9hn8

Apo Structure of Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis

Method: X-RAY DIFFRACTION D_max: 97.0 Å Quality: EXCELLENT

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	9hn8
沉积日期 deposition_date	2024-12-10
最后修订 last_revision	2025-01-22
结构标题 title	Apo Structure of Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis
关键词 keywords	apo, thiamine-dependent enzyme, synthase, 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	31.27 Å
回转半径 Rg (电子) rg_electron	30.19 Å
零角强度 I(0) i0	164161000.00
分子量 molecular_weight	101700.0 kDa
排除体积 excluded_volume	127450 Å³
包络体积 envelope_volume	156590 Å³
水化壳体积 shell_volume	42619 Å³
包络直径 envelope_diameter	97.9 Å
壳层 Rg shell_rg	37.90 Å
包络 Rg envelope_rg	30.27 Å
形状 Rg shape_rg	30.20 Å
总 Rg total_rg	30.81 Å
总原子数 total_atoms	7163
残基数 n_residues	954
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	97.0 Å
Rg (实空间) rg_real	31.10 Å
Rg 误差 (实空间) rg_real_error	0.60 Å
I(0) (实空间) i0_real	1.6420e+08
I(0) 误差 (实空间) i0_real_error	2.5110e+06
Rg (倒空间) rg_reciprocal	31.18 Å
I(0) (倒空间) i0_reciprocal	164200000.0000
解质量估计 total_estimate	0.9056
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	41.8 Å
偏度 Skewness skewness	0.132
峰度 Kurtosis kurtosis	-0.568
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	102800000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.946

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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 (2)

Entity 1 polymer

描述 description	1-deoxy-D-xylulose-5-phosphate synthase
分子量 formula_weight	63623.1 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	7205

GAMGMLQQIRGPADLQHLSQAQLRELAAEIREFLIHKVAATGGHLGPNLGVVELTLALHRVFDSPHDPIIFDTGHQAYVHKMLTGRSQDFATLRKKGGLSGYPSRAESEHDWVESSHASAALSYADGLAKAFELTGHRNRHVVAVVGDGALTGGMCWEALNNIAASRRPVIIVVNDNGRSYAPTIGGVADHLAGGGGGGGPQLLFTDLGLKYVGPVDGHDERAVEVALRSARRFGAPVIVHVVTRKGMGYPPAEADQAEQMHSTVPIDPATGQATKVAGVGWTATFSDALIGYAQKRRDIVAITAAMPGPTGLTAFGQRFPDRLFDVGIAEQHAMTSAAGLAMGGLHPVVAIYSTFLNRAFDQIMMDVALHKLPVTMVLDRAGITGSDGASHNGMWDLSMLGIVPGIRVAAPRDATRLREELGEALDVDDGPTALRFPKGDVGEDISALERRGGVDVLAAPADGLNHDVLLVAIGAFAPMALAVAKRLHNQGIGVTVIDPRWVLPVSDGVRELAVQHKLLVTLEDNGVNGGAGSAVSAALRRAEIDVPCRDVGLPQEFVEHASRSEVLADLGLTDQDVARRITGWVAALGTGVCASDAIPEHLD

来源 Source

来源生物 organism	Mycobacterium tuberculosis H37Rv
NCBI 分类编号 ncbi_taxonomy_id	83332
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 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	20

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7. 引用文献 (1)

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晶胞边长 a length_a	67.180 Å
晶胞边长 b length_b	126.772 Å
晶胞边长 c length_c	80.553 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.70 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	monoclinic

分辨率 resolution	2.650 Å
最低分辨率 resolution_low	48.870 Å
R 因子 r_factor	0.2486
R_work r_work	0.2474
R_free r_free	0.2733

fit	/app/data/saxs_computation/hn/9hn8/9hn8.fit
pddf	/app/data/pr_computation/hn/9hn8/9hn8.pr.out
profile	/app/data/saxs_computation/hn/9hn8/9hn8.dat

Apo Structure of Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis

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 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)