SAXSdb — 1j3j

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1j3j
沉积日期 deposition_date	2003-02-03
结构标题 title	;Double mutant (C59R+S108N) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with pyrimethamine, NADPH, and dUMP ;
关键词 keywords	bifunctional, OXIDOREDUCTASE, TRANSFERASE; OXIDOREDUCTASE, TRANSFERASE
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	34.75 Å
回转半径 Rg (电子) rg_electron	33.70 Å
零角强度 I(0) i0	255683000.00
分子量 molecular_weight	131140.0 kDa
排除体积 excluded_volume	164940 Å³
包络体积 envelope_volume	211560 Å³
水化壳体积 shell_volume	50937 Å³
包络直径 envelope_diameter	110.5 Å
壳层 Rg shell_rg	41.63 Å
包络 Rg envelope_rg	33.58 Å
形状 Rg shape_rg	33.66 Å
总 Rg total_rg	34.43 Å
总原子数 total_atoms	9228
残基数 n_residues	1089
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	104.6 Å
Rg (实空间) rg_real	34.63 Å
Rg 误差 (实空间) rg_real_error	0.52 Å
I(0) (实空间) i0_real	2.5570e+08
I(0) 误差 (实空间) i0_real_error	3.6180e+06
Rg (倒空间) rg_reciprocal	34.71 Å
I(0) (倒空间) i0_reciprocal	255700000.0000
解质量估计 total_estimate	0.6721
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	43.2 Å
偏度 Skewness skewness	0.170
峰度 Kurtosis kurtosis	-0.598
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	55920000.0000
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: 0.980; Stabil: 1.000; Sysdev: 0.038; Positv: 1.000; Valcen: 0.997; Smooth: 0.684

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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	33214.3 kDa
EC 编号 ec_number	1.5.1.3, 2.1.1.45
突变 mutation	C59R, S108N
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	9961

MMEQVCDVFDIYAICACCKVESKNEGKKNEVFNNYTFRGLGNKGVLPWKCNSLDMKYFRAVTTYVNESKYEKLKYKRCKYLNKETVDNVNDMPNSKKLQNVVVMGRTNWESIPKKFKPLSNRINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFIIGGSVVYQEFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTLDFIIYKKTNNKMLNEQNCIKGEEKNNDMPLKNDDKDTCHMKKLTEFYKNVDKYKINYEN

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 polymer

描述 description	Bifunctional dihydrofolate reductase-thymidylate synthase
分子量 formula_weight	38712.9 kDa
EC 编号 ec_number	1.5.1.3, 2.1.1.45
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	C,D

DDDDEEEDDFVYFNFNKEKEEKNKNSIHPNDFQIYNSLKYKYHPEYQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLFLRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVNDLGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLCAWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASYSIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLKLNPDIKNIEDFTISDFTIQNYVHHEKISMDMAA

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 3 non-polymer

描述 description	5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE
分子量 formula_weight	248.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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 5 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 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	733

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1j3ja_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.71 — Dihydrofolate reductase-like
超家族 Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
家族 Family family	c.71.1.1 — Dihydrofolate reductases

结构域编号 domain_id	d1j3jb_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.71 — Dihydrofolate reductase-like
超家族 Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
家族 Family family	c.71.1.1 — Dihydrofolate reductases

结构域编号 domain_id	d1j3jc_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

结构域编号 domain_id	d1j3jd_
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.117 — Thymidylate synthase/dCMP hydroxymethylase
超家族 Superfamily superfamily	d.117.1 — Thymidylate synthase/dCMP hydroxymethylase
家族 Family family	d.117.1.1 — Thymidylate synthase/dCMP hydroxymethylase

CATH v4.4 (4 domains)

结构域编号 domain_id	1j3jA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	430 — Dihydrofolate Reductase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

结构域编号 domain_id	1j3jB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	430 — Dihydrofolate Reductase, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

结构域编号 domain_id	1j3jC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

结构域编号 domain_id	1j3jD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	572 — Thymidylate Synthase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Thymidylate synthase/dCMP hydroxymethylase domain

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7. 引用文献 (1)

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晶胞边长 a length_a	56.343 Å
晶胞边长 b length_b	154.999 Å
晶胞边长 c length_c	164.001 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	2.300 Å
最低分辨率 resolution_low	23.830 Å
R 因子 r_factor	0.2000
R_work r_work	0.1980
R_free r_free	0.2310

fit	/app/data/saxs_computation/j3/1j3j/1j3j.fit
pddf	/app/data/pr_computation/j3/1j3j/1j3j.pr.out
profile	/app/data/saxs_computation/j3/1j3j/1j3j.dat

;Double mutant (C59R+S108N) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with pyrimethamine, 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

5. 实体与聚合体信息 (6)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)