8v9i

;1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus radiodurans with D-phenylalanine-derived triazole acetylphosphonate (D-PheTrAP) bound ;

Method: X-RAY DIFFRACTION D_max: 96.7 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

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8v9i
沉积日期 deposition_date	2023-12-08
结构标题 title	;1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus radiodurans with D-phenylalanine-derived triazole acetylphosphonate (D-PheTrAP) bound ;
关键词 keywords	;1-DEOXY-D-XYLULOSE 5-PHOSPHATE SYNTHASE, DXPS, THIAMINE DIPHOSPHATE, THIAMINE PYROPHOSPHATE, THDP, TPP, THE MEP PATHWAY, TRANSFERASE, TRANSFERASE-INHIBITOR complex ;; TRANSFERASE/INHIBITOR
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	30.71 Å
回转半径 Rg (电子) rg_electron	29.76 Å
零角强度 I(0) i0	257112000.00
分子量 molecular_weight	127320.0 kDa
排除体积 excluded_volume	158900 Å³
包络体积 envelope_volume	184300 Å³
水化壳体积 shell_volume	48911 Å³
包络直径 envelope_diameter	102.3 Å
壳层 Rg shell_rg	39.04 Å
包络 Rg envelope_rg	30.16 Å
形状 Rg shape_rg	29.78 Å
总 Rg total_rg	30.45 Å
总原子数 total_atoms	8958
残基数 n_residues	1171
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	96.7 Å
Rg (实空间) rg_real	30.52 Å
Rg 误差 (实空间) rg_real_error	0.47 Å
I(0) (实空间) i0_real	2.5710e+08
I(0) 误差 (实空间) i0_real_error	3.7090e+06
Rg (倒空间) rg_reciprocal	30.61 Å
I(0) (倒空间) i0_reciprocal	257100000.0000
解质量估计 total_estimate	0.8978
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	39.0 Å
偏度 Skewness skewness	0.150
峰度 Kurtosis kurtosis	-0.483
角度范围 angular_range	— – 0.2600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	125300000.0000
实空间数据点数 n_real_points	53
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.982

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (6)

Entity 1 polymer

描述 description	1-deoxy-D-xylulose-5-phosphate synthase
分子量 formula_weight	70029.5 kDa
EC 编号 ec_number	2.2.1.7
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	9628

MGSSHHHHHHSSGLVPRGSHMMNELPGTSDTPLLDQIHGPKDLKRLSREQLPALTEELRGEIVRVCSRGGLHLASSLGAVDIITALHYVLDSPRDRILFDVGHQAYAHKILTGRRDQMADIKKEGGISGFTKVSESEHDAITVGHASTSLANALGMALARDAQGKDFHVAAVIGDGSLTGGMALAALNTIGDMGRKMLIVLNDNEMSISENVGAMNKFMRGLQVQKWFQEGEGAGKKAVEAVSKPLADFMSRAKNSTRHFFDPASVNPFAAMGVRYVGPVDGHNVQELVWLLERLVDLDGPTILHIVTTKGKGLSYAEADPIYWHGPAKFDPATGEYVPSSAYSWSAAFGEAVTEWAKTDPRTFVVTPAMREGSGLVEFSRVHPHRYLDVGIAEEVAVTTAAGMALQGMRPVVAIYSTFLQRAYDQVLHDVAIEHLNVTFCIDRAGIVGADGATHNGVFDLSFLRSIPGVRIGLPKDAAELRGMLKYAQTHDGPFAIRYPRGNTAQVPAGTWPDLKWGEWERLKGGDDVVILAGGKALDYALKAAEDLPGVGVVNARFVKPLDEEMLREVGGRARALITVEDNTVVGGFGGAVLEALNSMNLHPTVRVLGIPDEFQEHATAESVHARAGIDAPAIRTVLAELGVDVPIEV

来源 Source

来源生物 organism	Deinococcus radiodurans
NCBI 分类编号 ncbi_taxonomy_id	1299
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	;3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-[(S)-(2-{1-[(1R)-1-carboxy-2-phenylethyl]-1H-1,2,3-triazol-4-yl}ethoxy)(hydroxy)phosphoryl]-1-hydroxyethyl}-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium ;
分子量 formula_weight	792.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	2

Entity 4 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	2-HYDROXY BUTANE-1,4-DIOL
分子量 formula_weight	106.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	580

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	78.616 Å
晶胞边长 b length_b	125.321 Å
晶胞边长 c length_c	152.017 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	1.981 Å
最低分辨率 resolution_low	66.597 Å
R 因子 r_factor	0.1611
R_work r_work	0.1601
R_free r_free	0.1812

fit	/app/data/saxs_computation/v9/8v9i/8v9i.fit
pddf	/app/data/pr_computation/v9/8v9i/8v9i.pr.out
profile	/app/data/saxs_computation/v9/8v9i/8v9i.dat