8i66

;Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with isoorotic acid (2,4-Dihydroxypyrimidine-5-carboxylic Acid) and citric acid, Form I ;

Method: X-RAY DIFFRACTION D_max: 55.5 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	8i66
沉积日期 deposition_date	2023-01-27
结构标题 title	;Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with isoorotic acid (2,4-Dihydroxypyrimidine-5-carboxylic Acid) and citric acid, Form I ;
关键词 keywords	DNA repair, Base excision repair, Inhibitor-complex, HYDROLASE, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
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	18.07 Å
回转半径 Rg (电子) rg_electron	16.62 Å
零角强度 I(0) i0	11052700.00
分子量 molecular_weight	24800.0 kDa
排除体积 excluded_volume	31048 Å³
包络体积 envelope_volume	34572 Å³
水化壳体积 shell_volume	17237 Å³
包络直径 envelope_diameter	55.7 Å
壳层 Rg shell_rg	23.03 Å
包络 Rg envelope_rg	16.84 Å
形状 Rg shape_rg	16.60 Å
总 Rg total_rg	17.68 Å
总原子数 total_atoms	1752
残基数 n_residues	228
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	55.5 Å
Rg (实空间) rg_real	17.93 Å
Rg 误差 (实空间) rg_real_error	0.22 Å
I(0) (实空间) i0_real	1.1050e+07
I(0) 误差 (实空间) i0_real_error	1.1260e+05
Rg (倒空间) rg_reciprocal	17.95 Å
I(0) (倒空间) i0_reciprocal	11050000.0000
解质量估计 total_estimate	0.8975
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	23.2 Å
偏度 Skewness skewness	0.115
峰度 Kurtosis kurtosis	-0.416
角度范围 angular_range	— – 0.4400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1987000.0000
实空间数据点数 n_real_points	75
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.959

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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	Uracil-DNA glycosylase
分子量 formula_weight	25813.5 kDa
EC 编号 ec_number	3.2.2.27
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	A
原子数 atom_count	1788

MHHHHHHGMASMTARPLSELVERGWAAALEPVADQVAHMGQFLRAEIAAGRRYLPAGSNVLRAFTFPFDNVRVLIVGQDPYPTPGHAVGLSFSVAPDVRPWPRSLANIFDEYTADLGYPLPSNGDLTPWAQRGVLLLNRVLTVRPSNPASHRGKGWEAVTECAIRALAARAAPLVAILWGRDASTLKPMLAAGNCVAIESPHPSPLSASRGFFGSRPFSRANELLVGMGAEPIDWRLP

来源 Source

来源生物 organism	Mycobacterium tuberculosis H37Rv
NCBI 分类编号 ncbi_taxonomy_id	83332
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid
分子量 formula_weight	156.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	CITRIC ACID
分子量 formula_weight	192.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	36

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7. 引用文献 (2)

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晶胞边长 a length_a	39.120 Å
晶胞边长 b length_b	63.970 Å
晶胞边长 c length_c	45.390 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	112.29 °
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	—

分辨率 resolution	2.600 Å
最低分辨率 resolution_low	36.220 Å
R 因子 r_factor	0.1814
R_work r_work	0.1782
R_free r_free	0.2341

fit	/app/data/saxs_computation/i6/8i66/8i66.fit
pddf	/app/data/pr_computation/i6/8i66/8i66.pr.out
profile	/app/data/saxs_computation/i6/8i66/8i66.dat

;Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with isoorotic acid (2,4-Dihydroxypyrimidine-5-carboxylic Acid) and citric acid, Form I ;

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