8yq8

;Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB8, NADPH and dUMP ;

Method: X-RAY DIFFRACTION D_max: 108.6 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8yq8
沉积日期 deposition_date	2024-03-19
最后修订 last_revision	2024-09-11
结构标题 title	;Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB8, NADPH and dUMP ;
关键词 keywords	dihydrofolate reductase, thymidylate synthase, antifolate, Plasmodium falciparum, biphenyl, fragment, OXIDOREDUCTASE; OXIDOREDUCTASE
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	34.74 Å
回转半径 Rg (电子) rg_electron	33.75 Å
零角强度 I(0) i0	229913000.00
分子量 molecular_weight	125940.0 kDa
排除体积 excluded_volume	158970 Å³
包络体积 envelope_volume	198280 Å³
水化壳体积 shell_volume	47830 Å³
包络直径 envelope_diameter	108.9 Å
壳层 Rg shell_rg	41.53 Å
包络 Rg envelope_rg	33.53 Å
形状 Rg shape_rg	33.71 Å
总 Rg total_rg	34.45 Å
总原子数 total_atoms	8874
残基数 n_residues	1042
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	108.6 Å
Rg (实空间) rg_real	34.62 Å
Rg 误差 (实空间) rg_real_error	0.69 Å
I(0) (实空间) i0_real	2.2990e+08
I(0) 误差 (实空间) i0_real_error	3.3800e+06
Rg (倒空间) rg_reciprocal	34.70 Å
I(0) (倒空间) i0_reciprocal	229900000.0000
解质量估计 total_estimate	0.9084
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	42.5 Å
偏度 Skewness skewness	0.163
峰度 Kurtosis kurtosis	-0.631
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	47920000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.928

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Bifunctional dihydrofolate reductase-thymidylate synthase
分子量 formula_weight	71908.1 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,B
原子数 atom_count	9462

MMEQVCDVFDIYAICACCKVESKNEGKKNEVFNNYTFRGLGNKGVLPWKCISLDMKYFRAVTTYVNESKYEKLKYKRCKYLNKETVDNVNDMPNSKKLQNVVVMGRTNWESIPKKFKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFILGGSVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTLDFIIYKKTNNKMLNEQNCIKGEEKNNDMPLKNDDKDTCHMKKLTEFYKNVDKYKINYENDDDDEEEDDFVYFNFNKEKEEKNKNSIHPNDFQIYNSLKYKYHPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLNPDIKNIEDFTISDFTIQNYVHHEKISMDMAA

来源 Source

来源生物 organism	Plasmodium falciparum VS/1
NCBI 分类编号 ncbi_taxonomy_id	478864
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	4-[4-[4-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]oxybutoxy]phenyl]benzoic acid
分子量 formula_weight	422.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
分子量 formula_weight	745.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ;
分子量 formula_weight	308.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	588

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	57.763 Å
晶胞边长 b length_b	156.410 Å
晶胞边长 c length_c	165.065 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	2.100 Å
最低分辨率 resolution_low	26.096 Å
R 因子 r_factor	—
R_work r_work	0.1945
R_free r_free	0.2404

fit	/app/data/saxs_computation/yq/8yq8/8yq8.fit
pddf	/app/data/pr_computation/yq/8yq8/8yq8.pr.out
profile	/app/data/saxs_computation/yq/8yq8/8yq8.dat

;Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB8, NADPH and dUMP ;

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