/IMMUNE SYSTEM
实验方法 method	X-RAY DIFFRACTION

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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	39.85 Å
回转半径 Rg (电子) rg_electron	40.12 Å
零角强度 I(0) i0	147688000.00
分子量 molecular_weight	75716.0 kDa
排除体积 excluded_volume	85182 Å³
包络体积 envelope_volume	128990 Å³
水化壳体积 shell_volume	31923 Å³
包络直径 envelope_diameter	151.6 Å
壳层 Rg shell_rg	37.64 Å
包络 Rg envelope_rg	40.57 Å
形状 Rg shape_rg	39.93 Å
总 Rg total_rg	40.44 Å
总原子数 total_atoms	5201
残基数 n_residues	527
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	145.0 Å
Rg (实空间) rg_real	40.90 Å
Rg 误差 (实空间) rg_real_error	1.65 Å
I(0) (实空间) i0_real	1.4770e+08
I(0) 误差 (实空间) i0_real_error	2.6610e+06
Rg (倒空间) rg_reciprocal	40.25 Å
I(0) (倒空间) i0_reciprocal	147600000.0000
解质量估计 total_estimate	0.7156
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	29.0 Å
偏度 Skewness skewness	0.688
峰度 Kurtosis kurtosis	-0.186
角度范围 angular_range	— – 0.2000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	5155000.0000
实空间数据点数 n_real_points	41
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.502; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.255; Smooth: 0.538

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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	Fab BL3-6K170A heavy chain
分子量 formula_weight	24182.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H
原子数 atom_count	5226

EISEVQLVESGGGLVQPGGSLRLSCAASGFYISYSSIHWVRQAPGKGLEWVASISPYSGSTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARQGYRRRSGRGFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Fab BL3-6K170A light chain
分子量 formula_weight	23336.8 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	L

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQSYSFPSTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSADSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 3 polymer

描述 description	RNA (88-MER)
分子量 formula_weight	28444.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	R

GGUAGAACACGUGGGAUAGGGGAUGACCUUGUCGACCGAAACACGGUCCCCUGCUCCUUCGAGCUGGCAAGGCGCUCACAGGUUCUAC

Entity 4 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	25

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6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

结构域编号 domain_id	8sh5H01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8sh5H02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8sh5L01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

结构域编号 domain_id	8sh5L02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	10 — Immunoglobulins

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7. 引用文献 (2)

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晶胞边长 a length_a	63.346 Å
晶胞边长 b length_b	65.460 Å
晶胞边长 c length_c	89.817 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.29 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	monoclinic

分辨率 resolution	2.750 Å
最低分辨率 resolution_low	59.420 Å
R 因子 r_factor	0.2554
R_work r_work	0.2514
R_free r_free	0.2966

fit	/app/data/saxs_computation/sh/8sh5/8sh5.fit
pddf	/app/data/pr_computation/sh/8sh5/8sh5.pr.out
profile	/app/data/saxs_computation/sh/8sh5/8sh5.dat

;Crystal structure of 3'cap-independent translation enhancers (CITE) from Pea enation mosaic virus RNA 2 (PEMV2) with Fab BL3-6K170A ;

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

精修参数 Refinement

衍射实验 Diffraction

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 polymer

聚合体 Polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)