;Crystal structure of thiamine pyrophosphate (TPP)-dependent alpha-imino acid decarboxylase (AzcB and AzcC) from Streptomyces mobaraensis in complex with TPP and 5-azacytosine. ;

entry_id	9u8s
deposition_date	2025-03-26
last_revision	2026-04-01
title	;Crystal structure of thiamine pyrophosphate (TPP)-dependent alpha-imino acid decarboxylase (AzcB and AzcC) from Streptomyces mobaraensis in complex with TPP and 5-azacytosine. ;
keywords	thiamine pyrophosphate (TPP)-dependent decarboxylase, AzcB, AzcC, 5-azacytidine biosynthesis, 5-azacytosine, LYASE; LYASE
method	X-RAY DIFFRACTION

rg_guinier	37.22 Å
rg_electron	36.84 Å
i0	828738000.00
molecular_weight	232360.0 kDa
excluded_volume	289590 ų
envelope_volume	339970 ų
shell_volume	72034 ų
envelope_diameter	123.3 Å
shell_rg	46.41 Å
envelope_rg	36.69 Å
shape_rg	36.87 Å
total_rg	37.22 Å
total_atoms	16246
n_residues	2157
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	115.4 Å
rg_real	37.00 Å
rg_real_error	0.56 Å
i0_real	8.2870e+08
i0_real_error	1.1550e+07
rg_reciprocal	37.14 Å
i0_reciprocal	828900000.0000
total_estimate	0.8969
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.7 Å
skewness	0.154
kurtosis	-0.502
angular_range	— – 0.2100 Å−1
current_alpha	0.0000
highest_alpha	443700000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.917

Unit Cell

length_a	119.465 Å
length_b	96.918 Å
length_c	130.285 Å
angle_alpha	90.00 °
angle_beta	113.39 °
angle_gamma	90.00 °
z_pdb	12

Symmetry

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

Refinement

resolution	2.460 Å
resolution_low	48.460 Å
r_factor	0.1909
r_work	0.1900
r_free	0.2328

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/u8/9u8s/pr_distribution.json
• pr_output /app/data/pr_computation/u8/9u8s/9u8s.pr.out
• pr_plot /app/data/visualization/pr_computation/u8/9u8s/9u8s_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/u8/9u8s/9u8s.dat
• saxs_fit /app/data/saxs_computation/u8/9u8s/9u8s.fit
• saxs_log /app/data/saxs_computation/u8/9u8s/9u8s.log
• saxs_plot /app/data/visualization/saxs_computation/u8/9u8s/9u8s_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/u8/9u8s/9u8s.fit
pddf	/app/data/pr_computation/u8/9u8s/9u8s.pr.out
profile	/app/data/saxs_computation/u8/9u8s/9u8s.dat