Crystal structure of the WRKY DNA-binding domain in complex with the W-box DNA motif

条目编号 entry_id	9m0k
沉积日期 deposition_date	2025-02-25
结构标题 title	Crystal structure of the WRKY DNA-binding domain in complex with the W-box DNA motif
关键词 keywords	DNA recognition mechanism, Complex, Gene regulation, Binding specificity, DNA BINDING PROTEIN/DNA, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
实验方法 method	X-RAY DIFFRACTION

回转半径 Rg (Guinier) rg_guinier	18.64 Å
回转半径 Rg (电子) rg_electron	17.69 Å
零角强度 I(0) i0	12948500.00
分子量 molecular_weight	21261.0 kDa
排除体积 excluded_volume	24147 ų
包络体积 envelope_volume	31190 ų
水化壳体积 shell_volume	15372 ų
包络直径 envelope_diameter	65.8 Å
壳层 Rg shell_rg	22.97 Å
包络 Rg envelope_rg	17.81 Å
形状 Rg shape_rg	17.62 Å
总 Rg total_rg	18.58 Å
总原子数 total_atoms	1462
残基数 n_residues	142
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	65.1 Å
Rg (实空间) rg_real	18.61 Å
Rg 误差 (实空间) rg_real_error	0.43 Å
I(0) (实空间) i0_real	1.2950e+07
I(0) 误差 (实空间) i0_real_error	1.6330e+05
Rg (倒空间) rg_reciprocal	18.61 Å
I(0) (倒空间) i0_reciprocal	12950000.0000
解质量估计 total_estimate	0.8739
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	23.2 Å
偏度 Skewness skewness	0.277
峰度 Kurtosis kurtosis	-0.329
角度范围 angular_range	— – 0.4250 Å−1
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1466000.0000
实空间数据点数 n_real_points	74
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 1.000

晶胞参数 Unit Cell

晶胞边长 a length_a	54.111 Å
晶胞边长 b length_b	93.285 Å
晶胞边长 c length_c	83.694 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	16

对称性 Symmetry

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

精修参数 Refinement

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	46.810 Å
R 因子 r_factor	0.2470
R_work r_work	0.2470
R_free r_free	0.2803

衍射实验 Diffraction

实验温度 temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/m0/9m0k/pr_distribution.json
• pr_output /app/data/pr_computation/m0/9m0k/9m0k.pr.out
• pr_plot /app/data/visualization/pr_computation/m0/9m0k/9m0k_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/m0/9m0k/9m0k.dat
• saxs_fit /app/data/saxs_computation/m0/9m0k/9m0k.fit
• saxs_log /app/data/saxs_computation/m0/9m0k/9m0k.log
• saxs_plot /app/data/visualization/saxs_computation/m0/9m0k/9m0k_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/m0/9m0k/9m0k.fit
pddf	/app/data/pr_computation/m0/9m0k/9m0k.pr.out
profile	/app/data/saxs_computation/m0/9m0k/9m0k.dat