8tlc

Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and tri-glutamate AGF347 inhibitor

Method: X-RAY DIFFRACTION D_max: 91.5 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	8tlc
沉积日期 deposition_date	2023-07-26
最后修订 last_revision	2024-02-21
结构标题 title	Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and tri-glutamate AGF347 inhibitor
关键词 keywords	SHMT2, tetramer, glycine synthesis, inhibitor, polyglutamate, 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	28.61 Å
回转半径 Rg (电子) rg_electron	27.60 Å
零角强度 I(0) i0	162367000.00
分子量 molecular_weight	99287.0 kDa
排除体积 excluded_volume	123470 Å³
包络体积 envelope_volume	147700 Å³
水化壳体积 shell_volume	42552 Å³
包络直径 envelope_diameter	96.2 Å
壳层 Rg shell_rg	36.62 Å
包络 Rg envelope_rg	27.98 Å
形状 Rg shape_rg	27.60 Å
总 Rg total_rg	28.42 Å
总原子数 total_atoms	6993
残基数 n_residues	902
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	91.5 Å
Rg (实空间) rg_real	28.52 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	1.6240e+08
I(0) 误差 (实空间) i0_real_error	2.4110e+06
Rg (倒空间) rg_reciprocal	28.56 Å
I(0) (倒空间) i0_reciprocal	162400000.0000
解质量估计 total_estimate	0.8924
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	34.9 Å
偏度 Skewness skewness	0.280
峰度 Kurtosis kurtosis	-0.313
角度范围 angular_range	— – 0.2750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	83200000.0000
实空间数据点数 n_real_points	56
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.966

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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 (3)

Entity 1 polymer

描述 description	Serine hydroxymethyltransferase, mitochondrial
分子量 formula_weight	54834.0 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	7003

MGSSHHHHHHSSGLVPRSNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGFDEH

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 BL21(DE3)

Entity 2 non-polymer

描述 description	;N-{4-[4-(2-amino-4-oxo-1,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-2-fluorobenzoyl}-D-gamma-glutamyl-L-gamma-glutamyl-D-glutamic acid ;
分子量 formula_weight	731.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	10

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7. 引用文献 (1)

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晶胞边长 a length_a	158.718 Å
晶胞边长 b length_b	158.718 Å
晶胞边长 c length_c	207.155 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	120.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 65 2 2
空间群编号 int_tables_number	179
晶系 crystal_system	—

分辨率 resolution	2.720 Å
最低分辨率 resolution_low	48.712 Å
R 因子 r_factor	0.3085
R_work r_work	0.3060
R_free r_free	0.3594

fit	/app/data/saxs_computation/tl/8tlc/8tlc.fit
pddf	/app/data/pr_computation/tl/8tlc/8tlc.pr.out
profile	/app/data/saxs_computation/tl/8tlc/8tlc.dat

Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and tri-glutamate AGF347 inhibitor

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