8t1t

Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA with QSY deletion) heteromeric complex (bound to SAM)

Method: X-RAY DIFFRACTION D_max: 75.7 Å Quality: EXCELLENT

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	8t1t
沉积日期 deposition_date	2023-06-03
最后修订 last_revision	2023-11-22
结构标题 title	Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA with QSY deletion) heteromeric complex (bound to SAM)
关键词 keywords	alpha-N-methyltransferase, borosin, natural products, TRANSFERASE; TRANSFERASE
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	25.85 Å
回转半径 Rg (电子) rg_electron	24.61 Å
零角强度 I(0) i0	82323200.00
分子量 molecular_weight	70907.0 kDa
排除体积 excluded_volume	88734 Å³
包络体积 envelope_volume	105830 Å³
水化壳体积 shell_volume	34437 Å³
包络直径 envelope_diameter	76.5 Å
壳层 Rg shell_rg	33.03 Å
包络 Rg envelope_rg	24.67 Å
形状 Rg shape_rg	24.62 Å
总 Rg total_rg	25.50 Å
总原子数 total_atoms	4985
残基数 n_residues	635
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	75.7 Å
Rg (实空间) rg_real	25.66 Å
Rg 误差 (实空间) rg_real_error	0.28 Å
I(0) (实空间) i0_real	8.2320e+07
I(0) 误差 (实空间) i0_real_error	1.0230e+06
Rg (倒空间) rg_reciprocal	25.72 Å
I(0) (倒空间) i0_reciprocal	82330000.0000
解质量估计 total_estimate	0.9101
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	33.5 Å
偏度 Skewness skewness	0.085
峰度 Kurtosis kurtosis	-0.520
角度范围 angular_range	— – 0.3050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19190000.0000
实空间数据点数 n_real_points	62
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.968

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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 (5)

Entity 1 polymer

描述 description	Alpha-N-methyltransferase (SonM)
分子量 formula_weight	29068.3 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	A,C
原子数 atom_count	5608

MGSLVCVGTGLQLAGQISVLSRSYIEHADIVFSLLPDGFSQRWLTKLNPNVINLQQFYAQNGEVKNRRDTYEQMVNAILDAVRAGKKTVCALYGHPGVFACVSHMAITRAKAEGFSAKMEPGISAEACLWADLGIDPGNSGHQSFEASQFMFFNHVPDPTTHLLLWQIAIAGEHTLTQFHTSSDRLQILVEQLNQWYPLDHEVVIYEAANLPIQAPRIERLPLANLPQAHLMPISTLLIPPAKKLEYNYAILAKLGIGPEDLG

来源 Source

来源生物 organism	Shewanella oneidensis
NCBI 分类编号 ncbi_taxonomy_id	211586
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	RiPP precursor (SonA)
分子量 formula_weight	8404.3 kDa
突变 mutation	Deletion of sequence QSY
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,D

MHHHHHHMSGLSDFFTQLGQDAQLMEDYKQNPEAVMRAHGLTDEQINAVMTGDMEKLKTLSGDSSYLVISHGNGD

来源 Source

来源生物 organism	Shewanella oneidensis
NCBI 分类编号 ncbi_taxonomy_id	211586
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	S-ADENOSYLMETHIONINE
分子量 formula_weight	398.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	488

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7. 引用文献 (1)

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晶胞边长 a length_a	52.500 Å
晶胞边长 b length_b	59.300 Å
晶胞边长 c length_c	60.100 Å
晶胞夹角 α angle_alpha	95.90 °
晶胞夹角 β angle_beta	96.50 °
晶胞夹角 γ angle_gamma	112.60 °
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	1.550 Å
最低分辨率 resolution_low	46.130 Å
R 因子 r_factor	0.1749
R_work r_work	0.1731
R_free r_free	0.2087

fit	/app/data/saxs_computation/t1/8t1t/8t1t.fit
pddf	/app/data/pr_computation/t1/8t1t/8t1t.pr.out
profile	/app/data/saxs_computation/t1/8t1t/8t1t.dat

Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA with QSY deletion) heteromeric complex (bound to SAM)

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 (5)

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

Entity 5 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)