9imb

;The crystal structure of human m5C methyltransferase NSUN6 bound to its S-adenosyl-L-methionine analog and a NECTIN-2 3'-UTR RNA substrate ;

Method: X-RAY DIFFRACTION D_max: 108.6 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	9imb
沉积日期 deposition_date	2024-07-02
结构标题 title	;The crystal structure of human m5C methyltransferase NSUN6 bound to its S-adenosyl-L-methionine analog and a NECTIN-2 3'-UTR RNA substrate ;
关键词 keywords	m5C methyltransferase, RNA BINDING PROTEIN/RNA, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/RNA
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	33.18 Å
回转半径 Rg (电子) rg_electron	33.16 Å
零角强度 I(0) i0	230607000.00
分子量 molecular_weight	112850.0 kDa
排除体积 excluded_volume	137360 Å³
包络体积 envelope_volume	178140 Å³
水化壳体积 shell_volume	44487 Å³
包络直径 envelope_diameter	111.7 Å
壳层 Rg shell_rg	40.08 Å
包络 Rg envelope_rg	32.79 Å
形状 Rg shape_rg	33.18 Å
总 Rg total_rg	33.59 Å
总原子数 total_atoms	7866
残基数 n_residues	960
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	108.6 Å
Rg (实空间) rg_real	33.19 Å
Rg 误差 (实空间) rg_real_error	0.69 Å
I(0) (实空间) i0_real	2.3060e+08
I(0) 误差 (实空间) i0_real_error	3.5390e+06
Rg (倒空间) rg_reciprocal	33.19 Å
I(0) (倒空间) i0_reciprocal	230600000.0000
解质量估计 total_estimate	0.8901
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	36.2 Å
偏度 Skewness skewness	0.342
峰度 Kurtosis kurtosis	-0.405
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	58570000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.894

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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	tRNA (cytosine(72)-C(5))-methyltransferase NSUN6
分子量 formula_weight	51834.1 kDa
EC 编号 ec_number	2.1.1.-
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	7873

MSIFPKISLRPEVENYLKEGFMNKEIVTALGKQEAERKFETLLKHLSHPPSFTTVRVNTHLASVQHVKNLLLDELQKQFNGLSVPILQHPDLQDVLLIPVIGPRKNIKKQQCEAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKCKKGAKEFDGTKVFLGNGISELSRKEIFSGLPELKGMGIRMTEPVYLSPSFDSVLPRYLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKAVKLDMVEDTEGEPPFLPESFDRILLDAPCSGMGQRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGLSCEQLKQLQRFDPSAVPLPDTDMDSLREARREDMLRLANKDSIGFFIAKFVKCKST

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	;RNA (5'-R(GPCPCPCPUPCPUPUPCPAPUPCPUPCPCPAPAPAPGPAPGPGPGPC)-3') ;
分子量 formula_weight	7604.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polyribonucleotide
链编号 strand_id	D,C

GCCCUCUUCAUCUCCAAAGAGGGC

Entity 3 non-polymer

描述 description	SINEFUNGIN
分子量 formula_weight	381.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	7

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7. 引用文献 (1)

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晶胞边长 a length_a	61.814 Å
晶胞边长 b length_b	72.441 Å
晶胞边长 c length_c	77.150 Å
晶胞夹角 α angle_alpha	62.48 °
晶胞夹角 β angle_beta	83.38 °
晶胞夹角 γ angle_gamma	69.62 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.900 Å
最低分辨率 resolution_low	43.000 Å
R 因子 r_factor	0.2101
R_work r_work	0.2068
R_free r_free	0.2638

fit	/app/data/saxs_computation/im/9imb/9imb.fit
pddf	/app/data/pr_computation/im/9imb/9imb.pr.out
profile	/app/data/saxs_computation/im/9imb/9imb.dat

;The crystal structure of human m5C methyltransferase NSUN6 bound to its S-adenosyl-L-methionine analog and a NECTIN-2 3'-UTR RNA substrate ;

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

Entity 3 non-polymer

Entity 4 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)