9lac

Comparative analysis of functions and catalytic mechanisms of methyltransferases involved in anthracycline biosynthesis

Method: X-RAY DIFFRACTION D_max: 100.1 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	9lac
沉积日期 deposition_date	2025-01-02
最后修订 last_revision	2026-01-07
结构标题 title	Comparative analysis of functions and catalytic mechanisms of methyltransferases involved in anthracycline biosynthesis
关键词 keywords	DnrK, TRANSFERASE; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

▼

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

回转半径 Rg (Guinier) rg_guinier	29.31 Å
回转半径 Rg (电子) rg_electron	28.94 Å
零角强度 I(0) i0	172415000.00
分子量 molecular_weight	69519.0 kDa
排除体积 excluded_volume	66945 Å³
包络体积 envelope_volume	109980 Å³
水化壳体积 shell_volume	32943 Å³
包络直径 envelope_diameter	104.5 Å
壳层 Rg shell_rg	34.82 Å
包络 Rg envelope_rg	29.15 Å
形状 Rg shape_rg	28.91 Å
总 Rg total_rg	29.35 Å
总原子数 total_atoms	5283
残基数 n_residues	671
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	100.1 Å
Rg (实空间) rg_real	29.50 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	1.7240e+08
I(0) 误差 (实空间) i0_real_error	2.5690e+06
Rg (倒空间) rg_reciprocal	29.42 Å
I(0) (倒空间) i0_reciprocal	172400000.0000
解质量估计 total_estimate	0.8471
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	29.7 Å
偏度 Skewness skewness	0.577
峰度 Kurtosis kurtosis	-0.078
角度范围 angular_range	— – 0.2700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	47940000.0000
实空间数据点数 n_real_points	55
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.810

▶

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	Methyltransferase domain-containing protein
分子量 formula_weight	40942.4 kDa
突变 mutation	E299A
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,B
原子数 atom_count	6049

MGSSHHHHHHSSGLVPRGSHMTAEPTVAARPQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHILAGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGRPTYESIYGKPFYEDLAGRPDLRASFDSLLACDQDVAFDAPAAAYDWTNVRHVLDVGGGKGGFAAAIARRAPHVSATVLEMAGTVDTARSYLKDEGLSDRVDVVEGDFFEPLPRKADAIILSFVLLNWPDHDAVRILTRCAEALEPGGRILIHERDDLHENSFNEQFTALDLRMLVFLGGALRTREKWDGLAASAGLVVEEVRQLPSPTIPYDLSLLVLAPAATGA

来源 Source

来源生物 organism	Streptomyces coeruleorubidus
NCBI 分类编号 ncbi_taxonomy_id	116188
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;(7S,9R,10R)-7-[(2R,4S,5S,6S)-4-azanyl-6-methyl-5-oxidanyl-oxan-2-yl]oxy-9-ethyl-4-methoxy-6,9,10,11-tetrakis(oxidanyl)-8,10-dihydro-7H-tetracene-5,12-dione ;
分子量 formula_weight	529.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	S-ADENOSYL-L-HOMOCYSTEINE
分子量 formula_weight	384.4 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	766

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	60.501 Å
晶胞边长 b length_b	104.553 Å
晶胞边长 c length_c	120.296 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	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	33.049 Å
R 因子 r_factor	—
R_work r_work	0.1962
R_free r_free	0.2218

fit	/app/data/saxs_computation/la/9lac/9lac.fit
pddf	/app/data/pr_computation/la/9lac/9lac.pr.out
profile	/app/data/saxs_computation/la/9lac/9lac.dat

Comparative analysis of functions and catalytic mechanisms of methyltransferases involved in anthracycline biosynthesis

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