8tgs

;The crystal structure of the post-reactive state of UDP-sugar pyrophosphorylase from Leishmania major in complex with product UDP-Glucose and by-product analog VO4 (orthovanadate) ;

Method: X-RAY DIFFRACTION D_max: 93.1 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	8tgs
沉积日期 deposition_date	2023-07-13
最后修订 last_revision	2025-01-22
结构标题 title	;The crystal structure of the post-reactive state of UDP-sugar pyrophosphorylase from Leishmania major in complex with product UDP-Glucose and by-product analog VO4 (orthovanadate) ;
关键词 keywords	carbohydrate biosynthesis, nucleotidyltransferase, catalysis, molecular mechanism, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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	27.49 Å
回转半径 Rg (电子) rg_electron	26.36 Å
零角强度 I(0) i0	75769400.00
分子量 molecular_weight	67534.0 kDa
排除体积 excluded_volume	84287 Å³
包络体积 envelope_volume	106420 Å³
水化壳体积 shell_volume	33641 Å³
包络直径 envelope_diameter	96.9 Å
壳层 Rg shell_rg	33.85 Å
包络 Rg envelope_rg	26.54 Å
形状 Rg shape_rg	26.36 Å
总 Rg total_rg	27.14 Å
总原子数 total_atoms	4748
残基数 n_residues	608
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	93.1 Å
Rg (实空间) rg_real	27.43 Å
Rg 误差 (实空间) rg_real_error	0.81 Å
I(0) (实空间) i0_real	7.5770e+07
I(0) 误差 (实空间) i0_real_error	1.2140e+06
Rg (倒空间) rg_reciprocal	27.45 Å
I(0) (倒空间) i0_reciprocal	75770000.0000
解质量估计 total_estimate	0.7996
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	32.1 Å
偏度 Skewness skewness	0.326
峰度 Kurtosis kurtosis	-0.261
角度范围 angular_range	— – 0.2900 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16050000.0000
实空间数据点数 n_real_points	59
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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 (5)

Entity 1 polymer

描述 description	UTP-monosaccharide-1-phosphate uridylyltransferase
分子量 formula_weight	66935.9 kDa
EC 编号 ec_number	2.7.7.64
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	4992

NPSNSNLQALREELCTPGLDQGHLFEGWPETVDECNERQIALLTDLYMFSNMYPGGVAQYIRNGHELLARESEEVDFAALEMPPLIFEAPSLHRRTAERTALENAGTAMLCKTVFVLVAGGLGERLGYSSIKVSLPVETATNTTYLAYYLRWAQRVGGKEVPFVIMTSDDTHDRTLQLLRELQLEVPNLHVLKQGQVFCFADSAAHLALDETGKLLRKPHGHGDVHSLIYNATVKRDVVPDSGDGTATAQPLVNDWLAAGYESIVFIQDTNAGATITIPISLALSAEHSLDMNFTCIPRVPKEPIGLLCRTKKNSGDPWLVANVEYNVFAEVSRALNKDGGDEVSDPTGFSPFPGSVNTLVFKLSSYVDRLRESHGIVPEFINPKYSDETRRSFKKPARIESLMQDIALLFSEDDYRVGGTVFERFSYQPVKNSLEEAAGLVAQGNGAYCAATGEAAFYELQRRRLKAIGLPLFYSSQPEVTVAKDAFGVRLFPIIVLDTVCASSGSLDDLARVFPTPEKVHIDQHSTLIVEGRVIIESLELYGALTIRGPTDSMALPHVVRNAVVRNAGWSVHAILSLCAGRDSRLSEVDRIRGFVLKKTAMAVMDC

来源 Source

来源生物 organism	Leishmania major
NCBI 分类编号 ncbi_taxonomy_id	5664
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	URIDINE-5'-DIPHOSPHATE-GLUCOSE
分子量 formula_weight	566.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	VANADATE ION
分子量 formula_weight	114.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 4 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	244

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7. 引用文献 (1)

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晶胞边长 a length_a	108.080 Å
晶胞边长 b length_b	122.420 Å
晶胞边长 c length_c	61.240 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	105.55 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	59.070 Å
R 因子 r_factor	0.2127
R_work r_work	0.2111
R_free r_free	0.2422

fit	/app/data/saxs_computation/tg/8tgs/8tgs.fit
pddf	/app/data/pr_computation/tg/8tgs/8tgs.pr.out
profile	/app/data/saxs_computation/tg/8tgs/8tgs.dat

;The crystal structure of the post-reactive state of UDP-sugar pyrophosphorylase from Leishmania major in complex with product UDP-Glucose and by-product analog VO4 (orthovanadate) ;

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