The toxin-antitoxin complex Fic-1-AntF is a deAMPylase that regulates the activity of DNA gyrase

条目编号 entry_id	8wt0
沉积日期 deposition_date	2023-10-17
最后修订 last_revision	2024-10-23
结构标题 title	The toxin-antitoxin complex Fic-1-AntF is a deAMPylase that regulates the activity of DNA gyrase
关键词 keywords	;Toxin-antitoxin, AMPylation, deAMPylation, Posttranslational Modification, Filamentation, cyclic adenosine monophosphate protein, STRUCTURAL PROTEIN ;; STRUCTURAL PROTEIN
实验方法 method	X-RAY DIFFRACTION

回转半径 Rg (Guinier) rg_guinier	18.22 Å
回转半径 Rg (电子) rg_electron	17.11 Å
零角强度 I(0) i0	12617300.00
分子量 molecular_weight	26121.0 kDa
排除体积 excluded_volume	32442 ų
包络体积 envelope_volume	36923 ų
水化壳体积 shell_volume	17831 ų
包络直径 envelope_diameter	59.4 Å
壳层 Rg shell_rg	23.48 Å
包络 Rg envelope_rg	17.40 Å
形状 Rg shape_rg	17.08 Å
总 Rg total_rg	18.15 Å
总原子数 total_atoms	1835
残基数 n_residues	225
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/ų
壳层衬度 contrast_shell	0.0300 e/ų
CRYSOL 版本 crysol_version	4.1.3

最大尺寸 Dmax dmax	58.8 Å
Rg (实空间) rg_real	18.11 Å
Rg 误差 (实空间) rg_real_error	0.30 Å
I(0) (实空间) i0_real	1.2620e+07
I(0) 误差 (实空间) i0_real_error	1.4550e+05
Rg (倒空间) rg_reciprocal	18.13 Å
I(0) (倒空间) i0_reciprocal	12620000.0000
解质量估计 total_estimate	0.8869
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	23.8 Å
偏度 Skewness skewness	0.164
峰度 Kurtosis kurtosis	-0.371
角度范围 angular_range	— – 0.4350 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3280000.0000
实空间数据点数 n_real_points	75
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.999

晶胞参数 Unit Cell

晶胞边长 a length_a	107.026 Å
晶胞边长 b length_b	107.026 Å
晶胞边长 c length_c	113.529 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	12

对称性 Symmetry

空间群 space_group	P 63 2 2
空间群编号 int_tables_number	182
晶系 crystal_system	—

精修参数 Refinement

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	48.410 Å
R 因子 r_factor	—
R_work r_work	0.2117
R_free r_free	0.2685

衍射实验 Diffraction

实验温度 temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/wt/8wt0/pr_distribution.json
• pr_output /app/data/pr_computation/wt/8wt0/8wt0.pr.out
• pr_plot /app/data/visualization/pr_computation/wt/8wt0/8wt0_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/wt/8wt0/8wt0.dat
• saxs_fit /app/data/saxs_computation/wt/8wt0/8wt0.fit
• saxs_log /app/data/saxs_computation/wt/8wt0/8wt0.log
• saxs_plot /app/data/visualization/saxs_computation/wt/8wt0/8wt0_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/wt/8wt0/8wt0.fit
pddf	/app/data/pr_computation/wt/8wt0/8wt0.pr.out
profile	/app/data/saxs_computation/wt/8wt0/8wt0.dat