8yq9

;Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB6, NADPH and dUMP ;

Method: X-RAY DIFFRACTION D_max: 108.9 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	8yq9
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 FB6, 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

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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	34.59 Å
回转半径 Rg (电子) rg_electron	33.62 Å
零角强度 I(0) i0	231693000.00
分子量 molecular_weight	126200.0 kDa
排除体积 excluded_volume	159210 Å³
包络体积 envelope_volume	198630 Å³
水化壳体积 shell_volume	48154 Å³
包络直径 envelope_diameter	108.7 Å
壳层 Rg shell_rg	41.38 Å
包络 Rg envelope_rg	33.44 Å
形状 Rg shape_rg	33.58 Å
总 Rg total_rg	34.32 Å
总原子数 total_atoms	8892
残基数 n_residues	1043
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	108.9 Å
Rg (实空间) rg_real	34.48 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	2.3170e+08
I(0) 误差 (实空间) i0_real_error	3.8240e+06
Rg (倒空间) rg_reciprocal	34.55 Å
I(0) (倒空间) i0_reciprocal	231700000.0000
解质量估计 total_estimate	0.8354
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	42.6 Å
偏度 Skewness skewness	0.169
峰度 Kurtosis kurtosis	-0.622
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	49580000.0000
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: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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 (6)

Entity 1 polymer

描述 description	Bifunctional dihydrofolate reductase-thymidylate synthase
分子量 formula_weight	71908.1 kDa
突变 mutation	N51I, C59R, S108N, I164L
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	9243

MMEQVCDVFDIYAICACCKVESKNEGKKNEVFNNYTFRGLGNKGVLPWKCISLDMKYFRAVTTYVNESKYEKLKYKRCKYLNKETVDNVNDMPNSKKLQNVVVMGRTNWESIPKKFKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFILGGSVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTLDFIIYKKTNNKMLNEQNCIKGEEKNNDMPLKNDDKDTCHMKKLTEFYKNVDKYKINYENDDDDEEEDDFVYFNFNKEKEEKNKNSIHPNDFQIYNSLKYKYHPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLNPDIKNIEDFTISDFTIQNYVHHEKISMDMAA

来源 Source

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite P. falciparum
NCBI 分类编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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 3 non-polymer

描述 description	4-[4-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]oxypropoxy]phenyl]benzoic acid
分子量 formula_weight	408.4 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 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	351

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7. 引用文献 (1)

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晶胞边长 a length_a	58.064 Å
晶胞边长 b length_b	156.496 Å
晶胞边长 c length_c	164.865 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	2.400 Å
最低分辨率 resolution_low	24.629 Å
R 因子 r_factor	—
R_work r_work	0.2171
R_free r_free	0.2909

fit	/app/data/saxs_computation/yq/8yq9/8yq9.fit
pddf	/app/data/pr_computation/yq/8yq9/8yq9.pr.out
profile	/app/data/saxs_computation/yq/8yq9/8yq9.dat