The structure of dUTPase in complex with dUTP from Methanosarcina mazei

entry_id	9w5a
deposition_date	2025-08-01
last_revision	2026-04-29
title	The structure of dUTPase in complex with dUTP from Methanosarcina mazei
keywords	Archaea; dUTPase; trimeric enzyme; crystal structure; subdomain I; evolutionary divergence, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

rg_guinier	22.28 Å
rg_electron	21.07 Å
i0	45921600.00
molecular_weight	53035.0 kDa
excluded_volume	66628 ų
envelope_volume	74883 ų
shell_volume	28176 ų
envelope_diameter	71.7 Å
shell_rg	29.14 Å
envelope_rg	21.38 Å
shape_rg	21.07 Å
total_rg	21.98 Å
total_atoms	3715
n_residues	465
n_harmonics	20
q_range	— – 0.5000 Å−1
n_points	101
shell_type	directional
solvent_density	0.3340 e/ų
contrast_shell	0.0300 e/ų
crysol_version	4.1.3

dmax	67.4 Å
rg_real	22.11 Å
rg_real_error	0.24 Å
i0_real	4.5920e+07
i0_real_error	4.8670e+05
rg_reciprocal	22.15 Å
i0_reciprocal	45920000.0000
total_estimate	0.8965
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.6 Å
skewness	0.033
kurtosis	-0.518
angular_range	— – 0.3550 Å−1
current_alpha	0.0000
highest_alpha	13880000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.967

Unit Cell

length_a	81.971 Å
length_b	81.971 Å
length_c	81.704 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

Symmetry

space_group	P 43
int_tables_number	78
crystal_system	tetragonal

Refinement

resolution	1.530 Å
resolution_low	27.310 Å
r_factor	0.1750
r_work	0.1743
r_free	0.2038

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/w5/9w5a/pr_distribution.json
• pr_output /app/data/pr_computation/w5/9w5a/9w5a.pr.out
• pr_plot /app/data/visualization/pr_computation/w5/9w5a/9w5a_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/w5/9w5a/9w5a.dat
• saxs_fit /app/data/saxs_computation/w5/9w5a/9w5a.fit
• saxs_log /app/data/saxs_computation/w5/9w5a/9w5a.log
• saxs_plot /app/data/visualization/saxs_computation/w5/9w5a/9w5a_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/w5/9w5a/9w5a.fit
pddf	/app/data/pr_computation/w5/9w5a/9w5a.pr.out
profile	/app/data/saxs_computation/w5/9w5a/9w5a.dat