9mp1

Crystal structure of mithramycin analogue MTM SA-7-methyl-Trp in complex with double-stranded DNA AGAGGCCTCT

Method: X-RAY DIFFRACTION D_max: 43.2 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	9mp1
沉积日期 deposition_date	2024-12-29
结构标题 title	Crystal structure of mithramycin analogue MTM SA-7-methyl-Trp in complex with double-stranded DNA AGAGGCCTCT
关键词 keywords	DNA-drug complex, transcription, minor groove, natural product, DNA; DNA
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	12.86 Å
回转半径 Rg (电子) rg_electron	12.16 Å
零角强度 I(0) i0	4269400.00
分子量 molecular_weight	8648.0 kDa
排除体积 excluded_volume	7450 Å³
包络体积 envelope_volume	11167 Å³
水化壳体积 shell_volume	8244 Å³
包络直径 envelope_diameter	42.6 Å
壳层 Rg shell_rg	17.15 Å
包络 Rg envelope_rg	12.44 Å
形状 Rg shape_rg	12.11 Å
总 Rg total_rg	12.95 Å
总原子数 total_atoms	590
残基数 n_residues	20
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	43.2 Å
Rg (实空间) rg_real	12.83 Å
Rg 误差 (实空间) rg_real_error	0.32 Å
I(0) (实空间) i0_real	4.2690e+06
I(0) 误差 (实空间) i0_real_error	4.9290e+04
Rg (倒空间) rg_reciprocal	12.83 Å
I(0) (倒空间) i0_reciprocal	4269000.0000
解质量估计 total_estimate	0.6638
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.7 Å
偏度 Skewness skewness	0.275
峰度 Kurtosis kurtosis	-0.366
角度范围 angular_range	— – 0.5000 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	278400.0000
实空间数据点数 n_real_points	80
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.855; Stabil: 0.997; Sysdev: 0.368; Positv: 1.000; Valcen: 0.965; Smooth: 0.000

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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	;DNA (5'-D(APGPAPGPGPCPCPTPCPT)-3') ;
分子量 formula_weight	3045.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polydeoxyribonucleotide
链编号 strand_id	A,B
原子数 atom_count	663

AGAGGCCTCT

Entity 2 non-polymer

描述 description	;methyl (2S)-2-({(2S)-2-[(2R,3S)-3-{[(2S,4R,5R,6R)-4-{[(2S,4R,5S,6R)-4-{[(2S,4S,5R,6R)-4,5-dihydroxy-4,6-dimethyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl]oxy}-7-{[(2S,4R,5R,6R)-4-{[(2S,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]oxy}-5-hydroxy-6-methyloxan-2-yl]oxy}-5,10-dihydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-2-methoxyacetyl}amino)-3-(7-methyl-1H-indol-3-yl)propanoate (non-preferred name) ;
分子量 formula_weight	1241.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	7

Entity 4 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	73

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7. 引用文献 (1)

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晶胞边长 a length_a	94.184 Å
晶胞边长 b length_b	94.184 Å
晶胞边长 c length_c	94.184 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	48

空间群 space_group	P 41 3 2
空间群编号 int_tables_number	213
晶系 crystal_system	—

分辨率 resolution	2.080 Å
最低分辨率 resolution_low	38.480 Å
R 因子 r_factor	0.2206
R_work r_work	0.2194
R_free r_free	0.2481

fit	/app/data/saxs_computation/mp/9mp1/9mp1.fit
pddf	/app/data/pr_computation/mp/9mp1/9mp1.pr.out
profile	/app/data/saxs_computation/mp/9mp1/9mp1.dat

Crystal structure of mithramycin analogue MTM SA-7-methyl-Trp in complex with double-stranded DNA AGAGGCCTCT

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

Entity 2 non-polymer

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)