9box

;Room-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase (hSHMT2) with PLP-glycine external aldimine and 5-formyltetrahydrofolate (folinic acid) ;

Method: X-RAY DIFFRACTION D_max: 146.6 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	9box
沉积日期 deposition_date	2024-05-06
最后修订 last_revision	2024-08-28
结构标题 title	;Room-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase (hSHMT2) with PLP-glycine external aldimine and 5-formyltetrahydrofolate (folinic acid) ;
关键词 keywords	;PYRIDOXAL 5'-PHOSPHATE, PLP, FOLD TYPE 1, ONE CARBON METABOLISM, TRANSFERASE ;; 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	44.24 Å
回转半径 Rg (电子) rg_electron	44.18 Å
零角强度 I(0) i0	636052000.00
分子量 molecular_weight	206170.0 kDa
排除体积 excluded_volume	257060 Å³
包络体积 envelope_volume	323040 Å³
水化壳体积 shell_volume	59812 Å³
包络直径 envelope_diameter	156.7 Å
壳层 Rg shell_rg	49.87 Å
包络 Rg envelope_rg	43.84 Å
形状 Rg shape_rg	44.16 Å
总 Rg total_rg	44.45 Å
总原子数 total_atoms	14508
残基数 n_residues	1830
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	146.6 Å
Rg (实空间) rg_real	44.36 Å
Rg 误差 (实空间) rg_real_error	1.23 Å
I(0) (实空间) i0_real	6.3610e+08
I(0) 误差 (实空间) i0_real_error	1.1040e+07
Rg (倒空间) rg_reciprocal	44.25 Å
I(0) (倒空间) i0_reciprocal	636000000.0000
解质量估计 total_estimate	0.8659
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	0
主峰位置 r_peak_primary	— Å
偏度 Skewness skewness	0.299
峰度 Kurtosis kurtosis	-0.755
角度范围 angular_range	— – 0.1800 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	153900000.0000
实空间数据点数 n_real_points	37
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 0.888

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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	Serine hydroxymethyltransferase, mitochondrial
分子量 formula_weight	51329.5 kDa
EC 编号 ec_number	2.1.2.1
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	15295

WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGFDEH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)glycine
分子量 formula_weight	304.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
分子量 formula_weight	473.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	765

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7. 引用文献 (1)

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晶胞边长 a length_a	142.980 Å
晶胞边长 b length_b	119.300 Å
晶胞边长 c length_c	134.627 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	16

空间群 space_group	P 2 2 21
空间群编号 int_tables_number	17
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	42.820 Å
R 因子 r_factor	0.1636
R_work r_work	0.1623
R_free r_free	0.1886

fit	/app/data/saxs_computation/bo/9box/9box.fit
pddf	/app/data/pr_computation/bo/9box/9box.pr.out
profile	/app/data/saxs_computation/bo/9box/9box.dat

;Room-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase (hSHMT2) with PLP-glycine external aldimine and 5-formyltetrahydrofolate (folinic acid) ;

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